Proposed Changes to the Enzyme List

References:

Mihasan, M., Chiribau, C.B., Friedrich, T., Artenie, V. and Brandsch, R. An NAD(P)H-nicotine blue oxidoreductase is part of the nicotine regulon and may protect Arthrobacter nicotinovorans from oxidative stress during nicotine catabolism. Appl. Environ. Microbiol. 73 (2007) 2479–2485. [DOI] [PMID: 17293530]

[EC 1.1.1.328 created 2012]

1.1.1.329

Accepted name:

2-deoxy-scyllo-inosamine dehydrogenase

Reaction:

2-deoxy-scyllo-inosamine + NAD(P)⁺ = 3-amino-2,3-dideoxy-scyllo-inosose + NAD(P)H + H⁺

For diagram of paromamine biosynthesis, click here

Glossary:

2-deoxy-scyllo-inosamine = (1R,2S,3S,4R,5S)-5-aminocyclohexane-1,2,3,4-tetrol

Other name(s):

neoA (gene name); kanK (gene name, ambiguous); kanE (gene name, ambiguous)

Systematic name:

2-deoxy-scyllo-inosamine:NAD(P)⁺ 1-oxidoreductase

Comments:

Requires zinc. Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin, neomycin and ribostamycin. cf. EC 1.1.99.38, 2-deoxy-scyllo-inosamine dehydrogenase (AdoMet-dependent).

Links to other databases:

References:

1.	Kudo, F., Yamamoto, Y., Yokoyama, K., Eguchi, T. and Kakinuma, K. Biosynthesis of 2-deoxystreptamine by three crucial enzymes in Streptomyces fradiae NBRC 12773. J. Antibiot. (Tokyo) 58 (2005) 766–774. [DOI] [PMID: 16506694]
2.	Nepal, K.K., Oh, T.J. and Sohng, J.K. Heterologous production of paromamine in Streptomyces lividans TK24 using kanamycin biosynthetic genes from Streptomyces kanamyceticus ATCC12853. Mol. Cells 27 (2009) 601–608. [DOI] [PMID: 19466609]

[EC 1.1.1.329 created 2012]

1.1.1.330

Accepted name:

very-long-chain 3-oxoacyl-CoA reductase

Reaction:

a very-long-chain (3R)-3-hydroxyacyl-CoA + NADP⁺ = a very-long-chain 3-oxoacyl-CoA + NADPH + H⁺

Glossary:

a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.

Other name(s):

very-long-chain 3-ketoacyl-CoA reductase; very-long-chain β-ketoacyl-CoA reductase; KCR (gene name); IFA38 (gene name)

Systematic name:

(3R)-3-hydroxyacyl-CoA:NADP⁺ oxidoreductase

Comments:

The second component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long-chain acyl CoAs. The enzyme is active with substrates with chain length of C₁₆ to C₃₄, depending on the species. cf. EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 4.2.1.134, very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase.

Links to other databases:

References:

1.	Beaudoin, F., Gable, K., Sayanova, O., Dunn, T. and Napier, J.A. A Saccharomyces cerevisiae gene required for heterologous fatty acid elongase activity encodes a microsomal β-keto-reductase. J. Biol. Chem. 277 (2002) 11481–11488. [DOI] [PMID: 11792704]
2.	Han, G., Gable, K., Kohlwein, S.D., Beaudoin, F., Napier, J.A. and Dunn, T.M. The Saccharomyces cerevisiae YBR159w gene encodes the 3-ketoreductase of the microsomal fatty acid elongase. J. Biol. Chem. 277 (2002) 35440–35449. [DOI] [PMID: 12087109]
3.	Beaudoin, F., Wu, X., Li, F., Haslam, R.P., Markham, J.E., Zheng, H., Napier, J.A. and Kunst, L. Functional characterization of the Arabidopsis β-ketoacyl-coenzyme A reductase candidates of the fatty acid elongase. Plant Physiol. 150 (2009) 1174–1191. [DOI] [PMID: 19439572]

[EC 1.1.1.330 created 2012]

1.1.1.331

Accepted name:

secoisolariciresinol dehydrogenase

Reaction:

(–)-secoisolariciresinol + 2 NAD⁺ = (–)-matairesinol + 2 NADH + 2 H⁺

For diagram of matairesinol biosynthesis, click here

Systematic name:

(–)-secoisolariciresinol:NAD⁺ oxidoreductase

Comments:

Isolated from the plants Forsythia intermedia [1] and Podophyllum peltatum [1-3]. An intermediate lactol is detected in vitro.

Links to other databases:

References:

1.	Xia, Z.Q., Costa, M.A., Pelissier, H.C., Davin, L.B. and Lewis, N.G. Secoisolariciresinol dehydrogenase purification, cloning, and functional expression. Implications for human health protection. J. Biol. Chem. 276 (2001) 12614–12623. [DOI] [PMID: 11278426]
2.	Youn, B., Moinuddin, S.G., Davin, L.B., Lewis, N.G. and Kang, C. Crystal structures of apo-form and binary/ternary complexes of Podophyllum secoisolariciresinol dehydrogenase, an enzyme involved in formation of health-protecting and plant defense lignans. J. Biol. Chem. 280 (2005) 12917–12926. [DOI] [PMID: 15653677]
3.	Moinuddin, S.G., Youn, B., Bedgar, D.L., Costa, M.A., Helms, G.L., Kang, C., Davin, L.B. and Lewis, N.G. Secoisolariciresinol dehydrogenase: mode of catalysis and stereospecificity of hydride transfer in Podophyllum peltatum. Org. Biomol. Chem. 4 (2006) 808–816. [DOI] [PMID: 16493463]

[EC 1.1.1.331 created 2012]

1.1.1.332

Accepted name:

chanoclavine-I dehydrogenase

Reaction:

chanoclavine-I + NAD⁺ = chanoclavine-I aldehyde + NADH + H⁺

For diagram of ergot alkaloid biosynthesis, click here

Glossary:

chanoclavine-I = (1E)-2-methyl-3-[(4R,5R)-4-(methylamino)-1,3,4,5-tetrahydrobenz[cd]indol-5-yl]prop-2-en-1-ol
chanoclavine-I aldehyde = (1E)-2-methyl-3-[(4R,5R)-4-(methylamino)-1,3,4,5-tetrahydrobenz[cd]indol-5-yl]prop-2-enal

Other name(s):

easD (gene name); fgaDH (gene name)

Systematic name:

chanoclavine-I:NAD⁺ oxidoreductase

Comments:

The enzyme catalyses a step in the pathway of ergot alkaloid biosynthesis in certain fungi.

Links to other databases:

References:

1.	Wallwey, C., Matuschek, M. and Li, S.M. Ergot alkaloid biosynthesis in Aspergillus fumigatus: conversion of chanoclavine-I to chanoclavine-I aldehyde catalyzed by a short-chain alcohol dehydrogenase FgaDH. Arch. Microbiol. 192 (2010) 127–134. [DOI] [PMID: 20039019]
2.	Wallwey, C., Heddergott, C., Xie, X., Brakhage, A.A. and Li, S.M. Genome mining reveals the presence of a conserved gene cluster for the biosynthesis of ergot alkaloid precursors in the fungal family Arthrodermataceae. Microbiology 158 (2012) 1634–1644. [DOI] [PMID: 22403186]

[EC 1.1.1.332 created 2012]

1.1.1.333

Accepted name:

decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose 2-reductase

Reaction:

trans,octacis-decaprenylphospho-β-D-arabinofuranose + NAD⁺ = trans,octacis-decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose + NADH + H⁺

For diagram of decaprenylphosphoarabinofuranose biosynthesis, click here

Other name(s):

decaprenylphospho-β-D-ribofuranose 2′-epimerase; Rv3791; DprE2

Systematic name:

trans,octacis-decaprenylphospho-β-D-arabinofuranose:NAD⁺ 2-oxidoreductase

Comments:

The reaction is catalysed in the reverse direction. The enzyme, isolated from the bacterium Mycobacterium smegmatis, is involved, along with EC 1.1.98.3, decaprenylphospho-β-D-ribofuranose 2-oxidase, in the epimerization of trans,octacis-decaprenylphospho-β-D-ribofuranose to trans,octacis-decaprenylphospho-β-D-arabinoofuranose, the arabinosyl donor for the biosynthesis of mycobacterial cell wall arabinan polymers.

Links to other databases:

References:

Trefzer, C., Škovierová, H., Buroni, S., Bobovská, A., Nenci, S., Molteni, E., Pojer, F., Pasca, M.R., Makarov, V., Cole, S.T., Riccardi, G., Mikušová, K. and Johnsson, K. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2′-oxidase DprE1. J. Am. Chem. Soc. 134 (2012) 912–915. [DOI] [PMID: 22188377]

[EC 1.1.1.333 created 2012]

1.1.1.334

Accepted name:

methylecgonone reductase

Reaction:

ecgonine methyl ester + NADP⁺ = ecgonone methyl ester + NADPH + H⁺

Glossary:

ecgonine methyl ester = 2β-carbomethoxy-3β-tropine = methyl (1R,2R,3S,5S)-3-hydroxy-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate
ecgonone methyl ester = 2β-carbomethoxy-3-tropinone = methyl (1R,2R,5S)-8-methyl-3-oxo-8-azabicyclo[3.2.1]octane-2-carboxylate

Other name(s):

MecgoR (gene name)

Systematic name:

ecgonine methyl ester:NADP⁺ oxidoreductase

Comments:

The enzyme from the plant Erythroxylum coca catalyses the penultimate step in the biosynthesis of cocaine. In vivo the reaction proceeds in the opposite direction. With NADH instead of NADPH the reaction rate is reduced to 14%. The enzyme also reduces tropinone, nortropinone and 6-hydroxytropinone but with lower reaction rates.

Links to other databases:

References:

1.	Jirschitzka, J., Schmidt, G.W., Reichelt, M., Schneider, B., Gershenzon, J. and D'Auria, J.C. Plant tropane alkaloid biosynthesis evolved independently in the Solanaceae and Erythroxylaceae. Proc. Natl. Acad. Sci. USA 109 (2012) 10304–10309. [DOI] [PMID: 22665766]

[EC 1.1.1.334 created 2012]

1.1.1.335

Accepted name:

UDP-N-acetyl-2-amino-2-deoxyglucuronate dehydrogenase

Reaction:

UDP-N-acetyl-2-amino-2-deoxy-α-D-glucuronate + NAD⁺ = UDP-2-acetamido-2-deoxy-α-D-ribo-hex-3-uluronate + NADH + H⁺

For diagram of UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronate biosynthesis, click here

Other name(s):

WlbA; WbpB

Systematic name:

UDP-N-acetyl-2-amino-2-deoxy-α-D-glucuronate:NAD⁺ 3-oxidoreductase

Comments:

This enzyme participates in the biosynthetic pathway for UDP-α-D-ManNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronic acid), an important precursor of B-band lipopolysaccharide. The enzymes from Pseudomonas aeruginosa serotype O5 and Thermus thermophilus form a complex with the the enzyme catalysing the next step the pathway (EC 2.6.1.98, UDP-2-acetamido-2-deoxy-ribo-hexuluronate aminotransferase). The enzyme also possesses an EC 1.1.99.2 (L-2-hydroxyglutarate dehydrogenase) activity, and utilizes the 2-oxoglutarate produced by EC 2.6.1.98 to regenerate the tightly bound NAD⁺. The enzymes from Bordetella pertussis and Chromobacterium violaceum do not bind NAD⁺ as tightly and do not require 2-oxoglutarate to function.

Links to other databases:

References:

1.	Westman, E.L., McNally, D.J., Charchoglyan, A., Brewer, D., Field, R.A. and Lam, J.S. Characterization of WbpB, WbpE, and WbpD and reconstitution of a pathway for the biosynthesis of UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronic acid in Pseudomonas aeruginosa. J. Biol. Chem. 284 (2009) 11854–11862. [DOI] [PMID: 19282284]
2.	Larkin, A. and Imperiali, B. Biosynthesis of UDP-GlcNAc(3NAc)A by WbpB, WbpE, and WbpD: enzymes in the Wbp pathway responsible for O-antigen assembly in Pseudomonas aeruginosa PAO1. Biochemistry 48 (2009) 5446–5455. [DOI] [PMID: 19348502]
3.	Thoden, J.B. and Holden, H.M. Structural and functional studies of WlbA: A dehydrogenase involved in the biosynthesis of 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid. Biochemistry 49 (2010) 7939–7948. [DOI] [PMID: 20690587]
4.	Thoden, J.B. and Holden, H.M. Biochemical and structural characterization of WlbA from Bordetella pertussis and Chromobacterium violaceum: enzymes required for the biosynthesis of 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid. Biochemistry 50 (2011) 1483–1491. [DOI] [PMID: 21241053]

[EC 1.1.1.335 created 2012]

1.1.1.336

Accepted name:

UDP-N-acetyl-D-mannosamine dehydrogenase

Reaction:

UDP-N-acetyl-α-D-mannosamine + 2 NAD⁺ + H₂O = UDP-N-acetyl-α-D-mannosaminuronate + 2 NADH + 2 H⁺

For diagram of UDP-N-acetylgalactosamine and UDP-N-acetylmannosamine biosynthesis, click here

Other name(s):

UDP-ManNAc 6-dehydrogenase; wecC (gene name)

Systematic name:

UDP-N-acetyl-α-D-mannosamine:NAD⁺ 6-oxidoreductase

Comments:

Part of the pathway for acetamido sugar biosynthesis in bacteria and archaea. The enzyme has no activity with NADP⁺.

Links to other databases:

References:

1.	Namboori, S.C. and Graham, D.E. Acetamido sugar biosynthesis in the Euryarchaea. J. Bacteriol. 190 (2008) 2987–2996. [DOI] [PMID: 18263721]

[EC 1.1.1.336 created 2012]

1.1.1.337

Accepted name:

L-2-hydroxycarboxylate dehydrogenase (NAD⁺)

Reaction:

a (2S)-2-hydroxycarboxylate + NAD⁺ = a 2-oxocarboxylate + NADH + H⁺

Other name(s):

(R)-sulfolactate:NAD⁺ oxidoreductase; L-sulfolactate dehydrogenase; (R)-sulfolactate dehydrogenase; L-2-hydroxyacid dehydrogenase (NAD⁺); ComC

Systematic name:

(2S)-2-hydroxycarboxylate:NAD⁺ oxidoreductase

Comments:

The enzyme from the archaeon Methanocaldococcus jannaschii acts on multiple (S)-2-hydroxycarboxylates including (2R)-3-sulfolactate, (S)-malate, (S)-lactate, and (S)-2-hydroxyglutarate [3]. Note that (2R)-3-sulfolactate has the same stereo configuration as (2S)-2-hydroxycarboxylates.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 81210-65-3

References:

1.	Graupner, M., Xu, H. and White, R.H. Identification of an archaeal 2-hydroxy acid dehydrogenase catalyzing reactions involved in coenzyme biosynthesis in methanoarchaea. J. Bacteriol. 182 (2000) 3688–3692. [DOI] [PMID: 10850983]
2.	Graupner, M. and White, R.H. The first examples of (S)-2-hydroxyacid dehydrogenases catalyzing the transfer of the pro-4S hydrogen of NADH are found in the archaea. Biochim. Biophys. Acta 1548 (2001) 169–173. [DOI] [PMID: 11451450]
3.	Graham, D.E. and White, R.H. Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat. Prod. Rep. 19 (2002) 133–147. [PMID: 12013276]
4.	Rein, U., Gueta, R., Denger, K., Ruff, J., Hollemeyer, K. and Cook, A.M. Dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in Paracoccus pantotrophus NKNCYSA. Microbiology 151 (2005) 737–747. [DOI] [PMID: 15758220]

[EC 1.1.1.337 created 2012]

1.1.1.338

Accepted name:

(2R)-3-sulfolactate dehydrogenase (NADP⁺)

Reaction:

(2R)-3-sulfolactate + NADP⁺ = 3-sulfopyruvate + NADPH + H⁺

For diagram of coenzyme-M biosynthesis, click here

Other name(s):

(R)-sulfolactate:NADP⁺ oxidoreductase; L-sulfolactate dehydrogenase; (R)-sulfolactate dehydrogenase; ComC

Systematic name:

(2R)-3-sulfolactate:NADP⁺ oxidoreductase

Comments:

The enzyme from the bacterium Chromohalobacter salexigens can only utilize NADP⁺. It functions both biosynthetically in coenzyme M biosynthesis and degradatively, in the degradation of sulfolactate. It can not use (S)-malate and (S)-lactate.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 81210-65-3

References:

1.	Denger, K. and Cook, A.M. Racemase activity effected by two dehydrogenases in sulfolactate degradation by Chromohalobacter salexigens: purification of (S)-sulfolactate dehydrogenase. Microbiology 156 (2010) 967–974. [DOI] [PMID: 20007648]

[EC 1.1.1.338 created 2012]

1.1.1.339

Accepted name:

dTDP-6-deoxy-L-talose 4-dehydrogenase (NAD⁺)

Reaction:

dTDP-6-deoxy-β-L-talose + NAD⁺ = dTDP-4-dehydro-β-L-rhamnose + NADH + H⁺

Glossary:

dTDP-4-dehydro-β-L-rhamnose = dTDP-4-dehydro-6-deoxy-β-L-mannose
dTDP-6-deoxy-β-L-talose = dTDP-β-L-pneumose

Other name(s):

tll (gene name)

Systematic name:

dTDP-6-deoxy-β-L-talose:NAD⁺ 4-oxidoreductase

Comments:

The enzyme has been characterized from the bacterium Aggregatibacter actinomycetemcomitans, in which it participates in the biosynthesis of the serotype c-specific polysaccharide antigen. Shows no activity with NADP⁺.

Links to other databases:

References:

1.	Nakano, Y., Suzuki, N., Yoshida, Y., Nezu, T., Yamashita, Y. and Koga, T. Thymidine diphosphate-6-deoxy-L-lyxo-4-hexulose reductase synthesizing dTDP-6-deoxy-L-talose from Actinobacillus actinomycetemcomitans. J. Biol. Chem. 275 (2000) 6806–6812. [DOI] [PMID: 10702238]

[EC 1.1.1.339 created 2012]

1.1.1.340

Accepted name:

1-deoxy-11β-hydroxypentalenate dehydrogenase

Reaction:

1-deoxy-11β-hydroxypentalenate + NAD⁺ = 1-deoxy-11-oxopentalenate + NADH + H⁺

For diagram of pentalenolactone biosynthesis, click here

Glossary:

1-deoxy-11β-hydroxypentalenate = (1S,2R,3aR,5aS,8aR)-2-hydroxy-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate
1-deoxy-11-oxopentalenate = (1S,3aR,5aS)-1,7,7-trimethyl-2-oxo-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate

Other name(s):

1-deoxy-11β-hydroxypentalenic acid dehydrogenase; ptlF (gene name); penF (gene name)

Systematic name:

1-deoxy-11β-hydroxypentalenate:NAD⁺ oxidoreductase

Comments:

Isolated from the bacterium Streptomyces avermitilis and present in many other Streptomyces species. Part of the pathway for pentalenolactone biosynthesis.

Links to other databases:

References:

You, Z., Omura, S., Ikeda, H. and Cane, D.E. Pentalenolactone biosynthesis: Molecular cloning and assignment of biochemical function to PtlF, a short-chain dehydrogenase from Streptomyces avermitilis, and identification of a new biosynthetic intermediate. Arch. Biochem. Biophys. 459 (2007) 233–240. [DOI] [PMID: 17178094]

[EC 1.1.1.340 created 2012]

1.1.1.341

Accepted name:

CDP-abequose synthase

Reaction:

CDP-α-D-abequose + NADP⁺ = CDP-4-dehydro-3,6-dideoxy-α-D-glucose + NADPH + H⁺

For diagram of CDP-abequose, CDP-ascarylose, CDP-paratose and CDP-tyrelose biosynthesis, click here

Glossary:

CDP-α-D-abequose = CDP-3,6-dideoxy-α-D-xylo-hexose

Other name(s):

rfbJ (gene name)

Systematic name:

CDP-α-D-abequose:NADP⁺ 4-oxidoreductase

Comments:

Isolated from Yersinia pseudotuberculosis [1,3] and Salmonella enterica [1,2].

Links to other databases:

References:

1.	Kessler, A.C., Brown, P.K., Romana, L.K. and Reeves, P.R. Molecular cloning and genetic characterization of the rfb region from Yersinia pseudotuberculosis serogroup IIA, which determines the formation of the 3,6-dideoxyhexose abequose. J. Gen. Microbiol. 137 (1991) 2689–2695. [DOI] [PMID: 1724263]
2.	Wyk, P. and Reeves, P. Identification and sequence of the gene for abequose synthase, which confers antigenic specificity on group B salmonellae: homology with galactose epimerase. J. Bacteriol. 171 (1989) 5687–5693. [DOI] [PMID: 2793832]
3.	Thorson, J.S., Lo, S.F., Ploux, O., He, X. and Liu, H.W. Studies of the biosynthesis of 3,6-dideoxyhexoses: molecular cloning and characterization of the asc (ascarylose) region from Yersinia pseudotuberculosis serogroup VA. J. Bacteriol. 176 (1994) 5483–5493. [DOI] [PMID: 8071227]

[EC 1.1.1.341 created 2012]

1.1.1.342

Accepted name:

CDP-paratose synthase

Reaction:

CDP-α-D-paratose + NADP⁺ = CDP-4-dehydro-3,6-dideoxy-α-D-glucose + NADPH + H⁺

For diagram of CDP-abequose, CDP-ascarylose, CDP-paratose and CDP-tyrelose biosynthesis, click here

Glossary:

CDP-α-D-paratose = CDP-3,6-dideoxy-α-D-glucose = CDP-3,6-dideoxy-α-D-ribo-hexose

Other name(s):

rfbS (gene name)

Systematic name:

CDP-α-D-paratose:NADP⁺ 4-oxidoreductase

Comments:

The enzyme is involved in synthesis of paratose and tyvelose, unusual 3,6-dideoxyhexose sugars that form part of the O-antigen in the lipopolysaccharides of several enteric bacteria. Isolated from Salmonella enterica subsp. enterica serovar Typhi (Salmonella typhi).

Links to other databases:

References:

1.	Verma, N. and Reeves, P. Identification and sequence of rfbS and rfbE, which determine antigenic specificity of group A and group D salmonellae. J. Bacteriol. 171 (1989) 5694–5701. [DOI] [PMID: 2793833]
2.	Hallis, T.M., Lei, Y., Que, N.L. and Liu, H. Mechanistic studies of the biosynthesis of paratose: purification and characterization of CDP-paratose synthase. Biochemistry 37 (1998) 4935–4945. [DOI] [PMID: 9538012]

[EC 1.1.1.342 created 2012]

1.1.3.43

Accepted name:

paromamine 6′-oxidase

Reaction:

paromamine + O₂ = 6′-dehydroparomamine + H₂O₂

For diagram of neamine and ribostamycin biosynthesis, click here

Other name(s):

btrQ (gene name); neoG (gene name); kanI (gene name); tacB (gene name); neoQ (obsolete gene name)

Systematic name:

paromamine:oxygen 6′-oxidoreductase

Comments:

Contains FAD. Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin, butirosin, neomycin and ribostamycin. Works in combination with EC 2.6.1.93, neamine transaminase, to replace the 6′-hydroxy group of paromamine with an amino group. The enzyme from the bacterium Streptomyces fradiae also catalyses EC 1.1.3.44, 6′′′-hydroxyneomycin C oxidase.

Links to other databases:

References:

1.	Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem 8 (2007) 283–288. [DOI] [PMID: 17206729]
2.	Yu, Y., Hou, X., Ni, X. and Xia, H. Biosynthesis of 3′-deoxy-carbamoylkanamycin C in a Streptomyces tenebrarius mutant strain by tacB gene disruption. J. Antibiot. (Tokyo) 61 (2008) 63–69. [DOI] [PMID: 18408324]
3.	Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6′-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642–651. [DOI] [PMID: 21689223]

[EC 1.1.3.43 created 2012]

1.1.3.44

Accepted name:

6′′′-hydroxyneomycin C oxidase

Reaction:

6′′′-deamino-6′′′-hydroxyneomycin C + O₂ = 6′′′-deamino-6′′′-oxoneomycin C + H₂O₂

Other name(s):

neoG (gene name); neoQ (obsolete gene name)

Systematic name:

6′′′-deamino-6′′′-hydroxyneomycin C:oxygen 6′′′-oxidoreductase

Comments:

Contains FAD. Involved in the biosynthetic pathway of aminoglycoside antibiotics of the neomycin family. Works in combination with EC 2.6.1.95, neomycin C transaminase, to replace the 6′′′-hydroxy group of 6′′′-hydroxyneomycin C with an amino group. Also catalyses EC 1.1.3.43, paromamine 6′-oxidase.

Links to other databases:

References:

1.	Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem 8 (2007) 283–288. [DOI] [PMID: 17206729]
2.	Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6′-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642–651. [DOI] [PMID: 21689223]

[EC 1.1.3.44 created 2012]

1.1.98.3

Accepted name:

decaprenylphospho-β-D-ribofuranose 2-dehydrogenase

Reaction:

trans,octacis-decaprenylphospho-β-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose + FADH₂

For diagram of decaprenylphosphoarabinofuranose biosynthesis, click here

Other name(s):

decaprenylphosphoryl-β-D-ribofuranose 2′-epimerase; Rv3790; DprE1; decaprenylphospho-β-D-ribofuranose 2-oxidase

Systematic name:

trans,octacis-decaprenylphospho-β-D-ribofuranose:FAD 2-oxidoreductase

Comments:

The enzyme, isolated from the bacterium Mycobacterium smegmatis, is involved, along with EC 1.1.1.333, decaprenylphospho-D-erythro-pentofuranosid-2-ulose 2-reductase, in the epimerization of trans,octacis-decaprenylphospho-β-D-ribofuranose to trans,octacis-decaprenylphospho-β-D-arabinofuranose, the arabinosyl donor for the biosynthesis of mycobacterial cell wall arabinan polymers.

Links to other databases:

References:

1.	Ribeiro, A.L., Degiacomi, G., Ewann, F., Buroni, S., Incandela, M.L., Chiarelli, L.R., Mori, G., Kim, J., Contreras-Dominguez, M., Park, Y.S., Han, S.J., Brodin, P., Valentini, G., Rizzi, M., Riccardi, G. and Pasca, M.R. Analogous mechanisms of resistance to benzothiazinones and dinitrobenzamides in Mycobacterium smegmatis. PLoS One 6:e26675 (2011). [DOI] [PMID: 22069462]
2.	Trefzer, C., Škovierová, H., Buroni, S., Bobovská, A., Nenci, S., Molteni, E., Pojer, F., Pasca, M.R., Makarov, V., Cole, S.T., Riccardi, G., Mikušová, K. and Johnsson, K. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2′-oxidase DprE1. J. Am. Chem. Soc. 134 (2012) 912–915. [DOI] [PMID: 22188377]

[EC 1.1.98.3 created 2012, modified 2014]

1.1.99.38

Accepted name:

2-deoxy-scyllo-inosamine dehydrogenase (AdoMet-dependent)

Reaction:

2-deoxy-scyllo-inosamine + S-adenosyl-L-methionine = 3-amino-2,3-dideoxy-scyllo-inosose + 5′-deoxyadenosine + L-methionine

For diagram of paromamine biosynthesis, click here

Other name(s):

btrN (gene name); 2-deoxy-scyllo-inosamine dehydrogenase (SAM-dependent)

Systematic name:

2-deoxy-scyllo-inosamine:S-adenosyl-L-methionine 1-oxidoreductase

Comments:

Involved in the biosynthetic pathway of the aminoglycoside antibiotics of the butirosin family. The enzyme from Bacillus circulans was shown to be a radical S-adenosyl-L-methionine (SAM) enzyme. cf. EC 1.1.1.329, 2-deoxy-scyllo-inosamine dehydrogenase.

Links to other databases:

References:

1.	Yokoyama, K., Numakura, M., Kudo, F., Ohmori, D. and Eguchi, T. Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin. J. Am. Chem. Soc. 129 (2007) 15147–15155. [DOI] [PMID: 18001019]
2.	Yokoyama, K., Ohmori, D., Kudo, F. and Eguchi, T. Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy. Biochemistry 47 (2008) 8950–8960. [DOI] [PMID: 18672902]

[EC 1.1.99.38 created 2012, modified 2013]

1.2.1.40

Deleted entry:

3α,7α,12α-trihydroxycholestan-26-al 26-oxidoreductase. The activity is part of EC 1.14.13.15, cholestanetriol 26-monooxygenase

[EC 1.2.1.40 created 1976, deleted 2012]

1.2.1.83

Accepted name:

3-succinoylsemialdehyde-pyridine dehydrogenase

Reaction:

4-oxo-4-(pyridin-3-yl)butanal + NADP⁺ + H₂O = 4-oxo-4-(pyridin-3-yl)butanoate + NADPH + H⁺

Glossary:

4-oxo-4-(pyridin-3-yl)butanal = 3-succinoylsemialdehyde-pyridine
4-oxo-4-(3-pyridyl)-butanoate = 3-succinoyl-pyridine

Systematic name:

4-oxo-4-(pyridin-3-yl)butanal:NADP⁺ oxidoreductase

Comments:

The enzyme has been characterized from the soil bacterium Pseudomonas sp. HZN6. It participates in the nicotine degradation pathway.

Links to other databases:

References:

1.	Qiu, J., Ma, Y., Wen, Y., Chen, L., Wu, L. and Liu, W. Functional identification of two novel genes from Pseudomonas sp. strain HZN6 involved in the catabolism of nicotine. Appl. Environ. Microbiol. 78 (2012) 2154–2160. [DOI] [PMID: 22267672]

[EC 1.2.1.83 created 2012]

1.2.1.84

Accepted name:

alcohol-forming fatty acyl-CoA reductase

Reaction:

a long-chain acyl-CoA + 2 NADPH + 2 H⁺ = a long-chain alcohol + 2 NADP⁺ + CoA

Glossary:

a long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 13 to 22 carbon atoms.

Other name(s):

FAR (gene name); long-chain acyl-CoA:NADPH reductase

Systematic name:

NADPH:long-chain acyl-CoA reductase

Comments:

The enzyme has been characterized from the plant Simmondsia chinensis (jojoba). The alcohol is formed by a four-electron reduction of fatty acyl-CoA. Although the reaction proceeds through an aldehyde intermediate, a free aldehyde is not released. The recombinant enzyme was shown to accept saturated and mono-unsaturated fatty acyl-CoAs of 16 to 22 carbons.

Links to other databases:

References:

1.	Metz, J.G., Pollard, M.R., Anderson, L., Hayes, T.R. and Lassner, M.W. Purification of a jojoba embryo fatty acyl-coenzyme A reductase and expression of its cDNA in high erucic acid rapeseed. Plant Physiol. 122 (2000) 635–644. [PMID: 10712526]

[EC 1.2.1.84 created 2012]

1.2.1.85

Accepted name:

2-hydroxymuconate-6-semialdehyde dehydrogenase

Reaction:

2-hydroxymuconate-6-semialdehyde + NAD⁺ + H₂O = (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H⁺

For diagram of catechol catabolism (meta ring cleavage), click here

Glossary:

2-hydroxymuconate-6-semialdehyde = (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate

Other name(s):

xylG (gene name); praB (gene name)

Systematic name:

2-hydroxymuconate-6-semialdehyde:NAD⁺ oxidoreductase

Comments:

This substrate for this enzyme is formed by meta ring cleavage of catechol (EC 1.13.11.2, catechol 2,3-dioxygenase), and is an intermediate in the bacterial degradation of several aromatic compounds. Has lower activity with benzaldehyde [1]. Activity with NAD⁺ is more than 10-fold higher than with NADP⁺ [3]. cf. EC 1.2.1.32, aminomuconate-semialdehyde dehydrogenase.

Links to other databases:

References:

1.	Inoue, J., Shaw, J.P., Rekik, M. and Harayama, S. Overlapping substrate specificities of benzaldehyde dehydrogenase (the xylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the xylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas putida. J. Bacteriol. 177 (1995) 1196–1201. [DOI] [PMID: 7868591]
2.	Orii, C., Takenaka, S., Murakami, S. and Aoki, K. Metabolism of 4-amino-3-hydroxybenzoic acid by Bordetella sp. strain 10d: A different modified meta-cleavage pathway for 2-aminophenols. Biosci. Biotechnol. Biochem. 70 (2006) 2653–2661. [DOI] [PMID: 17090920]
3.	Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758–6768. [DOI] [PMID: 19717587]

[EC 1.2.1.85 created 2012]

1.2.1.86

Accepted name:

geranial dehydrogenase

Reaction:

geranial + H₂O + NAD⁺ = geranate + NADH + H⁺

For diagram of acyclic monoterpenoid biosynthesis, click here

Other name(s):

GaDH; geoB (gene name)

Systematic name:

geranial:NAD⁺ oxidoreductase

Comments:

Does not act on neral.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG

References:

1.	Wolken, W.A. and van der Werf, M.J. Geraniol biotransformation-pathway in spores of Penicillium digitatum. Appl. Microbiol. Biotechnol. 57 (2001) 731–737. [PMID: 11778886]
2.	Lüddeke, F., Wülfing, A., Timke, M., Germer, F., Weber, J., Dikfidan, A., Rahnfeld, T., Linder, D., Meyerdierks, A. and Harder, J. Geraniol and geranial dehydrogenases induced in anaerobic monoterpene degradation by Castellaniella defragrans. Appl. Environ. Microbiol. 78 (2012) 2128–2136. [DOI] [PMID: 22286981]

[EC 1.2.1.86 created 2012]

*EC

1.2.3.1

Accepted name:

aldehyde oxidase

Reaction:

an aldehyde + H₂O + O₂ = a carboxylate + H₂O₂

Other name(s):

quinoline oxidase; retinal oxidase

Systematic name:

aldehyde:oxygen oxidoreductase

Comments:

Contains molybdenum, [2Fe-2S] centres and FAD. The enzyme from liver exhibits a broad substrate specificity, and is involved in the metabolism of xenobiotics, including the oxidation of N-heterocycles and aldehydes and the reduction of N-oxides, nitrosamines, hydroxamic acids, azo dyes, nitropolycyclic aromatic hydrocarbons, and sulfoxides [4,6].The enzyme is also responsible for the oxidation of retinal, an activity that was initially attributed to a distinct enzyme, retinal oxidase (formerly EC 1.2.3.11) [5,7].

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 9029-07-6

References:

1.	Gordon, A.H., Green, D.E. and Subrahmanyan, V. Liver aldehyde oxidase. Biochem. J. 34 (1940) 764–774. [PMID: 16747217]
2.	Knox, W.E. The quinine-oxidizing enzyme and liver aldehyde oxidase. J. Biol. Chem. 163 (1946) 699–711. [PMID: 20985642]
3.	Mahler, H.R., Mackler, B., Green, D.E. and Bock, R.M. Studies on metalloflavoproteins. III. Aldehyde oxidase: a molybdoflavoprotein. J. Biol. Chem. 210 (1954) 465–480. [PMID: 13201608]
4.	Krenitsky, T.A., Neil, S.M., Elion, G.B. and Hitchings, G.H. A comparison of the specificities of xanthine oxidase and aldehyde oxidase. Arch. Biochem. Biophys. 150 (1972) 585–599. [DOI] [PMID: 5044040]
5.	Tomita, S., Tsujita, M. and Ichikawa, Y. Retinal oxidase is identical to aldehyde oxidase. FEBS Lett. 336 (1993) 272–274. [DOI] [PMID: 8262244]
6.	Yoshihara, S. and Tatsumi, K. Purification and characterization of hepatic aldehyde oxidase in male and female mice. Arch. Biochem. Biophys. 338 (1997) 29–34. [DOI] [PMID: 9015384]
7.	Huang, D.-Y., Furukawa, A. and Ichikawa, Y. Molecular cloning of retinal oxidase/aldehyde oxidase cDNAs from rabbit and mouse livers and functional expression of recombinant mouse retinal oxidase cDNA in Escherichia coli. Arch. Biochem. Biophys. 364 (1999) 264–272. [DOI] [PMID: 10190983]
8.	Uchida, H., Kondo, D., Yamashita, A., Nagaosa, Y., Sakurai, T., Fujii, Y., Fujishiro, K., Aisaka, K. and Uwajima, T. Purification and characterization of an aldehyde oxidase from Pseudomonas sp. KY 4690. FEMS Microbiol. Lett. 229 (2003) 31–36. [DOI] [PMID: 14659539]

[EC 1.2.3.1 created 1961, modified 2002, modified 2004, modified 2012]

1.2.3.11

Deleted entry:

retinal oxidase. Now included with EC 1.2.3.1, aldehyde oxidase

[EC 1.2.3.11 created 1990, modified 2002, deleted 2011]

1.3.1.4

Transferred entry:

EC 1.3.1.4, cortisone α-reductase, transferred to EC 1.3.1.22, 3-oxo-5α-steroid 4-dehydrogenase (NADP⁺)

[EC 1.3.1.4 created 1965, deleted 2012]

*EC

1.3.1.22

Accepted name:

3-oxo-5α-steroid 4-dehydrogenase (NADP⁺)

Reaction:

a 3-oxo-5α-steroid + NADP⁺ = a 3-oxo-Δ⁴-steroid + NADPH + H⁺

Other name(s):

cholestenone 5α-reductase; testosterone Δ⁴-5α-reductase; steroid 5α-reductase; 3-oxosteroid Δ⁴-dehydrogenase; 5α-reductase; steroid 5α-hydrogenase; 3-oxosteroid 5α-reductase; testosterone Δ⁴-hydrogenase; 4-ene-3-oxosteroid 5α-reductase; reduced nicotinamide adenine dinucleotide phosphate:Δ⁴-3-ketosteroid 5α-oxidoreductase; 4-ene-5α-reductase; Δ⁴-3-ketosteroid 5α-oxidoreductase; cholest-4-en-3-one 5α-reductase; testosterone 5α-reductase; 3-oxo-5α-steroid 4-dehydrogenase

Systematic name:

3-oxo-5α-steroid:NADP⁺ Δ⁴-oxidoreductase

Comments:

The enzyme catalyses the conversion of assorted 3-oxo-Δ⁴ steroids into their corresponding 5α form. Substrates for the mammalian enzyme include testosterone, progesterone, and corticosterone. Substrates for the plant enzyme are brassinosteroids such as campest-4-en-3-one and (22α)-hydroxy-campest-4-en-3-one. cf. EC 1.3.99.5, 3-oxo-5α-steroid 4-dehydrogenase (acceptor).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37255-34-8

References:

1.	Levy, H.R. and Talalay, P. Bacterial oxidation of steroids. II. Studies on the enzymatic mechanisms of ring A dehydrogenation. J. Biol. Chem. 234 (1959) 2014–2021. [PMID: 13673006]
2.	Shefer, S., Hauser, S. and Mosbach, E.H. Studies on the biosynthesis of 5α-cholestan-3β-ol. I. Cholestenone 5α-reductase of rat liver. J. Biol. Chem. 241 (1966) 946–952. [PMID: 5907469]
3.	Cheng, Y.-J. and Karavolas, H.J. Properties and subcellular distribution of Δ⁴-steroid (progesterone) 5α-reductase in rat anterior pituitary. Steroids 26 (1975) 57–71. [DOI] [PMID: 1166484]
4.	Sargent, N.S. and Habib, F.K. Partial purification of human prostatic 5α-reductase (3-oxo-5α-steroid:NADP⁺ 4-ene-oxido-reductase; EC 1.3.1.22) in a stable and active form. J. Steroid Biochem. Mol. Biol. 38 (1991) 73–77. [DOI] [PMID: 1705142]
5.	Quemener, E., Amet, Y., di Stefano, S., Fournier, G., Floch, H.H. and Abalain, J.H. Purification of testosterone 5α-reductase from human prostate by a four-step chromatographic procedure. Steroids 59 (1994) 712–718. [DOI] [PMID: 7900170]
6.	Poletti, A., Celotti, F., Rumio, C., Rabuffetti, M. and Martini, L. Identification of type 1 5α-reductase in myelin membranes of male and female rat brain. Mol. Cell. Endocrinol. 129 (1997) 181–190. [DOI] [PMID: 9202401]
7.	Li, J., Biswas, M.G., Chao, A., Russell, D.W. and Chory, J. Conservation of function between mammalian and plant steroid 5α-reductases. Proc. Natl. Acad. Sci. USA 94 (1997) 3554–3559. [DOI] [PMID: 9108014]
8.	Rosati, F., Bardazzi, I., De Blasi, P., Simi, L., Scarpi, D., Guarna, A., Serio, M., Racchi, M.L. and Danza, G. 5α-Reductase activity in Lycopersicon esculentum: cloning and functional characterization of LeDET2 and evidence of the presence of two isoenzymes. J. Steroid Biochem. Mol. Biol. 96 (2005) 287–299. [DOI] [PMID: 15993049]

[EC 1.3.1.22 created 1972, modified 2012]

1.3.1.30

Transferred entry:

EC 1.3.1.30, progesterone 5α-reductase, transferred to EC 1.3.1.22, 3-oxo-5α-steroid 4-dehydrogenase (NADP⁺).

[EC 1.3.1.30 created 1978, deleted 2012]

1.3.1.93

Accepted name:

very-long-chain enoyl-CoA reductase

Reaction:

a very-long-chain acyl-CoA + NADP⁺ = a very-long-chain trans-2,3-dehydroacyl-CoA + NADPH + H⁺

Glossary:

a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.

Other name(s):

TSC13 (gene name); CER10 (gene name)

Systematic name:

very-long-chain acyl-CoA:NADP⁺ oxidoreductase

Comments:

This is the fourth component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long-chain acyl CoAs. cf. EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, and EC 4.2.1.134, very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase.

Links to other databases:

References:

1.	Kohlwein, S.D., Eder, S., Oh, C.S., Martin, C.E., Gable, K., Bacikova, D. and Dunn, T. Tsc13p is required for fatty acid elongation and localizes to a novel structure at the nuclear-vacuolar interface in Saccharomyces cerevisiae. Mol. Cell Biol. 21 (2001) 109–125. [DOI] [PMID: 11113186]
2.	Gable, K., Garton, S., Napier, J.A. and Dunn, T.M. Functional characterization of the Arabidopsis thaliana orthologue of Tsc13p, the enoyl reductase of the yeast microsomal fatty acid elongating system. J. Exp. Bot. 55 (2004) 543–545. [DOI] [PMID: 14673020]
3.	Kvam, E., Gable, K., Dunn, T.M. and Goldfarb, D.S. Targeting of Tsc13p to nucleus-vacuole junctions: a role for very-long-chain fatty acids in the biogenesis of microautophagic vesicles. Mol. Biol. Cell 16 (2005) 3987–3998. [DOI] [PMID: 15958487]
4.	Zheng, H., Rowland, O. and Kunst, L. Disruptions of the Arabidopsis enoyl-CoA reductase gene reveal an essential role for very-long-chain fatty acid synthesis in cell expansion during plant morphogenesis. Plant Cell 17 (2005) 1467–1481. [DOI] [PMID: 15829606]

[EC 1.3.1.93 created 2012]

1.3.1.94

Accepted name:

polyprenal reductase

Reaction:

a dolichal + NADP⁺ = a ditrans,polycis-polyprenal + NADPH + H⁺

Other name(s):

SRD5A3 (gene name); DFG10 (gene name); polyprenol reductase (incorrect); ditrans,polycis-dolichol:NADP⁺ 2,3-oxidoreductase (incorrect)

Systematic name:

dolichal:NADP⁺ 2,3-oxidoreductase

Comments:

The enzyme, isolated from human fetal brain tissue but present in all eukaryotes, catalyses the reduction of the terminal double bond next to the aldehyde group in ditrans,polycis-polyprenal, as part of the pathway that produces dolichol. In mammalian cells dolichols are predominantly 18-21 isoprene units in length.

Links to other databases:

References:

1.	Sagami, H., Kurisaki, A. and Ogura, K. Formation of dolichol from dehydrodolichol is catalyzed by NADPH-dependent reductase localized in microsomes of rat liver. J. Biol. Chem. 268 (1993) 10109–10113. [DOI] [PMID: 8486680]
2.	Cantagrel, V., Lefeber, D.J., Ng, B.G., Guan, Z., Silhavy, J.L., Bielas, S.L., Lehle, L., Hombauer, H., Adamowicz, M., Swiezewska, E., De Brouwer, A.P., Blumel, P., Sykut-Cegielska, J., Houliston, S., Swistun, D., Ali, B.R., Dobyns, W.B., Babovic-Vuksanovic, D., van Bokhoven, H., Wevers, R.A., Raetz, C.R., Freeze, H.H., Morava, E., Al-Gazali, L. and Gleeson, J.G. SRD5A3 is required for converting polyprenol to dolichol and is mutated in a congenital glycosylation disorder. Cell 142 (2010) 203–217. [DOI] [PMID: 20637498]
3.	Wilson, M.P., Kentache, T., Althoff, C.R., Schulz, C., de Bettignies, G., Mateu Cabrera, G., Cimbalistiene, L., Burnyte, B., Yoon, G., Costain, G., Vuillaumier-Barrot, S., Cheillan, D., Rymen, D., Rychtarova, L., Hansikova, H., Bury, M., Dewulf, J.P., Caligiore, F., Jaeken, J., Cantagrel, V., Van Schaftingen, E., Matthijs, G., Foulquier, F. and Bommer, G.T. A pseudoautosomal glycosylation disorder prompts the revision of dolichol biosynthesis. Cell (2024) . [DOI] [PMID: 38821050]

[EC 1.3.1.94 created 2012, modified 2024]

1.3.1.95

Accepted name:

acrylyl-CoA reductase (NADH)

Reaction:

propanoyl-CoA + NAD⁺ = acryloyl-CoA + NADH + H⁺

For diagram of 3-(dimethylsulfonio)propanoate metabolism, click here

Glossary:

propanoyl-CoA = propionyl-CoA

Systematic name:

propanoyl-CoA:NAD⁺ oxidoreductase

Comments:

Contains FAD. The reaction is catalysed in the opposite direction to that shown. The enzyme from the bacterium Clostridium propionicum is a complex that includes an electron-transfer flavoprotein (ETF). The ETF is reduced by NADH and transfers the electrons to the active site. Catalyses a step in a pathway for L-alanine fermentation to propanoate [1]. cf. EC 1.3.1.84, acrylyl-CoA reductase (NADPH).

Links to other databases:

References:

1.	Hetzel, M., Brock, M., Selmer, T., Pierik, A.J., Golding, B.T. and Buckel, W. Acryloyl-CoA reductase from Clostridium propionicum. An enzyme complex of propionyl-CoA dehydrogenase and electron-transferring flavoprotein. Eur. J. Biochem. 270 (2003) 902–910. [DOI] [PMID: 12603323]
2.	Kandasamy, V., Vaidyanathan, H., Djurdjevic, I., Jayamani, E., Ramachandran, K.B., Buckel, W., Jayaraman, G. and Ramalingam, S. Engineering Escherichia coli with acrylate pathway genes for propionic acid synthesis and its impact on mixed-acid fermentation. Appl. Microbiol. Biotechnol. 97 (2013) 1191–1200. [DOI] [PMID: 22810300]

[EC 1.3.1.95 created 2012]

1.3.1.96

Accepted name:

Botryococcus squalene synthase

Reaction:

squalene + diphosphate + NADP⁺ = presqualene diphosphate + NADPH + H⁺

For diagram of botryococcus braunii BOT22 squalene and botrycoccene biosynthesis, click here

Other name(s):

SSL-2 (gene name)

Systematic name:

squalene:NADP⁺ oxidoreductase

Comments:

Isolated from the green alga Botryococcus braunii BOT22. Acts in the reverse direction. cf. EC 2.5.1.21, squalene synthase, where squalene is formed directly from farnesyl diphosphate.

Links to other databases:

References:

1.	Niehaus, T.D., Okada, S., Devarenne, T.P., Watt, D.S., Sviripa, V. and Chappell, J. Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii. Proc. Natl. Acad. Sci. USA 108 (2011) 12260–12265. [DOI] [PMID: 21746901]

[EC 1.3.1.96 created 2012]

1.3.1.97

Accepted name:

botryococcene synthase

Reaction:

C₃₀ botryococcene + NADP⁺ + diphosphate = presqualene diphosphate + NADPH + H⁺

For diagram of botryococcus braunii BOT22 squalene and botrycoccene biosynthesis, click here

Glossary:

C₃₀ botryococcene = (10S,13R)-10-ethenyl-2,6,10,13,17,21-hexamethyldocosa-2,5,11,16,20-pentaene

Other name(s):

SSL-3 (gene name)

Systematic name:

C₃₀ botryococcene:NADP⁺ oxidoreductase

Comments:

Isolated from the green alga Botryococcus braunii BOT22. Acts in the reverse direction. Involved in the production of botryococcenes, which are triterpenoid hydrocarbons of isoprenoid origin produced in large amount by this alga.

Links to other databases:

References:

1.	Niehaus, T.D., Okada, S., Devarenne, T.P., Watt, D.S., Sviripa, V. and Chappell, J. Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii. Proc. Natl. Acad. Sci. USA 108 (2011) 12260–12265. [DOI] [PMID: 21746901]

[EC 1.3.1.97 created 2012]

1.3.7.10

Transferred entry:

pentalenolactone synthase. Now EC 1.14.19.8, pentalenolactone synthase

[EC 1.3.7.10 created 2012, deleted 2013]

*EC

1.3.99.5

Accepted name:

3-oxo-5α-steroid 4-dehydrogenase (acceptor)

Reaction:

a 3-oxo-5α-steroid + acceptor = a 3-oxo-Δ⁴-steroid + reduced acceptor

Other name(s):

steroid 5α-reductase; 3-oxosteroid Δ⁴-dehydrogenase; 3-oxo-5α-steroid Δ⁴-dehydrogenase; steroid Δ⁴-5α-reductase; Δ⁴-3-keto steroid 5α-reductase; Δ⁴-3-oxo steroid reductase; Δ⁴-3-ketosteroid5α-oxidoreductase; Δ⁴-3-oxosteroid-5α-reductase; 3-keto-Δ⁴-steroid-5α-reductase; 5α-reductase; testosterone 5α-reductase; 4-ene-3-ketosteroid-5α-oxidoreductase; Δ⁴-5α-dehydrogenase; 3-oxo-5α-steroid:(acceptor) Δ⁴-oxidoreductase; tesI (gene name)

Systematic name:

3-oxo-5α-steroid:acceptor Δ⁴-oxidoreductase

Comments:

A flavoprotein. This bacterial enzyme, characterized from Comamonas testosteroni, is involved in androsterone degradation. cf. EC 1.3.1.22, 3-oxo-5α-steroid 4-dehydrogenase (NADP⁺).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9036-43-5

References:

1.	Levy, H.R. and Talalay, P. Bacterial oxidation of steroids. II. Studies on the enzymatic mechanisms of ring A dehydrogenation. J. Biol. Chem. 234 (1959) 2014–2021. [PMID: 13673006]
2.	Florin, C., Kohler, T., Grandguillot, M. and Plesiat, P. Comamonas testosteroni 3-ketosteroid-Δ⁴(5α)-dehydrogenase: gene and protein characterization. J. Bacteriol. 178 (1996) 3322–3330. [DOI] [PMID: 8655514]
3.	Horinouchi, M., Hayashi, T., Yamamoto, T. and Kudo, T. A new bacterial steroid degradation gene cluster in Comamonas testosteroni TA441 which consists of aromatic-compound degradation genes for seco-steroids and 3-ketosteroid dehydrogenase genes. Appl. Environ. Microbiol. 69 (2003) 4421–4430. [DOI] [PMID: 12902225]

[EC 1.3.99.5 created 1965, modified 2012]

1.4.1.24

Accepted name:

3-dehydroquinate synthase II

Reaction:

2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate + H₂O + NAD⁺ = 3-dehydroquinate + NH₃ + NADH + H⁺

For diagram of 3-dehydroquinate biosynthesis in archaea, click here

Glossary:

2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate = 2-amino-2,3,7-trideoxy-D-lyxo-hept-6-ulosonate

Other name(s):

DHQ synthase II; MJ1249 (gene name); aroB′ (gene name)

Systematic name:

2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate:NAD⁺ oxidoreductase (deaminating)

Comments:

The enzyme, which was isolated from the archaeon Methanocaldococcus jannaschii, plays a key role in an alternative pathway for the biosynthesis of 3-dehydroquinate (DHQ), an intermediate of the canonical pathway for the biosynthesis of aromatic amino acids. The enzyme catalyses a two-step reaction - an oxidative deamination, followed by cyclization.

Links to other databases:

References:

1.	White, R.H. L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii. Biochemistry 43 (2004) 7618–7627. [DOI] [PMID: 15182204]

[EC 1.4.1.24 created 2012]

*EC

1.4.3.15

Accepted name:

D-glutamate(D-aspartate) oxidase

Reaction:

(1) D-glutamate + H₂O + O₂ = 2-oxoglutarate + NH₃ + H₂O₂
(2) D-aspartate + H₂O + O₂ = oxaloacetate + NH₃ + H₂O₂

Other name(s):

D-glutamic-aspartic oxidase; D-monoaminodicarboxylic acid oxidase

Systematic name:

D-glutamate(D-aspartate):oxygen oxidoreductase (deaminating)

Comments:

A flavoprotein (FAD). D-Glutamate and D-aspartate are oxidized at the same rate. Other D-monoaminodicarboxylates, and other D- and L-amino acids, are not oxidized. cf. EC 1.4.3.7, D-glutamate oxidase and EC 1.4.3.1, D-aspartate oxidase.

Links to other databases:

BRENDA, EXPASY, KEGG, CAS registry number: 9029-20-3

References:

1.	Mizushima, S. Purified D-glutamic-aspartic oxidase of Aspergillus ustus. J. Gen. Appl. Microbiol. 3 (1957) 233–239.

[EC 1.4.3.15 created 1983, modified 2012]

1.4.3.24

Transferred entry:

pseudooxynicotine oxidase, now classified as EC 1.4.2.3, pseudooxynicotine dehydrogenase

[EC 1.4.3.24 created 2012, deleted 2022]

1.5.1.43

Accepted name:

carboxynorspermidine synthase

Reaction:

(1) carboxynorspermidine + H₂O + NADP⁺ = L-aspartate 4-semialdehyde + propane-1,3-diamine + NADPH + H⁺
(2) carboxyspermidine + H₂O + NADP⁺ = L-aspartate 4-semialdehyde + putrescine + NADPH + H⁺

Other name(s):

carboxynorspermidine dehydrogenase; carboxyspermidine dehydrogenase; CASDH; CANSDH; VC1624 (gene name)

Systematic name:

carboxynorspermidine:NADP⁺ oxidoreductase

Comments:

The reaction takes place in the opposite direction. Part of a bacterial polyamine biosynthesis pathway. L-aspartate 4-semialdehyde and propane-1,3-diamine/putrescine form a Schiff base that is reduced to form carboxynorspermidine/carboxyspermidine, respectively [1]. The enzyme from the bacterium Vibrio cholerae is essential for biofilm formation [2]. The enzyme from Campylobacter jejuni only produces carboxyspermidine in vivo even though it also can produce carboxynorspermidine in vitro [3].

Links to other databases:

References:

1.	Nakao, H., Shinoda, S. and Yamamoto, S. Purification and some properties of carboxynorspermidine synthase participating in a novel biosynthetic pathway for norspermidine in Vibrio alginolyticus. J. Gen. Microbiol. 137 (1991) 1737–1742. [DOI] [PMID: 1955861]
2.	Lee, J., Sperandio, V., Frantz, D.E., Longgood, J., Camilli, A., Phillips, M.A. and Michael, A.J. An alternative polyamine biosynthetic pathway is widespread in bacteria and essential for biofilm formation in Vibrio cholerae. J. Biol. Chem. 284 (2009) 9899–9907. [DOI] [PMID: 19196710]
3.	Hanfrey, C.C., Pearson, B.M., Hazeldine, S., Lee, J., Gaskin, D.J., Woster, P.M., Phillips, M.A. and Michael, A.J. Alternative spermidine biosynthetic route is critical for growth of Campylobacter jejuni and is the dominant polyamine pathway in human gut microbiota. J. Biol. Chem. 286 (2011) 43301–43312. [DOI] [PMID: 22025614]

[EC 1.5.1.43 created 2012]

1.5.1.44

Accepted name:

festuclavine dehydrogenase

Reaction:

festuclavine + NAD⁺ = 6,8-dimethyl-6,7-didehydroergoline + NADH + H⁺

For diagram of fumigaclavin alkaloid biosynthesis, click here

Glossary:

festuclavine = 6,8β-dimethylergoline

Other name(s):

FgaFS; festuclavine synthase

Systematic name:

festuclavine:NAD⁺ oxidoreductase

Comments:

The enzyme participates in the biosynthesis of fumigaclavine C, an ergot alkaloid produced by some fungi of the Trichocomaceae family. The reaction proceeds in vivo in the opposite direction to the one shown here.

Links to other databases:

References:

Wallwey, C., Matuschek, M., Xie, X.L. and Li, S.M. Ergot alkaloid biosynthesis in Aspergillus fumigatus: Conversion of chanoclavine-I aldehyde to festuclavine by the festuclavine synthase FgaFS in the presence of the old yellow enzyme FgaOx3. Org. Biomol. Chem. 8 (2010) 3500–3508. [DOI] [PMID: 20526482]

[EC 1.5.1.44 created 2012]

1.5.1.45

Accepted name:

FAD reductase [NAD(P)H]

Reaction:

FADH₂ + NAD(P)⁺ = FAD + NAD(P)H + H⁺

For diagram of FAD biosynthesis, click here

Other name(s):

GTNG_3158 (gene name)

Systematic name:

FADH₂:NAD(P)⁺ oxidoreductase

Comments:

This enzyme, isolated from the bacterium Geobacillus thermodenitrificans, participates in the pathway of tryptophan degradation. The enzyme is part of a system that also includes a bifunctional riboflavin kinase/FMN adenylyltransferase and EC 1.14.14.8, anthranilate 3-monooxygenase (FAD). It can reduce either FAD or flavin mononucleotide (FMN) but prefers FAD. The enzyme has a slight preference for NADPH as acceptor. cf. EC 1.5.1.37, FAD reductase (NADH).

Links to other databases:

References:

1.	Liu, X., Dong, Y., Li, X., Ren, Y., Li, Y., Wang, W., Wang, L. and Feng, L. Characterization of the anthranilate degradation pathway in Geobacillus thermodenitrificans NG80-2. Microbiology 156 (2010) 589–595. [DOI] [PMID: 19942660]

[EC 1.5.1.45 created 2012]

1.5.3.19

Accepted name:

4-methylaminobutanoate oxidase (formaldehyde-forming)

Reaction:

4-methylaminobutanoate + O₂ + H₂O = 4-aminobutanoate + formaldehyde + H₂O₂

For diagram of nicotine catabolism by arthrobacter, click here

Other name(s):

mabO (gene name)

Systematic name:

4-methylaminobutanoate:oxygen oxidoreductase (formaldehyde-forming)

Comments:

A flavoprotein (FAD). In the enzyme from the soil bacterium Arthrobacter nicotinovorans the cofactor is covalently bound. Participates in the nicotine degradation pathway of this organism.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, KEGG

References:

1.	Chiribau, C.B., Sandu, C., Fraaije, M., Schiltz, E. and Brandsch, R. A novel γ-N-methylaminobutyrate demethylating oxidase involved in catabolism of the tobacco alkaloid nicotine by Arthrobacter nicotinovorans pAO1. Eur. J. Biochem. 271 (2004) 4677–4684. [DOI] [PMID: 15606755]

[EC 1.5.3.19 created 2012]

1.5.3.20

Accepted name:

N-alkylglycine oxidase

Reaction:

N-alkylglycine + H₂O + O₂ = alkylamine + glyoxalate + H₂O₂

Other name(s):

N-carboxymethylalkylamine:oxygen oxidoreductase (decarboxymethylating)

Systematic name:

N-alkylglycine:oxygen oxidoreductase (alkylamine-forming)

Comments:

Isolated from the mold Cladosporium sp. G-10. Acts on N⁶-(carboxymethyl)lysine, 6-[(carboxymethy)amino]hexanoic acid, sarcosine and N-ethylglycine. It has negligible action on glycine (cf. EC 1.4.3.19 glycine oxidase).

Links to other databases:

References:

1.	Gomi, K. and Horiuchi, T. Purification and characterization of a new enzyme, N-alkylglycine oxidase from Cladosporium sp. G-10. Biochim. Biophys. Acta 1429 (1999) 439–445. [DOI] [PMID: 9989229]

[EC 1.5.3.20 created 2012]

1.5.3.21

Accepted name:

4-methylaminobutanoate oxidase (methylamine-forming)

Reaction:

4-methylaminobutanoate + O₂ + H₂O = succinate semialdehyde + methylamine + H₂O₂

For diagram of nicotine catabolism by arthrobacter, click here

Other name(s):

mao (gene name, ambiguous)

Systematic name:

4-methylaminobutanoate methylamidohydrolase

Comments:

The enzyme participates in the nicotine degradation pathway of the soil bacterium Arthrobacter nicotinovorans. Has a very weak monoamine oxidase (EC 1.4.3.4) activity with 4-aminobutanoate [1].

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, KEGG, PDB

References:

1.	Chiribau, C.B., Sandu, C., Fraaije, M., Schiltz, E. and Brandsch, R. A novel γ-N-methylaminobutyrate demethylating oxidase involved in catabolism of the tobacco alkaloid nicotine by Arthrobacter nicotinovorans pAO1. Eur. J. Biochem. 271 (2004) 4677–4684. [DOI] [PMID: 15606755]
2.	Chiribau, C.B., Mihasan, M., Ganas, P., Igloi, G.L., Artenie, V. and Brandsch, R. Final steps in the catabolism of nicotine. FEBS J. 273 (2006) 1528–1536. [DOI] [PMID: 16689938]

[EC 1.5.3.21 created 2012]

1.5.99.14

Accepted name:

6-hydroxypseudooxynicotine dehydrogenase

Reaction:

1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one + acceptor + H₂O = 1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one + reduced acceptor

For diagram of nicotine catabolism by arthrobacter, click here

Glossary:

1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one = 6-hydroxypseudooxynicotine
1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one = 2,6-dihydroxypseudooxynicotine

Systematic name:

1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one:acceptor 6-oxidoreductase (hydroxylating)

Comments:

Contains a cytidylyl molybdenum cofactor [3]. The enzyme, which participates in the nicotine degradation pathway, has been characterized from the soil bacterium Arthrobacter nicotinovorans [1,2].

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB

References:

1.	Freudenberg, W., Konig, K. and Andreesen, J. R. Nicotine dehydrogenase from Arthrobacter oxidans: A molybdenum-containing hydroxylase. FEMS Microbiology Letters 52 (1988) 13–18.
2.	Grether-Beck, S., Igloi, G.L., Pust, S., Schilz, E., Decker, K. and Brandsch, R. Structural analysis and molybdenum-dependent expression of the pAO1-encoded nicotine dehydrogenase genes of Arthrobacter nicotinovorans. Mol. Microbiol. 13 (1994) 929–936. [DOI] [PMID: 7815950]
3.	Sachelaru, P., Schiltz, E. and Brandsch, R. A functional mobA gene for molybdopterin cytosine dinucleotide cofactor biosynthesis is required for activity and holoenzyme assembly of the heterotrimeric nicotine dehydrogenases of Arthrobacter nicotinovorans. Appl. Environ. Microbiol. 72 (2006) 5126–5131. [DOI] [PMID: 16820521]

[EC 1.5.99.14 created 2012]

1.7.2.6

Accepted name:

hydroxylamine dehydrogenase

Reaction:

hydroxylamine + H₂O + 4 ferricytochrome c = nitrite + 4 ferrocytochrome c + 5 H⁺

Other name(s):

HAO (ambiguous); hydroxylamine oxidoreductase (ambiguous); hydroxylamine oxidase (misleading)

Systematic name:

hydroxylamine:ferricytochrome-c oxidoreductase (nitrite-forming)

Comments:

The enzymes from the nitrifying bacterium Nitrosomonas europaea [1,4] and the methylotrophic bacterium Methylococcus capsulatus [5] are hemoproteins with seven c-type hemes and one specialized P-460-type heme per subunit. The enzyme converts hydroxylamine to nitrite via an enzyme-bound nitroxyl intermediate [3]. While nitrite is the main product, the enzyme from Nitrosomonas europaea can also produce nitric oxide by catalysing the activity of EC 1.7.2.9, hydroxylamine oxidase [2].

Links to other databases:

BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9075-43-8

References:

1.	Rees, M. Studies of the hydroxylamine metabolism of Nitrosomonas europaea. I. Purification of hydroxylamine oxidase. Biochemistry 7 (1968) 353–366. [PMID: 5758552]
2.	Hooper, A.B. and Terry, K.R. Hydroxylamine oxidoreductase of Nitrosomonas. Production of nitric oxide from hydroxylamine. Biochim. Biophys. Acta 571 (1979) 12–20. [DOI] [PMID: 497235]
3.	Hooper, A.B. and Balny, C. Reaction of oxygen with hydroxylamine oxidoreductase of Nitrosomonas: fast kinetics. FEBS Lett. 144 (1982) 299–303. [DOI] [PMID: 7117545]
4.	Lipscomb, J.D. and Hooper, A.B. Resolution of multiple heme centers of hydroxylamine oxidoreductase from Nitrosomonas. 1. Electron paramagnetic resonance spectroscopy. Biochemistry 21 (1982) 3965–3972. [PMID: 6289867]
5.	Poret-Peterson, A.T., Graham, J.E., Gulledge, J. and Klotz, M.G. Transcription of nitrification genes by the methane-oxidizing bacterium, Methylococcus capsulatus strain Bath. ISME J. 2 (2008) 1213–1220. [DOI] [PMID: 18650926]

[EC 1.7.2.6 created 1972 as EC 1.7.3.4, part transferred 2012 to EC 1.7.2.6, modifed 2021, modified 2021]

*EC

1.11.1.8

Accepted name:

iodide peroxidase

Reaction:

(1) 2 iodide + H₂O₂ + 2 H⁺ = diiodine + 2 H₂O
(2) [thyroglobulin]-L-tyrosine + iodide + H₂O₂ = [thyroglobulin]-3-iodo-L-tyrosine + 2 H₂O
(3) [thyroglobulin]-3-iodo-L-tyrosine + iodide + H₂O₂ = [thyroglobulin]-3,5-diiodo-L-tyrosine + 2 H₂O
(4) 2 [thyroglobulin]-3,5-diiodo-L-tyrosine + H₂O₂ = [thyroglobulin]-L-thyroxine + [thyroglobulin]-aminoacrylate + 2 H₂O
(5) [thyroglobulin]-3-iodo-L-tyrosine + [thyroglobulin]-3,5-diiodo-L-tyrosine + H₂O₂ = [thyroglobulin]-3,5,3′-triiodo-L-thyronine + [thyroglobulin]-aminoacrylate + 2 H₂O

Glossary:

3,5,3′-triiodo-L-thyronine = triiodo-L-thyronine

Other name(s):

thyroid peroxidase; iodoperoxidase (heme type); iodide peroxidase-tyrosine iodinase; thyroperoxidase; tyrosine iodinase; TPO; iodinase

Systematic name:

iodide:hydrogen-peroxide oxidoreductase

Comments:

Thyroid peroxidase catalyses the biosynthesis of the thyroid hormones L-thyroxine and triiodo-L-thyronine. It catalyses both the iodination of tyrosine residues in thyroglobulin (forming mono- and di-iodinated forms) and their coupling to form either L-thyroxine or triiodo-L-thyronine.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9031-28-1

References:

1.	Cunningham, B.A. and Kirkwood, S. Enzyme systems concerned with the synthesis of monoiodotyrosine. III. Ion requirements of the soluble system. J. Biol. Chem. 236 (1961) 485–489. [PMID: 13718859]
2.	Hosoya, T., Kondo, Y. and Ui, N. Peroxidase activity in thyroid gland and partial purification of the enzyme. J. Biochem. (Tokyo) 52 (1962) 180–189. [PMID: 13964156]
3.	Coval, M.L. and Taurog, A. Purification and iodinating activity of hog thyroid peroxidase. J. Biol. Chem. 242 (1967) 5510–5523. [PMID: 12325367]
4.	Gavaret, J.M., Cahnmann, H.J. and Nunez, J. Thyroid hormone synthesis in thyroglobulin. The mechanism of the coupling reaction. J. Biol. Chem. 256 (1981) 9167–9173. [PMID: 7021557]
5.	Ohtaki, S., Nakagawa, H., Nakamura, M. and Yamazaki, I. One- and two-electron oxidations of tyrosine, monoiodotyrosine, and diiodotyrosine catalyzed by hog thyroid peroxidase. J. Biol. Chem. 257 (1982) 13398–13403. [PMID: 7142155]
6.	Magnusson, R.P., Taurog, A. and Dorris, M.L. Mechanism of iodide-dependent catalatic activity of thyroid peroxidase and lactoperoxidase. J. Biol. Chem. 259 (1984) 197–205. [PMID: 6706930]
7.	Virion, A., Courtin, F., Deme, D., Michot, J.L., Kaniewski, J. and Pommier, J. Spectral characteristics and catalytic properties of thyroid peroxidase-H₂O₂ compounds in the iodination and coupling reactions. Arch. Biochem. Biophys. 242 (1985) 41–47. [DOI] [PMID: 2996435]
8.	Rawitch, A.B., Pollock, G., Yang, S.X. and Taurog, A. Thyroid peroxidase glycosylation: the location and nature of the N-linked oligosaccharide units in porcine thyroid peroxidase. Arch. Biochem. Biophys. 297 (1992) 321–327. [DOI] [PMID: 1497352]
9.	Sun, W. and Dunford, H.B. Kinetics and mechanism of the peroxidase-catalyzed iodination of tyrosine. Biochemistry 32 (1993) 1324–1331. [PMID: 8448141]
10.	Taurog, A., Dorris, M.L. and Doerge, D.R. Mechanism of simultaneous iodination and coupling catalyzed by thyroid peroxidase. Arch. Biochem. Biophys. 330 (1996) 24–32. [DOI] [PMID: 8651700]
11.	Ruf, J. and Carayon, P. Structural and functional aspects of thyroid peroxidase. Arch. Biochem. Biophys. 445 (2006) 269–277. [DOI] [PMID: 16098474]

[EC 1.11.1.8 created 1961, modified 2012]

*EC

1.13.11.12

Accepted name:

linoleate 13S-lipoxygenase

Reaction:

(1) linoleate + O₂ = (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate
(2) α-linolenate + O₂ = (9Z,11E,13S,15Z)-13-hydroperoxyoctadeca-9,11,15-trienoate

Glossary:

linoleate = (9Z,12Z)-octadeca-9,12-dienoate
α-linolenate = (9Z,12Z,15Z)-octadeca-9,12,15-trienoate

Other name(s):

13-lipoxidase; carotene oxidase; 13-lipoperoxidase; fat oxidase; 13-lipoxydase; lionoleate:O₂ 13-oxidoreductase

Systematic name:

linoleate:oxygen 13-oxidoreductase

Comments:

Contains nonheme iron. A common plant lipoxygenase that oxidizes linoleate and α-linolenate, the two most common polyunsaturated fatty acids in plants, by inserting molecular oxygen at the C-13 position with (S)-configuration. This enzyme produces precursors for several important compounds, including the plant hormone jasmonic acid. EC 1.13.11.58, linoleate 9S-lipoxygenase, catalyses a similar reaction at the second available position of these fatty acids.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9029-60-1

References:

1.	Christopher, J., Pistorius, E. and Axelrod, B. Isolation of an enzyme of soybean lipoxidase. Biochim. Biophys. Acta 198 (1970) 12–19. [DOI] [PMID: 5461103]
2.	Theorell, H., Holman, R.T. and Åkesson, Å. Crystalline lipoxidase. Acta Chem. Scand. 1 (1947) 571–576. [PMID: 18907700]
3.	Zimmerman, D.C. Specificity of flaxseed lipoxidase. Lipids 5 (1970) 392–397. [DOI] [PMID: 5447012]
4.	Royo, J., Vancanneyt, G., Perez, A.G., Sanz, C., Stormann, K., Rosahl, S. and Sanchez-Serrano, J.J. Characterization of three potato lipoxygenases with distinct enzymatic activities and different organ-specific and wound-regulated expression patterns. J. Biol. Chem. 271 (1996) 21012–21019. [DOI] [PMID: 8702864]
5.	Bachmann, A., Hause, B., Maucher, H., Garbe, E., Voros, K., Weichert, H., Wasternack, C. and Feussner, I. Jasmonate-induced lipid peroxidation in barley leaves initiated by distinct 13-LOX forms of chloroplasts. Biol. Chem. 383 (2002) 1645–1657. [DOI] [PMID: 12452441]

[EC 1.13.11.12 created 1961 as EC 1.99.2.1, transferred 1965 to EC 1.13.1.13, transferred 1972 to EC 1.13.11.12, modified 2011, modified 2012]

*EC

1.13.11.16

Accepted name:

3-carboxyethylcatechol 2,3-dioxygenase

Reaction:

(1) 3-(2,3-dihydroxyphenyl)propanoate + O₂ = (2Z,4E)-2-hydroxy-6-oxonona-2,4-diene-1,9-dioate
(2) (2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate + O₂ = (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioate

For diagram of 3-phenylpropanoate catabolism, click here and for diagram of cinnamate catabolism, click here

Glossary:

(2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate = trans-2,3-dihydroxycinnamate

Other name(s):

2,3-dihydroxy-β-phenylpropionic dioxygenase; 2,3-dihydroxy-β-phenylpropionate oxygenase; 3-(2,3-dihydroxyphenyl)propanoate:oxygen 1,2-oxidoreductase; 3-(2,3-dihydroxyphenyl)propanoate:oxygen 1,2-oxidoreductase (decyclizing)

Systematic name:

3-(2,3-dihydroxyphenyl)propanoate:oxygen 1,2-oxidoreductase (ring-opening)

Comments:

An iron protein. This enzyme catalyses a step in the pathway of phenylpropanoid compounds degradation.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 105503-63-7

References:

1.	Dagley, S., Chapman, P.J. and Gibson, D.T. The metabolism of β-phenylpropionic acid by an Achromobacter. Biochem. J. 97 (1965) 643–650. [PMID: 5881653]
2.	Lam, W. W. Y and Bugg, T. D. H. Chemistry of extradiol aromatic ring cleavage: isolation of a stable dienol ring fission intermediate and stereochemistry of its enzymatic hydrolytic clevage. J. Chem. Soc., Chem. Commun. 10 (1994) 1163–1164.
3.	Díaz, E., Ferrández, A. and García, J.L. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180 (1998) 2915–2923. [PMID: 9603882]

[EC 1.13.11.16 created 1972, modified 2011, modified 2012]

*EC

1.13.11.35

Accepted name:

pyrogallol 1,2-oxygenase

Reaction:

1,2,3-trihydroxybenzene + O₂ = (2Z,4E)-2-hydroxyhexa-2,4-dienedioate

Glossary:

(2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (2Z,4E)-2-hydroxymuconate
1,2,3-trihydroxybenzene = pyrogallol

Other name(s):

pyrogallol 1,2-dioxygenase; 1,2,3-trihydroxybenzene:oxygen 1,2-oxidoreductase (decyclizing)

Systematic name:

1,2,3-trihydroxybenzene:oxygen 1,2-oxidoreductase (ring-opening)

Links to other databases:

BRENDA, EXPASY, KEGG, CAS registry number: 78310-68-6

References:

1.	Groseclose, E.E. and Ribbons, D.W. Metabolism of resorcinylic compounds by bacteria: new pathway for resorcinol catabolism in Azotobacter vinelandii. J. Bacteriol. 146 (1981) 460–466. [PMID: 7217008]

[EC 1.13.11.35 created 1984, modified 2012]

1.13.11.64

Accepted name:

5-nitrosalicylate dioxygenase

Reaction:

5-nitrosalicylate + O₂ = 2-oxo-3-(5-oxofuran-2-ylidene)propanoate + nitrite (overall reaction)
(1a) 5-nitrosalicylate + O₂ = 4-nitro-6-oxohepta-2,4-dienedioate
(1b) 4-nitro-6-oxohepta-2,4-dienedioate = 2-oxo-3-(5-oxofuran-2-ylidene)propanoate + nitrite (spontaneous)

Other name(s):

naaB (gene name); 5-nitrosalicylate:oxygen 1,2-oxidoreductase (decyclizing)

Systematic name:

5-nitrosalicylate:oxygen 1,2-oxidoreductase (ring-opening)

Comments:

The enzyme, characterized from the soil bacterium Bradyrhizobium sp. JS329, is involved in the pathway of 5-nitroanthranilate degradation. It is unusual in being able to catalyse the ring fission without the requirement for prior removal of the nitro group. The product undergoes spontaneous lactonization, with concurrent elimination of the nitro group.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, KEGG, PDB

References:

1.	Qu, Y. and Spain, J.C. Biodegradation of 5-nitroanthranilic acid by Bradyrhizobium sp. strain JS329. Appl. Environ. Microbiol. 76 (2010) 1417–1422. [DOI] [PMID: 20081004]
2.	Qu, Y. and Spain, J.C. Molecular and biochemical characterization of the 5-nitroanthranilic acid degradation pathway in Bradyrhizobium sp. strain JS329. J. Bacteriol. 193 (2011) 3057–3063. [DOI] [PMID: 21498645]

[EC 1.13.11.64 created 2012]

1.13.11.65

Accepted name:

carotenoid isomerooxygenase

Reaction:

zeaxanthin + O₂ = (3R)-11-cis-3-hydroxyretinal + (3R)-all-trans-3-hydroxyretinal

For diagram of zeaxanthin biosynthesis, click here

Other name(s):

ninaB (gene name)

Systematic name:

zeaxanthin:oxygen 15,15′-oxidoreductase (bond-cleaving, cis-isomerizing)

Comments:

The enzyme, characterized from the moth Galleria mellonella and the fruit fly Drosophila melanogaster, is involved in the synthesis of retinal from dietary caroteoids in insects. The enzyme accepts different all-trans carotenoids, including β-carotene, α-carotene and lutein, and catalyses the symmetrical cleavage of the carotenoid and the simultaneous isomerization of only one of the products to a cis configuration. When the substrate is hydroxylated only in one side (as in cryptoxanthin), the enzyme preferentially isomerizes the hydroxylated part of the molecule.

Links to other databases:

References:

1.	Oberhauser, V., Voolstra, O., Bangert, A., von Lintig, J. and Vogt, K. NinaB combines carotenoid oxygenase and retinoid isomerase activity in a single polypeptide. Proc. Natl. Acad. Sci. USA 105 (2008) 19000–19005. [DOI] [PMID: 19020100]

[EC 1.13.11.65 created 2012 as EC 1.14.13.164, transferred 2012 to EC 1.13.11.65]

1.13.11.66

Accepted name:

hydroquinone 1,2-dioxygenase

Reaction:

benzene-1,4-diol + O₂ = (2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate

For diagram of 4-nitrophenol metabolism, click here

Glossary:

benzene-1,4-diol = hydroquinone
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate = 4-hydroxymuconic semialdehyde

Other name(s):

hydroquinone dioxygenase; benzene-1,4-diol:oxygen 1,2-oxidoreductase (decyclizing)

Systematic name:

benzene-1,4-diol:oxygen 1,2-oxidoreductase (ring-opening)

Comments:

The enzyme is an extradiol-type dioxygenase, and is a member of the nonheme-iron(II)-dependent dioxygenase family. It catalyses the ring cleavage of a wide range of hydroquinone substrates to produce the corresponding 4-hydroxymuconic semialdehydes.

Links to other databases:

References:

1.	Miyauchi, K., Adachi, Y., Nagata, Y. and Takagi, M. Cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of γ-hexachlorocyclohexane in Sphingomonas paucimobilis. J. Bacteriol. 181 (1999) 6712–6719. [PMID: 10542173]
2.	Moonen, M.J., Synowsky, S.A., van den Berg, W.A., Westphal, A.H., Heck, A.J., van den Heuvel, R.H., Fraaije, M.W. and van Berkel, W.J. Hydroquinone dioxygenase from pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases. J. Bacteriol. 190 (2008) 5199–5209. [DOI] [PMID: 18502867]
3.	Shen, W., Liu, W., Zhang, J., Tao, J., Deng, H., Cao, H. and Cui, Z. Cloning and characterization of a gene cluster involved in the catabolism of p-nitrophenol from Pseudomonas putida DLL-E4. Bioresour. Technol. 101 (2010) 7516–7522. [DOI] [PMID: 20466541]

[EC 1.13.11.66 created 2012]

1.13.11.67

Accepted name:

8′-apo-β-carotenoid 14′,13′-cleaving dioxygenase

Reaction:

8′-apo-β-carotenol + O₂ = 14′-apo-β-carotenal + an uncharacterized product

For diagram of 8′-apo-β-carotenal metabolites, click here

Other name(s):

8′-apo-β-carotenol:O₂ oxidoreductase (14′,13′-cleaving)

Systematic name:

8′-apo-β-carotenol:oxygen oxidoreductase (14′,13′-cleaving)

Comments:

A thiol-dependent enzyme isolated from rat and rabbit. Unlike EC 1.13.11.63, β-carotene-15,15′-dioxygenase, it is not active towards β-carotene. The secondary product has not been characterized, but may be (3E,5E)-7-hydroxy-6-methylhepta-3,5-dien-2-one.

Links to other databases:

BRENDA, EXPASY, KEGG, CAS registry number: 198028-39-6

References:

1.	Dmitrovskii, A.A., Gessler, N.N., Gomboeva, S.B., Ershov, Yu.V. and Bykhovsky, V.Ya. Enzymatic oxidation of β-apo-8′-carotenol to β-apo-14′-carotenal by an enzyme different from β-carotene-15,15′-dioxygenase. Biochemistry (Mosc.) 62 (1997) 787–792. [PMID: 9331970]

[EC 1.13.11.67 created 2000 as EC 1.13.12.12, transferred 2012 to EC 1.13.11.67]

1.13.11.68

Accepted name:

9-cis-β-carotene 9′,10′-cleaving dioxygenase

Reaction:

9-cis-β-carotene + O₂ = 9-cis-10′-apo-β-carotenal + β-ionone

For diagram of strigol biosynthesis, click here

Glossary:

β-ionone = (3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one

Other name(s):

CCD7 (gene name); MAX3 (gene name); NCED7 (gene name)

Systematic name:

9-cis-β-carotene:oxygen oxidoreductase (9′,10′-cleaving)

Comments:

Requires Fe²⁺. The enzyme participates in a pathway leading to biosynthesis of strigolactones, plant hormones involved in promotion of symbiotic associations known as arbuscular mycorrhiza.

Links to other databases:

References:

1.	Booker, J., Auldridge, M., Wills, S., McCarty, D., Klee, H. and Leyser, O. MAX3/CCD7 is a carotenoid cleavage dioxygenase required for the synthesis of a novel plant signaling molecule. Curr. Biol. 14 (2004) 1232–1238. [DOI] [PMID: 15268852]
2.	Alder, A., Jamil, M., Marzorati, M., Bruno, M., Vermathen, M., Bigler, P., Ghisla, S., Bouwmeester, H., Beyer, P. and Al-Babili, S. The path from β-carotene to carlactone, a strigolactone-like plant hormone. Science 335 (2012) 1348–1351. [DOI] [PMID: 22422982]

[EC 1.13.11.68 created 2012]

1.13.11.69

Accepted name:

carlactone synthase

Reaction:

9-cis-10′-apo-β-carotenal + 2 O₂ = carlactone + (2E,4E,6E)-7-hydroxy-4-methylhepta-2,4,6-trienal

For diagram of strigol biosynthesis, click here

Glossary:

carlactone = 3-methyl-5-{[(1Z,3E)-2-methyl-4-(2,6,6-trimethylcyclohex-1-en-1-yl)buta-1,3-dien-1-yl]oxy}-5H-furan-2-one

Other name(s):

CCD8 (gene name); MAX4 (gene name); NCED8 (gene name)

Systematic name:

9-cis-10′-apo-β-carotenal:oxygen oxidoreductase (14,15-cleaving, carlactone-forming)

Comments:

Requires Fe²⁺. The enzyme participates in a pathway leading to biosynthesis of strigolactones, plant hormones involved in promotion of symbiotic associations known as arbuscular mycorrhiza. Also catalyses EC 1.13.11.70, all-trans-10′-apo-β-carotenal 13,14-cleaving dioxygenase, but 10-fold slower.

Links to other databases:

References:

1.	Sorefan, K., Booker, J., Haurogne, K., Goussot, M., Bainbridge, K., Foo, E., Chatfield, S., Ward, S., Beveridge, C., Rameau, C. and Leyser, O. MAX4 and RMS1 are orthologous dioxygenase-like genes that regulate shoot branching in Arabidopsis and pea. Genes Dev. 17 (2003) 1469–1474. [DOI] [PMID: 12815068]
2.	Schwartz, S.H., Qin, X. and Loewen, M.C. The biochemical characterization of two carotenoid cleavage enzymes from Arabidopsis indicates that a carotenoid-derived compound inhibits lateral branching. J. Biol. Chem. 279 (2004) 46940–46945. [DOI] [PMID: 15342640]
3.	Alder, A., Jamil, M., Marzorati, M., Bruno, M., Vermathen, M., Bigler, P., Ghisla, S., Bouwmeester, H., Beyer, P. and Al-Babili, S. The path from β-carotene to carlactone, a strigolactone-like plant hormone. Science 335 (2012) 1348–1351. [DOI] [PMID: 22422982]

[EC 1.13.11.69 created 2012]

1.13.11.70

Accepted name:

all-trans-10′-apo-β-carotenal 13,14-cleaving dioxygenase

Reaction:

all-trans-10′-apo-β-carotenal + O₂ = 13-apo-β-carotenone + (2E,4E,6E)-4-methylocta-2,4,6-trienedial

For diagram of 10′-apo-β-carotenal biosynthesis, click here

Other name(s):

CCD8 (gene name); MAX4 (gene name); NCED8 (gene name); all-trans-10′-apo-β-carotenal:O₂ oxidoreductase (13,14-cleaving)

Systematic name:

all-trans-10′-apo-β-carotenal:oxygen oxidoreductase (13,14-cleaving)

Comments:

Requires Fe²⁺. The enzyme from the plant Arabidopsis thaliana also catalyses EC 1.13.11.69, carlactone synthase, 10-fold faster.

Links to other databases:

References:

1.	Schwartz, S.H., Qin, X. and Loewen, M.C. The biochemical characterization of two carotenoid cleavage enzymes from Arabidopsis indicates that a carotenoid-derived compound inhibits lateral branching. J. Biol. Chem. 279 (2004) 46940–46945. [DOI] [PMID: 15342640]

[EC 1.13.11.70 created 2012]

1.13.11.71

Accepted name:

carotenoid-9′,10′-cleaving dioxygenase

Reaction:

all-trans-β-carotene + O₂ = all-trans-10′-apo-β-carotenal + β-ionone

For diagram of 10′-apo-β-carotenal biosynthesis, click here

Other name(s):

BCO₂ (gene name); β-carotene 9′,10′-monooxygenase (misleading); all-trans-β-carotene:O₂ oxidoreductase (9′,10′-cleaving)

Systematic name:

all-trans-β-carotene:oxygen oxidoreductase (9′,10′-cleaving)

Comments:

Requires Fe²⁺. The enzyme catalyses the asymmetric oxidative cleavage of carotenoids. The mammalian enzyme can also cleave all-trans-lycopene.

Links to other databases:

References:

1.	Kiefer, C., Hessel, S., Lampert, J.M., Vogt, K., Lederer, M.O., Breithaupt, D.E. and von Lintig, J. Identification and characterization of a mammalian enzyme catalyzing the asymmetric oxidative cleavage of provitamin A. J. Biol. Chem. 276 (2001) 14110–14116. [DOI] [PMID: 11278918]
2.	Lindqvist, A., He, Y.G. and Andersson, S. Cell type-specific expression of β-carotene 9′,10′-monooxygenase in human tissues. J. Histochem. Cytochem. 53 (2005) 1403–1412. [DOI] [PMID: 15983114]

[EC 1.13.11.71 created 2012]

1.13.11.72

Accepted name:

2-hydroxyethylphosphonate dioxygenase

Reaction:

2-hydroxyethylphosphonate + O₂ = hydroxymethylphosphonate + formate

For diagram of phosphonate metabolism, click here

Other name(s):

HEPD; phpD (gene name); 2-hydroxyethylphosphonate:O₂ 1,2-oxidoreductase (hydroxymethylphosphonate forming)

Systematic name:

2-hydroxyethylphosphonate:oxygen 1,2-oxidoreductase (hydroxymethylphosphonate-forming)

Comments:

Requires non-heme-iron(II). Isolated from some bacteria including Streptomyces hygroscopicus and Streptomyces viridochromogenes. The pro-R hydrogen at C-2 of the ethyl group is retained by the formate ion. Any stereochemistry at C-1 of the ethyl group is lost. One atom from dioxygen is present in each product. Involved in phosphinothricin biosynthesis.

Links to other databases:

References:

1.	Cicchillo, R.M., Zhang, H., Blodgett, J.A., Whitteck, J.T., Li, G., Nair, S.K., van der Donk, W.A. and Metcalf, W.W. An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis. Nature 459 (2009) 871–874. [DOI] [PMID: 19516340]
2.	Whitteck, J.T., Malova, P., Peck, S.C., Cicchillo, R.M., Hammerschmidt, F. and van der Donk, W.A. On the stereochemistry of 2-hydroxyethylphosphonate dioxygenase. J. Am. Chem. Soc. 133 (2011) 4236–4239. [DOI] [PMID: 21381767]
3.	Peck, S.C., Cooke, H.A., Cicchillo, R.M., Malova, P., Hammerschmidt, F., Nair, S.K. and van der Donk, W.A. Mechanism and substrate recognition of 2-hydroxyethylphosphonate dioxygenase. Biochemistry 50 (2011) 6598–6605. [DOI] [PMID: 21711001]

[EC 1.13.11.72 created 2012]

1.13.11.73

Accepted name:

methylphosphonate synthase

Reaction:

2-hydroxyethylphosphonate + O₂ = methylphosphonate + hydrogen carbonate

For diagram of phosphonate metabolism, click here

Other name(s):

mpnS (gene name); 2-hydroxyethylphosphonate:O₂ 1,2-oxidoreductase (methylphosphonate-forming)

Systematic name:

2-hydroxyethylphosphonate:oxygen 1,2-oxidoreductase (methylphosphonate-forming)

Comments:

Isolated from the marine archaeon Nitrosopumilus maritimus.

Links to other databases:

References:

Metcalf, W.W., Griffin, B.M., Cicchillo, R.M., Gao, J., Janga, S.C., Cooke, H.A., Circello, B.T., Evans, B.S., Martens-Habbena, W., Stahl, D.A. and van der Donk, W.A. Synthesis of methylphosphonic acid by marine microbes: a source for methane in the aerobic ocean. Science 337 (2012) 1104–1107. [DOI] [PMID: 22936780]

[EC 1.13.11.73 created 2012]

1.13.12.12

Transferred entry:

apo-β-carotenoid-14′,13′-dioxygenase. The enzyme was misclassified and has been transferred to EC 1.13.11.67, 8-apo-β-carotenoid 14′,13′-cleaving dioxygenase

[EC 1.13.12.12 created 2000, modified 2001, deleted 2012]

1.14.11.35

Accepted name:

1-deoxypentalenic acid 11β-hydroxylase

Reaction:

1-deoxypentalenate + 2-oxoglutarate + O₂ = 1-deoxy-11β-hydroxypentalenate + succinate + CO₂

For diagram of pentalenolactone biosynthesis, click here

Glossary:

1-deoxypentalenate = (1R,3aR,5aS,8aR)-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate
1-deoxy-11β-hydroxypentalenate = (1S,2R,3aR,5aS,8aR)-2-hydroxy-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate

Other name(s):

ptlH (gene name); sav2991 (gene name); pntH (gene name)

Systematic name:

1-deoxypentalenic acid,2-oxoglutarate:oxygen oxidoreductase

Comments:

The enzyme requires iron(II) and ascorbate. Isolated from the bacterium Streptomyces avermitilis. Part of the pathway for pentalenolactone biosynthesis.

Links to other databases:

References:

1.	You, Z., Omura, S., Ikeda, H. and Cane, D.E. Pentalenolactone biosynthesis. Molecular cloning and assignment of biochemical function to PtlH, a non-heme iron dioxygenase of Streptomyces avermitilis. J. Am. Chem. Soc. 128 (2006) 6566–6567. [DOI] [PMID: 16704250]
2.	You, Z., Omura, S., Ikeda, H., Cane, D.E. and Jogl, G. Crystal structure of the non-heme iron dioxygenase PtlH in pentalenolactone biosynthesis. J. Biol. Chem. 282 (2007) 36552–36560. [DOI] [PMID: 17942405]

[EC 1.14.11.35 created 2012]

1.14.11.36

Accepted name:

pentalenolactone F synthase

Reaction:

pentalenolactone D + 2 2-oxoglutarate + 2 O₂ = pentalenolactone F + 2 succinate + 2 CO₂ + H₂O (overall reaction)
(1a) pentalenolactone D + 2-oxoglutarate + O₂ = pentalenolactone E + succinate + CO₂ + H₂O
(1b) pentalenolactone E + 2-oxoglutarate + O₂ = pentalenolactone F + succinate + CO₂

For diagram of pentalenolactone biosynthesis, click here

Glossary:

pentalenolactone D = (1S,4aR,6aS,9aR)-1,8,8-trimethyl-2-oxo-1,2,4,4a,6a,7,8,9-octahydropentaleno[1,6a-c]pyran-5-carboxylate
pentalenolactone E = (4aR,6aS,9aR)-8,8-dimethyl-1-methylene-2-oxo-1,2,4,4a,6a,7,8,9-octahydropentaleno[1,6a-c]pyran-5-carboxylate
pentalenolactone F = (1′R,4′aR,6′aS,9′aR)-8′,8′-dimethyl-2′-oxo-4′,4′a,6′a,8′,9′-hexahydrospiro[oxirane-2,1′-pentaleno[1,6a-c]pyran]-5′-carboxylic acid

Other name(s):

penD (gene name); pntD (gene name); ptlD (gene name)

Systematic name:

pentalenolactone-D,2-oxoglutarate:oxygen oxidoreductase

Comments:

Requires iron(II) and ascorbate. Isolated from the bacteria Streptomyces exfoliatus, Streptomyces arenae and Streptomyces avermitilis. Part of the pentalenolactone biosynthesis pathway.

Links to other databases:

References:

Seo, M.J., Zhu, D., Endo, S., Ikeda, H. and Cane, D.E. Genome mining in Streptomyces. Elucidation of the role of Baeyer-Villiger monooxygenases and non-heme iron-dependent dehydrogenase/oxygenases in the final steps of the biosynthesis of pentalenolactone and neopentalenolactone. Biochemistry 50 (2011) 1739–1754. [DOI] [PMID: 21250661]

[EC 1.14.11.36 created 2012]

*EC

1.14.12.13

Accepted name:

2-halobenzoate 1,2-dioxygenase

Reaction:

a 2-halobenzoate + NADH + H⁺ + O₂ = catechol + a halide anion + NAD⁺ + CO₂

For diagram of benzoate metabolism, click here, and for mechanism, click here

Other name(s):

2-chlorobenzoate 1,2-dioxygenase

Systematic name:

2-halobenzoate,NADH:oxygen oxidoreductase (1,2-hydroxylating, dehalogenating, decarboxylating)

Comments:

A multicomponent enzyme system composed of a dioxygenase component and an electron transfer component. The latter contains FAD. The enzyme, characterized from the bacterium Burkholderia cepacia 2CBS, has a broad substrate specificity. Substrates include 2-fluorobenzoate, 2-chlorobenzoate, 2-bromobenzoate, and 2-iodobenzoate, which are processed in this order of preference.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, CAS registry number: 125268-83-9

References:

1.	Fetzner, S., Mueller, R. and Lingens, F. Degradation of 2-chlorobenzoate by Pseudomonas cepacia 2CBS. Biol. Chem. Hoppe-Seyler 370 (1989) 1173–1182. [PMID: 2610934]
2.	Fetzner, S., Muller, R. and Lingens, F. Purification and some properties of 2-halobenzoate 1,2-dioxygenase, a two-component enzyme system from Pseudomonas cepacia 2CBS. J. Bacteriol. 174 (1992) 279–290. [DOI] [PMID: 1370284]
3.	Haak, B., Fetzner, S. and Lingens, F. Cloning, nucleotide sequence, and expression of the plasmid-encoded genes for the two-component 2-halobenzoate 1,2-dioxygenase from Pseudomonas cepacia 2CBS. J. Bacteriol. 177 (1995) 667–675. [DOI] [PMID: 7530709]

[EC 1.14.12.13 created 1992, modified 2012]

*EC

1.14.13.15

Transferred entry:

cholestanetriol 26-monooxygenase. Now EC 1.14.15.15, cholestanetriol 26-monooxygenase.

[EC 1.14.13.15 created 1976, modified 2005, modified 2012, deleted 2016]

*EC

1.14.13.39

Accepted name:

nitric-oxide synthase (NADPH)

Reaction:

2 L-arginine + 3 NADPH + 3 H⁺ + 4 O₂ = 2 L-citrulline + 2 nitric oxide + 3 NADP⁺ + 4 H₂O (overall reaction)
(1a) 2 L-arginine + 2 NADPH + 2 H⁺ + 2 O₂ = 2 N^ω-hydroxy-L-arginine + 2 NADP⁺ + 2 H₂O
(1b) 2 N^ω-hydroxy-L-arginine + NADPH + H⁺ + 2 O₂ = 2 L-citrulline + 2 nitric oxide + NADP⁺ + 2 H₂O

Glossary:

nitric oxide = NO = nitrogen(II) oxide

Other name(s):

NOS (gene name); nitric oxide synthetase (ambiguous); endothelium-derived relaxation factor-forming enzyme; endothelium-derived relaxing factor synthase; NO synthase (ambiguous); NADPH-diaphorase (ambiguous)

Systematic name:

L-arginine,NADPH:oxygen oxidoreductase (nitric-oxide-forming)

Comments:

The enzyme consists of linked oxygenase and reductase domains. The eukaryotic enzyme binds FAD, FMN, heme (iron protoporphyrin IX) and tetrahydrobiopterin, and its two domains are linked via a regulatory calmodulin-binding domain. Upon calcium-induced calmodulin binding, the reductase and oxygenase domains form a complex, allowing electrons to flow from NADPH via FAD and FMN to the active center. The reductase domain of the enzyme from the bacterium Sorangium cellulosum utilizes a [2Fe-2S] cluster to transfer the electrons from NADPH to the active center. cf. EC 1.14.14.47, nitric-oxide synthase (flavodoxin).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 125978-95-2

References:

1.	Bredt, D.S. and Snyder, S.H. Isolation of nitric oxide synthetase, a calmodulin-requiring enzyme. Proc. Natl. Acad. Sci. USA 87 (1990) 682–685. [DOI] [PMID: 1689048]
2.	Stuehr, D.J., Kwon, N.S., Nathan, C.F., Griffith, O.W., Feldman, P.L. and Wiseman, J. N^ω-hydroxy-L-arginine is an intermediate in the biosynthesis of nitric oxide from L-arginine. J. Biol. Chem. 266 (1991) 6259–6263. [PMID: 1706713]
3.	Stuehr, D., Pou, S. and Rosen, G.M. Oxygen reduction by nitric-oxide synthases. J. Biol. Chem. 276 (2001) 14533–14536. [DOI] [PMID: 11279231]
4.	Agapie, T., Suseno, S., Woodward, J.J., Stoll, S., Britt, R.D. and Marletta, M.A. NO formation by a catalytically self-sufficient bacterial nitric oxide synthase from Sorangium cellulosum. Proc. Natl. Acad. Sci. USA 106 (2009) 16221–16226. [DOI] [PMID: 19805284]
5.	Foresi, N., Correa-Aragunde, N., Parisi, G., Calo, G., Salerno, G. and Lamattina, L. Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent. Plant Cell 22 (2010) 3816–3830. [DOI] [PMID: 21119059]

[EC 1.14.13.39 created 1992, modified 2012, modified 2017]

*EC

1.14.13.59

Accepted name:

L-lysine N⁶-monooxygenase (NADPH)

Reaction:

L-lysine + NADPH + H⁺ + O₂ = N⁶-hydroxy-L-lysine + NADP⁺ + H₂O

For diagram of aerobactin biosynthesis, click here

Other name(s):

lysine N⁶-hydroxylase; L-lysine 6-monooxygenase (NADPH) (ambiguous)

Systematic name:

L-lysine,NADPH:oxygen oxidoreductase (6-hydroxylating)

Comments:

A flavoprotein (FAD). The enzyme from strain EN 222 of Escherichia coli is highly specific for L-lysine; L-ornithine and L-homolysine are, for example, not substrates.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 64295-82-5

References:

1.	Plattner, H.J., Pfefferle, P., Romaguera, A., Waschutza, S. and Diekmann, H. Isolation and some properties of lysine N⁶-hydroxylase from Escherichia coli strain EN222. Biol. Met. 2 (1989) 1–5. [PMID: 2518519]
2.	Macheroux, P., Plattner, H.J., Romaguera, A. and Diekmann, H. FAD and substrate analogs as probes for lysine N⁶-hydroxylase from Escherichia coli EN 222. Eur. J. Biochem. 213 (1993) 995–1002. [DOI] [PMID: 8504838]
3.	Thariath, A.M., Fatum, K.L., Valvano, M.A. and Viswanatha, T. Physico-chemical characterization of a recombinant cytoplasmic form of lysine: N⁶-hydroxylase. Biochim. Biophys. Acta 1203 (1993) 27–35. [DOI] [PMID: 8218389]
4.	de Lorenzo, V., Bindereif, A., Paw, B.H. and Neilands, J.B. Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12. J. Bacteriol. 165 (1986) 570–578. [DOI] [PMID: 2935523]
5.	Marrone, L., Siemann, S., Beecroft, M. and Viswanatha, T. Specificity of lysine:N-6-hydroxylase: A hypothesis for a reactive substrate intermediate in the catalytic mechanism. Bioorg. Chem. 24 (1996) 401–406.
6.	Goh, C.J., Szczepan, E.W., Menhart, N. and Viswanatha, T. Studies on lysine: N⁶-hydroxylation by cell-free system of Aerobacter aerogenes 62-1. Biochim. Biophys. Acta 990 (1989) 240–245. [DOI] [PMID: 2493814]

[EC 1.14.13.59 created 1999, modified 2001, modified 2012]

1.14.13.163

Accepted name:

6-hydroxy-3-succinoylpyridine 3-monooxygenase

Reaction:

4-(6-hydroxypyridin-3-yl)-4-oxobutanoate + 2 NADH + 2 H⁺ + O₂ = 2,5-dihydroxypyridine + succinate semialdehyde + 2 NAD⁺ + H₂O

Glossary:

4-(6-hydroxypyridin-3-yl)-4-oxobutanoate = 6-hydroxy-3-succinoyl-pyridine

Other name(s):

6-hydroxy-3-succinoylpyridine hydroxylase; hspA (gene name); hspB (gene name)

Systematic name:

4-(6-hydroxypyridin-3-yl)-4-oxobutanoate,NADH:oxygen oxidoreductase (3-hydroxylating, succinate semialdehyde releasing)

Comments:

The enzyme catalyses a reaction in the nicotine degradation pathway of Pseudomonas species. One of the enzymes from the soil bacterium Pseudomonas putida S16 contains an FAD cofactor [2].

Links to other databases:

References:

1.	Tang, H., Wang, S., Ma, L., Meng, X., Deng, Z., Zhang, D., Ma, C. and Xu, P. A novel gene, encoding 6-hydroxy-3-succinoylpyridine hydroxylase, involved in nicotine degradation by Pseudomonas putida strain S16. Appl. Environ. Microbiol. 74 (2008) 1567–1574. [DOI] [PMID: 18203859]
2.	Tang, H., Yao, Y., Zhang, D., Meng, X., Wang, L., Yu, H., Ma, L. and Xu, P. A novel NADH-dependent and FAD-containing hydroxylase is crucial for nicotine degradation by Pseudomonas putida. J. Biol. Chem. 286 (2011) 39179–39187. [DOI] [PMID: 21949128]

[EC 1.14.13.163 created 2012]

1.14.13.165

Transferred entry:

nitric-oxide synthase [NAD(P)H]. Now classified as EC 1.14.14.47, nitric-oxide synthase (flavodoxin)

[EC 1.14.13.165 created 2012, deleted 2017]

1.14.13.166

Accepted name:

4-nitrocatechol 4-monooxygenase

Reaction:

4-nitrocatechol + NAD(P)H + H⁺ + O₂ = 2-hydroxy-1,4-benzoquinone + nitrite + NAD(P)⁺ + H₂O

For diagram of 4-nitrophenol metabolism, click here

Systematic name:

4-nitrocatechol,NAD(P)H:oxygen 4-oxidoreductase (4-hydroxylating, nitrite-forming)

Comments:

Contains FAD. The enzyme catalyses the oxidation of 4-nitrocatechol with the concomitant removal of the nitro group as nitrite. Forms a two-component system with a flavoprotein reductase [1]. The enzymes from the bacteria Lysinibacillus sphaericus JS905 and Rhodococcus sp. strain PN1 were shown to also catalyse EC 1.14.13.29, 4-nitrophenol 2-monooxygenase [1,2] while the enzyme from Pseudomonas sp. WBC-3 was shown to also catalyse EC 1.14.13.167, 4-nitrophenol 4-monooxygenase [3].

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, KEGG

References:

1.	Kadiyala, V. and Spain, J.C. A two-component monooxygenase catalyzes both the hydroxylation of p-nitrophenol and the oxidative release of nitrite from 4-nitrocatechol in Bacillus sphaericus JS905. Appl. Environ. Microbiol. 64 (1998) 2479–2484. [PMID: 9647818]
2.	Kitagawa, W., Kimura, N. and Kamagata, Y. A novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, Rhodococcus opacus SAO101. J. Bacteriol. 186 (2004) 4894–4902. [DOI] [PMID: 15262926]
3.	Zhang, J.J., Liu, H., Xiao, Y., Zhang, X.E. and Zhou, N.Y. Identification and characterization of catabolic para-nitrophenol 4-monooxygenase and para-benzoquinone reductase from Pseudomonas sp. strain WBC-3. J. Bacteriol. 191 (2009) 2703–2710. [DOI] [PMID: 19218392]

[EC 1.14.13.166 created 2012]

1.14.13.167

Accepted name:

4-nitrophenol 4-monooxygenase

Reaction:

4-nitrophenol + NADPH + H⁺ + O₂ = 1,4-benzoquinone + nitrite + NADP⁺ + H₂O

For diagram of 4-nitrophenol metabolism, click here

Other name(s):

pnpA (gene name); pdcA (gene name)

Systematic name:

4-nitrophenol,NAD(P)H:oxygen 4-oxidoreductase (4-hydroxylating, nitrite-forming)

Comments:

Contains FAD. The enzyme catalyses the first step in a degradation pathway for 4-nitrophenol, the oxidation of 4-nitrophenol at position 4 with the concomitant removal of the nitro group as nitrite. The enzyme from the bacterium Pseudomonas sp. strain WBC-3 also catalyses EC 1.14.13.166, 4-nitrocatechol 4-monooxygenase.

Links to other databases:

References:

1.	Zhang, J.J., Liu, H., Xiao, Y., Zhang, X.E. and Zhou, N.Y. Identification and characterization of catabolic para-nitrophenol 4-monooxygenase and para-benzoquinone reductase from Pseudomonas sp. strain WBC-3. J. Bacteriol. 191 (2009) 2703–2710. [DOI] [PMID: 19218392]

[EC 1.14.13.167 created 2012]

1.14.13.168

Accepted name:

indole-3-pyruvate monooxygenase

Reaction:

(indol-3-yl)pyruvate + NADPH + H⁺ + O₂ = (indol-3-yl)acetate + NADP⁺ + H₂O + CO₂

For diagram of indoleacetic acid biosynthesis, click here

Glossary:

(indol-3-yl)pyruvate = 3-(1H-indol-3-yl)-2-oxopropanoate, (indol-3-yl)acetate = 2-(1H-indol-3-yl)acetate = indole-3-acetate

Other name(s):

YUC2 (gene name); spi1 (gene name)

Systematic name:

indole-3-pyruvate,NADPH:oxygen oxidoreductase (1-hydroxylating, decarboxylating)

Comments:

This plant enzyme, along with EC 2.6.1.99 L-tryptophan—pyruvate aminotransferase, is responsible for the biosynthesis of the plant hormone indole-3-acetate from L-tryptophan.

Links to other databases:

References:

1.	Mashiguchi, K., Tanaka, K., Sakai, T., Sugawara, S., Kawaide, H., Natsume, M., Hanada, A., Yaeno, T., Shirasu, K., Yao, H., McSteen, P., Zhao, Y., Hayashi, K., Kamiya, Y. and Kasahara, H. The main auxin biosynthesis pathway in Arabidopsis. Proc. Natl. Acad. Sci. USA 108 (2011) 18512–18517. [DOI] [PMID: 22025724]
2.	Zhao, Y. Auxin biosynthesis: a simple two-step pathway converts tryptophan to indole-3-acetic acid in plants. Mol. Plant 5 (2012) 334–338. [DOI] [PMID: 22155950]

[EC 1.14.13.168 created 2012]

1.14.13.169

Transferred entry:

sphinganine C4-monooxygenase. Now EC 1.14.18.5, sphingolipid C4-monooxygenase

[EC 1.14.13.169 created 2012, deleted 2015]

1.14.13.170

Accepted name:

pentalenolactone D synthase

Reaction:

1-deoxy-11-oxopentalenate + NADPH + H⁺ + O₂ = pentalenolactone D + NADP⁺ + H₂O

For diagram of pentalenolactone biosynthesis, click here

Glossary:

1-deoxy-11-oxopentalenate = (1S,3aR,5aS)-1,7,7-trimethyl-2-oxo-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate
pentalenolactone D = (1S,4aR,6aS,9aR)-1,8,8-trimethyl-2-oxo-1,2,4,4a,6a,7,8,9-octahydropentaleno[1,6a-c]pyran-5-carboxylate

Other name(s):

penE (gene name); pntE (gene name)

Systematic name:

1-deoxy-11-oxopentalenate,NADH:oxygen oxidoreductase (pentalenolactone-D-forming)

Comments:

A FAD-dependent oxygenase. Isolated from the bacteria Streptomyces exfoliatus and Streptomyces arenae. The ketone undergoes a biological Baeyer-Villiger reaction. Part of the pathway of pentalenolactone biosynthesis.

Links to other databases:

References:

[EC 1.14.13.170 created 2012]

1.14.13.171

Accepted name:

neopentalenolactone D synthase

Reaction:

1-deoxy-11-oxopentalenate + NADPH + H⁺ + O₂ = neopentalenolactone D + NADP⁺ + H₂O

For diagram of pentalenolactone biosynthesis, click here

Glossary:

1-deoxy-11-oxopentalenate = (1S,3aR,5aS)-1,7,7-trimethyl-2-oxo-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate
neopentalenolactone D = (1S,4aR,6aS)-1,7,7-trimethyl-3-oxo-4,4a,6a,7,8,9-hexahydro-3H-pentaleno[6a,1-c]pyran-5-carboxylate

Other name(s):

ptlE (gene name)

Systematic name:

1-deoxy-11-oxopentalenate,NADH:oxygen oxidoreductase (neopentalenolactone-D-forming)

Comments:

A FAD-dependent oxygenase. Isolated from the bacterium Streptomyces avermitilis. The ketone undergoes a biological Baeyer-Villiger reaction.

Links to other databases:

References:

[EC 1.14.13.171 created 2012]

1.14.14.13

Accepted name:

4-(γ-L-glutamylamino)butanoyl-[BtrI acyl-carrier protein] monooxygenase

Reaction:

4-(γ-L-glutamylamino)butanoyl-[BtrI acyl-carrier protein] + FMNH₂ + O₂ = 4-(γ-L-glutamylamino)-(2S)-2-hydroxybutanoyl-[BtrI acyl-carrier protein] + FMN + H₂O

Other name(s):

btrO (gene name)

Systematic name:

4-(γ-L-glutamylamino)butanoyl-[BtrI acyl-carrier protein],FMNH₂:oxygen oxidoreductase (2-hydroxylating)

Comments:

Catalyses a step in the biosynthesis of the side chain of the aminoglycoside antibiotics of the butirosin family. FMNH₂ is used as a free cofactor. Forms a complex with a dedicated NAD(P)H:FMN oxidoreductase. The enzyme is not able to hydroxylate free substrates, activation by the acyl-carrier protein is mandatory. Octanoyl-S-[BtrI acyl-carrier protein] is also accepted.

Links to other databases:

References:

1.	Li, Y., Llewellyn, N.M., Giri, R., Huang, F. and Spencer, J.B. Biosynthesis of the unique amino acid side chain of butirosin: possible protective-group chemistry in an acyl carrier protein-mediated pathway. Chem. Biol. 12 (2005) 665–675. [DOI] [PMID: 15975512]

[EC 1.14.14.13 created 2012]

1.14.15.2

Transferred entry:

camphor 1,2-monooxygenase. Now EC 1.14.13.162, 2,5-diketocamphane 1,2-monooxygenase.

[EC 1.14.15.2 created 1972, deleted 2012]

1.14.15.11

Accepted name:

pentalenic acid synthase

Reaction:

1-deoxypentalenate + reduced ferredoxin + O₂ = pentalenate + oxidized ferredoxin + H₂O

For diagram of pentalenolactone biosynthesis, click here

Glossary:

1-deoxypentalenate = (1R,3aR,5aS,8aR)-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate
pentalenate = (1R,3aR,5aS,6R,8aS)-6-hydroxy-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylate

Other name(s):

CYP105D7; sav7469 (gene name); 1-deoxypentalenate,reduced ferredoxin:O₂ oxidoreductase

Systematic name:

1-deoxypentalenate,reduced ferredoxin:oxygen oxidoreductase

Comments:

A heme-thiolate enzyme (P-450). Isolated from the bacterium Streptomyces avermitilis. The product, pentalenate, is a co-metabolite from pentalenolactone biosynthesis.

Links to other databases:

References:

Takamatsu, S., Xu, L.H., Fushinobu, S., Shoun, H., Komatsu, M., Cane, D.E. and Ikeda, H. Pentalenic acid is a shunt metabolite in the biosynthesis of the pentalenolactone family of metabolites: hydroxylation of 1-deoxypentalenic acid mediated by CYP105D7 (SAV_7469) of Streptomyces avermitilis. J. Antibiot. (Tokyo) 64 (2011) 65–71. [DOI] [PMID: 21081950]

[EC 1.14.15.11 created 2012]

*EC

1.14.18.1

Accepted name:

tyrosinase

Reaction:

(1) L-tyrosine + O₂ = dopaquinone + H₂O (overall reaction)
(1a) L-tyrosine + ½ O₂ = L-dopa
(1b) L-dopa + ½ O₂ = dopaquinone + H₂O
(2) 2 L-dopa + O₂ = 2 dopaquinone + 2 H₂O

For diagram of melanin biosynthesis, click here

Other name(s):

monophenol monooxygenase; phenolase; monophenol oxidase; cresolase; monophenolase; tyrosine-dopa oxidase; monophenol monooxidase; monophenol dihydroxyphenylalanine:oxygen oxidoreductase; N-acetyl-6-hydroxytryptophan oxidase; monophenol, dihydroxy-L-phenylalanine oxygen oxidoreductase; o-diphenol:O₂ oxidoreductase; phenol oxidase

Systematic name:

L-tyrosine,L-dopa:oxygen oxidoreductase

Comments:

A type III copper protein found in a broad variety of bacteria, fungi, plants, insects, crustaceans, and mammals, which is involved in the synthesis of betalains and melanin. The enzyme, which is activated upon binding molecular oxygen, can catalyse both a monophenolase reaction cycle (reaction 1) or a diphenolase reaction cycle (reaction 2). During the monophenolase cycle, one of the bound oxygen atoms is transferred to a monophenol (such as L-tyrosine), generating an o-diphenol intermediate, which is subsequently oxidized to an o-quinone and released, along with a water molecule. The enzyme remains in an inactive deoxy state, and is restored to the active oxy state by the binding of a new oxygen molecule. During the diphenolase cycle the enzyme binds an external diphenol molecule (such as L-dopa) and oxidizes it to an o-quinone that is released along with a water molecule, leaving the enzyme in the intermediate met state. The enzyme then binds a second diphenol molecule and repeats the process, ending in a deoxy state [7]. The second reaction is identical to that catalysed by the related enzyme catechol oxidase (EC 1.10.3.1). However, the latter can not catalyse the hydroxylation or monooxygenation of monophenols.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9002-10-2

References:

1.	Dawson, C.R. and Tarpley, W.B. The copper oxidases. In: Sumner, J.B. and Myrbäck, K. (Ed.), The Enzymes, 1st edn, vol. 2, Academic Press, New York, 1951, pp. 454–498.
2.	Patil, S.S. and Zucker, M. Potato phenolases. Purification and properties. J. Biol. Chem. 240 (1965) 3938–3943. [PMID: 5842066]
3.	Pomerantz, S.H. Separation, purification, and properties of two tyrosinases from hamster melanoma. J. Biol. Chem. 238 (1963) 2351–2357. [PMID: 13972077]
4.	Robb, D.A. `Tyrosinase. In: Lontie, R. (Ed.), Copper Proteins and Copper Enzymes, vol. 2, CRC Press, Boca Raton, FL, 1984, pp. 207–240.
5.	Sanchez-Ferrer, A., Rodriguez-Lopez, J.N., Garcia-Canovas, F. and Garcia-Carmona, F. Tyrosinase: a comprehensive review of its mechanism. Biochim. Biophys. Acta 1247 (1995) 1–11. [DOI] [PMID: 7873577]
6.	Steiner, U., Schliemann, W. and Strack, D. Assay for tyrosine hydroxylation activity of tyrosinase from betalain-forming plants and cell cultures. Anal. Biochem. 238 (1996) 72–75. [DOI] [PMID: 8660589]
7.	Rolff, M., Schottenheim, J., Decker, H. and Tuczek, F. Copper-O₂ reactivity of tyrosinase models towards external monophenolic substrates: molecular mechanism and comparison with the enzyme. Chem Soc Rev 40 (2011) 4077–4098. [DOI] [PMID: 21416076]

[EC 1.14.18.1 created 1972, modified 1976, modified 1980 (EC 1.14.17.2 created 1972, incorporated 1984), modified 2012]

1.14.99.47

Accepted name:

(+)-larreatricin hydroxylase

Reaction:

(+)-larreatricin + reduced acceptor + O₂ = (+)-3′-hydroxylarreatricin + acceptor + H₂O

Glossary:

(+)-larreatricin = 4,4′-[(2R,3R,4S,5R)-3,4-dimethyltetrahydrofuran-2,5-diyl]bisphenol

Systematic name:

(+)-larreatricin:oxygen 3′-hydroxylase

Comments:

Isolated from the plant Larrea tridentata (creosote bush). The enzyme has a strong preference for the 3′ position of (+)-larreatricin.

Links to other databases:

References:

1.	Cho, M.H., Moinuddin, S.G., Helms, G.L., Hishiyama, S., Eichinger, D., Davin, L.B. and Lewis, N.G. (+)-Larreatricin hydroxylase, an enantio-specific polyphenol oxidase from the creosote bush (Larrea tridentata). Proc. Natl. Acad. Sci. USA 100 (2003) 10641–10646. [DOI] [PMID: 12960376]

[EC 1.14.99.47 created 2012]

*EC

1.18.1.2

Accepted name:

ferredoxin—NADP⁺ reductase

Reaction:

2 reduced ferredoxin + NADP⁺ + H⁺ = 2 oxidized ferredoxin + NADPH

For diagram of reaction, click here

Other name(s):

ferredoxin-nicotinamide adenine dinucleotide phosphate reductase; ferredoxin-NADP⁺ reductase; TPNH-ferredoxin reductase; ferredoxin-NADP⁺ oxidoreductase; NADP⁺:ferredoxin oxidoreductase; ferredoxin-TPN reductase; ferredoxin-NADP⁺-oxidoreductase; NADPH:ferredoxin oxidoreductase; ferredoxin-nicotinamide-adenine dinucleotide phosphate (oxidized) reductase

Systematic name:

ferredoxin:NADP⁺ oxidoreductase

Comments:

A flavoprotein (FAD). In chloroplasts and cyanobacteria the enzyme acts on plant-type [2Fe-2S] ferredoxins, but in other bacteria it can also reduce bacterial [4Fe-4S] ferredoxins and flavodoxin.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9029-33-8

References:

1.	Shin, M., Tagawa, K. and Arnon, D.I. Crystallization of ferredoxin-TPN reductase and its role in the photosynthetic apparatus of chloroplasts. Biochem. Z. 338 (1963) 84–96. [PMID: 14087348]
2.	Knaff, D.B. and Hirasawa, M. Ferredoxin-dependent chloroplast enzymes. Biochim. Biophys. Acta 1056 (1991) 93–125. [DOI] [PMID: 1671559]
3.	Karplus, P.A., Daniels, M.J. and Herriott, J.R. Atomic structure of ferredoxin-NADP⁺ reductase: prototype for a structurally novel flavoenzyme family. Science 251 (1991) 60–66. [DOI] [PMID: 1986412]
4.	Morales, R., Charon, M.H., Kachalova, G., Serre, L., Medina, M., Gomez-Moreno, C. and Frey, M. A redox-dependent interaction between two electron-transfer partners involved in photosynthesis. EMBO Rep. 1 (2000) 271–276. [DOI] [PMID: 11256611]

[EC 1.18.1.2 created 1965 as EC 1.6.99.4, transferred 1972 as EC 1.6.7.1, transferred 1978 to EC 1.18.1.2, part transferred 2012 to EC 1.18.1.6, modified 2012]

1.18.1.6

Accepted name:

adrenodoxin-NADP⁺ reductase

Reaction:

2 reduced adrenodoxin + NADP⁺ + H⁺ = 2 oxidized adrenodoxin + NADPH

Other name(s):

adrenodoxin reductase; nicotinamide adenine dinucleotide phosphate-adrenodoxin reductase; AdR; NADPH:adrenal ferredoxin oxidoreductase; NADPH-adrenodoxin reductase

Systematic name:

reduced adrenodoxin:NADP⁺ oxidoreductase

Comments:

A flavoprotein (FAD). The enzyme, which transfers electrons from NADPH to adrenodoxin molecules, is the first component of the mitochondrial cytochrome P-450 electron transfer systems, and is involved in the biosynthesis of all steroid hormones.

Links to other databases:

References:

1.	Omura, T., Sanders, E., Estabrook, R.W., Cooper, D.Y. and Rosenthal, O. Isolation from adrenal cortex of a nonheme iron protein and a flavoprotein functional as a reduced triphosphopyridine nucleotide-cytochrome P-450 reductase. Arch. Biochem. Biophys. 117 (1966) 660–673.
2.	Chu, J.W. and Kimura, T. Studies on adrenal steroid hydroxylases. Molecular and catalytic properties of adrenodoxin reductase (a flavoprotein). J. Biol. Chem. 248 (1973) 2089–2094. [PMID: 4144106]
3.	Sugiyama, T. and Yamano, T. Purification and crystallization of NADPH-adrenodoxin reductase from bovine adrenocortical mitochondria. FEBS Lett. 52 (1975) 145–148. [DOI] [PMID: 235468]
4.	Hanukoglu, I. and Jefcoate, C.R. Mitochondrial cytochrome P-450_scc. Mechanism of electron transport by adrenodoxin. J. Biol. Chem. 255 (1980) 3057–3061. [PMID: 6766943]
5.	Hanukoglu, I. and Hanukoglu, Z. Stoichiometry of mitochondrial cytochromes P-450, adrenodoxin and adrenodoxin reductase in adrenal cortex and corpus luteum. Implications for membrane organization and gene regulation. Eur. J. Biochem. 157 (1986) 27–31. [DOI] [PMID: 3011431]
6.	Hanukoglu, I. and Gutfinger, T. cDNA sequence of adrenodoxin reductase. Identification of NADP-binding sites in oxidoreductases. Eur. J. Biochem. 180 (1989) 479–484. [DOI] [PMID: 2924777]
7.	Ziegler, G.A., Vonrhein, C., Hanukoglu, I. and Schulz, G.E. The structure of adrenodoxin reductase of mitochondrial P450 systems: electron transfer for steroid biosynthesis. J. Mol. Biol. 289 (1999) 981–990. [DOI] [PMID: 10369776]

[EC 1.18.1.6 created 1965 as EC 1.6.99.4, transferred 1972 as EC 1.6.7.1, transferred 1978 to EC 1.18.1.2, part transferred 2012 to EC 1.18.1.6, modified 2016]

*EC

1.21.3.6

Accepted name:

aureusidin synthase

Reaction:

(1) 2′,4,4′,6′-tetrahydroxychalcone 4′-O-β-D-glucoside + O₂ = aureusidin 6-O-β-D-glucoside + H₂O
(2) 2′,3,4,4′,6′-pentahydroxychalcone 4′-O-β-D-glucoside + ½ O₂ = aureusidin 6-O-β-D-glucoside + H₂O
(3) 2′,3,4,4′,6′-pentahydroxychalcone 4′-O-β-D-glucoside + O₂ = bracteatin 6-O-β-D-glucoside + H₂O

For diagram of aureusidin biosynthesis, click here

Glossary:

2′,4,4′,6′-tetrahydroxychalcone = 3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
aureusidin = 4,6-dihydroxy-2-[(3,4-dihydroxyphenyl)methylidene]benzofuran-3(2H)-one
bracteatin = 4,6-dihydroxy-2-[(3,4,5-trihydroxyphenyl)methylidene]benzofuran-3(2H)-one

Other name(s):

AmAS1

Systematic name:

2′,4,4′,6′-tetrahydroxychalcone 4′-O-β-D-glucoside:oxygen oxidoreductase

Comments:

A copper-containing glycoprotein that plays a key role in the yellow coloration of flowers such as Antirrhinum majus (snapdragon). The enzyme is a homologue of plant polyphenol oxidase [1] and catalyses two separate chemical transformations, i.e. 3-hydroxylation and oxidative cyclization (2′,-dehydrogenation). H₂O₂ activates reaction (1) but inhibits reaction (2). Originally considered to act on the phenol but now thought to act mainly on the 4′-O-β-D-glucoside in vivo [4].

Links to other databases:

BRENDA, EXPASY, KEGG, CAS registry number: 320784-48-3

References:

1.	Nakayama, T., Yonekura-Sakakibara, K., Sato, T., Kikuchi, S., Fukui, Y., Fukuchi-Mizutani, M., Ueda, T., Nakao, M., Tanaka, Y., Kusumi, T. and Nishino, T. Aureusidin synthase: A polyphenol oxidase homolog responsible for flower coloration. Science 290 (2000) 1163–1166. [DOI] [PMID: 11073455]
2.	Nakayama, T., Sato, T., Fukui, Y., Yonekura-Sakakibara, K., Hayashi, H., Tanaka, Y., Kusumi, T. and Nishino, T. Specificity analysis and mechanism of aurone synthesis catalyzed by aureusidin synthase, a polyphenol oxidase homolog responsible for flower coloration. FEBS Lett. 499 (2001) 107–111. [DOI] [PMID: 11418122]
3.	Sato, T., Nakayama, T., Kikuchi, S., Fukui, Y., Yonekura-Sakakibara, K., Ueda, T., Nishino, T., Tanaka, Y. and Kusumi, T. Enzymatic formation of aurones in the extracts of yellow snapdragon flowers. Plant Sci. 160 (2001) 229–236. [DOI] [PMID: 11164594]
4.	Ono, E., Fukuchi-Mizutani, M., Nakamura, N., Fukui, Y., Yonekura-Sakakibara, K., Yamaguchi, M., Nakayama, T., Tanaka, T., Kusumi, T. and Tanaka, Y. Yellow flowers generated by expression of the aurone biosynthetic pathway. Proc. Natl. Acad. Sci. USA 103 (2006) 11075–11080. [DOI] [PMID: 16832053]

[EC 1.21.3.6 created 2003, modified 2012]

1.21.3.7

Accepted name:

tetrahydrocannabinolic acid synthase

Reaction:

cannabigerolate + O₂ = Δ⁹-tetrahydrocannabinolate + H₂O₂

For diagram of cannabinoid biosynthesis, click here

Glossary:

Δ⁹-tetrahydrocannabinolate = Δ⁹-THCA = (6aR,10aR)-1-hydroxy-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydro-6H-benzo[c]chromene-2-carboxylate
cannabigerolate = CBGA = 3-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-2,4-dihydroxy-6-pentylbenzoate
cannabinerolate = 3-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-2,4-dihydroxy-6-pentylbenzoate

Other name(s):

THCA synthase; Δ¹-tetrahydrocannabinolic acid synthase

Systematic name:

cannabigerolate:oxygen oxidoreductase (cyclizing, Δ⁹-tetrahydrocannabinolate-forming)

Comments:

A flavoprotein (FAD). The cofactor is covalently bound. Part of the cannabinoids biosynthetic pathway in the plant Cannabis sativa. The enzyme can also convert cannabinerolate (the (Z)-isomer of cannabigerolate) to Δ⁹-THCA with lower efficiency. Whereas the product was originally called Δ¹-tetrahydrocannabinolate, the recommended name according to systematic peripheral numbering is Δ⁹-tetrahydrocannabinolate.

Links to other databases:

References:

1.	Taura, F., Morimoto, S. Shoyama, Y. and Mechoulam, R. First direct evidence for the mechanism of Δ¹-tetrahydrocannabinolic acid biosynthesis. J. Am. Chem. Soc. 117 (1995) 9766–9767.
2.	Sirikantaramas, S., Morimoto, S., Shoyama, Y., Ishikawa, Y., Wada, Y., Shoyama, Y. and Taura, F. The gene controlling marijuana psychoactivity: molecular cloning and heterologous expression of Δ¹-tetrahydrocannabinolic acid synthase from Cannabis sativa L. J. Biol. Chem. 279 (2004) 39767–39774. [DOI] [PMID: 15190053]
3.	Shoyama, Y., Takeuchi, A., Taura, F., Tamada, T., Adachi, M., Kuroki, R., Shoyama, Y. and Morimoto, S. Crystallization of Δ¹-tetrahydrocannabinolic acid (THCA) synthase from Cannabis sativa. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 61 (2005) 799–801. [DOI] [PMID: 16511162]
4.	Shoyama, Y., Tamada, T., Kurihara, K., Takeuchi, A., Taura, F., Arai, S., Blaber, M., Shoyama, Y., Morimoto, S. and Kuroki, R. Structure and function of 1-tetrahydrocannabinolic acid (THCA) synthase, the enzyme controlling the psychoactivity of Cannabis sativa. J. Mol. Biol. 423 (2012) 96–105. [DOI] [PMID: 22766313]

[EC 1.21.3.7 created 2012]

1.21.3.8

Accepted name:

cannabidiolic acid synthase

Reaction:

cannabigerolate + O₂ = cannabidiolate + H₂O₂

For diagram of cannabinoid biosynthesis, click here

Glossary:

cannabigerolate = CBGA = 3-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-2,4-dihydroxy-6-pentylbenzoate
cannabidiolate = 2,4-dihydroxy-3-[(1R,6R)-3-methyl-6-(prop-1-en-2-yl)cyclohex-2-en-1-yl]-6-pentylbenzoate

Other name(s):

CBDA synthase

Systematic name:

cannabigerolate:oxygen oxidoreductase (cyclizing, cannabidiolate-forming)

Comments:

Binds FAD covalently. Part of the cannabinoids biosynthetic pathway of the plant Cannabis sativa. The enzyme can also convert cannabinerolate to cannabidiolate with lower efficiency.

Links to other databases:

References:

1.	Taura, F., Morimoto, S. and Shoyama, Y. Purification and characterization of cannabidiolic-acid synthase from Cannabis sativa L.. Biochemical analysis of a novel enzyme that catalyzes the oxidocyclization of cannabigerolic acid to cannabidiolic acid. J. Biol. Chem. 271 (1996) 17411–17416. [DOI] [PMID: 8663284]
2.	Taura, F., Sirikantaramas, S., Shoyama, Y., Yoshikai, K., Shoyama, Y. and Morimoto, S. Cannabidiolic-acid synthase, the chemotype-determining enzyme in the fiber-type Cannabis sativa. FEBS Lett. 581 (2007) 2929–2934. [DOI] [PMID: 17544411]

[EC 1.21.3.8 created 2012]

*EC

2.1.1.61

Accepted name:

tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase

Reaction:

S-adenosyl-L-methionine + tRNA containing 5-(aminomethyl)-2-thiouridine = S-adenosyl-L-homocysteine + tRNA containing 5-[(methylamino)methyl]-2-thiouridylate

Other name(s):

transfer ribonucleate 5-methylaminomethyl-2-thiouridylate 5-methyltransferase; tRNA 5-methylaminomethyl-2-thiouridylate 5′-methyltransferase; S-adenosyl-L-methionine:tRNA (5-methylaminomethyl-2-thio-uridylate)-methyltransferase; tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase

Systematic name:

S-adenosyl-L-methionine:tRNA 5-(aminomethyl)-2-thiouridylate N-methyltransferase

Comments:

This enzyme specifically adds the terminal methyl group of 5-[(methylamino)methyl]-2-thiouridylate.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 39391-17-8

References:

1.	Taya, Y. and Nishimura, S. Biosynthesis of 5-methylaminomethyl-2-thiouridylate. I. Isolation of a new tRNA-methylase specific for 5-methylaminomethyl-2-thiouridylate. Biochem. Biophys. Res. Commun. 51 (1973) 1062–1068. [DOI] [PMID: 4703553]
2.	Taya, Y. and Nishimura, S. In: Salvatore, F., Borek, E., Zappia, V., Williams-Ashman, H.G. and Schlenk, F. (Ed.), The Biochemistry of Adenosylmethionine, Columbia University Press, New York, 1977, p. 251.
3.	Bujnicki, J.M., Oudjama, Y., Roovers, M., Owczarek, S., Caillet, J. and Droogmans, L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA 10 (2004) 1236–1242. [DOI] [PMID: 15247431]
4.	Kim, J. and Almo, S.C. Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC. BMC Struct Biol 13:5 (2013). [DOI] [PMID: 23617613]

[EC 2.1.1.61 created 1982, modified 2012, modified 2021]

*EC

2.1.1.127

Accepted name:

[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase

Reaction:

3 S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-L-lysine = 3 S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N⁶,N⁶,N⁶-trimethyl-L-lysine

Other name(s):

rubisco methyltransferase; ribulose-bisphosphate-carboxylase/oxygenase N-methyltransferase; ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit εN-methyltransferase; S-adenosyl-L-methionine:[3-phospho-D-glycerate-carboxy-lyase (dimerizing)]-lysine 6-N-methyltransferase; RuBisCO methyltransferase; RuBisCO LSMT

Systematic name:

S-adenosyl-L-methionine:[3-phospho-D-glycerate-carboxy-lyase (dimerizing)]-lysine N⁶-methyltransferase

Comments:

The enzyme catalyses three successive methylations of Lys-14 in the large subunits of hexadecameric higher plant ribulose-bisphosphate-carboxylase (EC 4.1.1.39). Only the three methylated form is observed [3]. The enzyme from pea (Pisum sativum) also three-methylates a specific lysine in the chloroplastic isoforms of fructose-bisphosphate aldolase (EC 4.1.2.13) [5].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 139171-98-5

References:

1.	Wang, P., Royer, M., Houtz, R.L. Affinity purification of ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit ^εN-methyltransferase. Protein Expr. Purif. 6 (1995) 528–536. [DOI] [PMID: 8527940]
2.	Ying, Z., Janney, N., Houtz, R.L. Organization and characterization of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit N-methyltransferase gene in tobacco. Plant Mol. Biol. 32 (1996) 663–672. [PMID: 8980518]
3.	Dirk, L.M., Flynn, E.M., Dietzel, K., Couture, J.F., Trievel, R.C. and Houtz, R.L. Kinetic manifestation of processivity during multiple methylations catalyzed by SET domain protein methyltransferases. Biochemistry 46 (2007) 3905–3915. [DOI] [PMID: 17338551]
4.	Magnani, R., Nayak, N.R., Mazarei, M., Dirk, L.M. and Houtz, R.L. Polypeptide substrate specificity of PsLSMT. A set domain protein methyltransferase. J. Biol. Chem. 282 (2007) 27857–27864. [DOI] [PMID: 17635932]
5.	Mininno, M., Brugiere, S., Pautre, V., Gilgen, A., Ma, S., Ferro, M., Tardif, M., Alban, C. and Ravanel, S. Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as lysine-methylated proteins in plants. J. Biol. Chem. 287 (2012) 21034–21044. [DOI] [PMID: 22547063]

[EC 2.1.1.127 created 1999, modified 2012]

2.1.1.258

Accepted name:

5-methyltetrahydrofolate—corrinoid/iron-sulfur protein Co-methyltransferase

Reaction:

a [methyl-Co(III) corrinoid Fe-S protein] + tetrahydrofolate = a [Co(I) corrinoid Fe-S protein] + 5-methyltetrahydrofolate

Other name(s):

acsE (gene name)

Systematic name:

5-methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase

Comments:

Catalyses the transfer of a methyl group from the N⁵ group of methyltetrahydrofolate to the 5-methoxybenzimidazolylcobamide cofactor of a corrinoid/Fe-S protein. Involved, together with EC 1.2.7.4, anaerobic carbon-monoxide dehydrogenase and EC 2.3.1.169, CO-methylating acetyl-CoA synthase, in the reductive acetyl coenzyme A (Wood-Ljungdahl) pathway of autotrophic carbon fixation in various bacteria and archaea.

Links to other databases:

References:

1.	Roberts, D.L., Zhao, S., Doukov, T. and Ragsdale, S.W. The reductive acetyl coenzyme A pathway: sequence and heterologous expression of active methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase from Clostridium thermoaceticum. J. Bacteriol. 176 (1994) 6127–6130. [DOI] [PMID: 7928975]
2.	Doukov, T., Seravalli, J., Stezowski, J.J. and Ragsdale, S.W. Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. Structure 8 (2000) 817–830. [DOI] [PMID: 10997901]
3.	Doukov, T.I., Hemmi, H., Drennan, C.L. and Ragsdale, S.W. Structural and kinetic evidence for an extended hydrogen-bonding network in catalysis of methyl group transfer. Role of an active site asparagine residue in activation of methyl transfer by methyltransferases. J. Biol. Chem. 282 (2007) 6609–6618. [DOI] [PMID: 17172470]

[EC 2.1.1.258 created 2012]

2.1.1.259

Accepted name:

[fructose-bisphosphate aldolase]-lysine N-methyltransferase

Reaction:

3 S-adenosyl-L-methionine + [fructose-bisphosphate aldolase]-L-lysine = 3 S-adenosyl-L-homocysteine + [fructose-bisphosphate aldolase]-N⁶,N⁶,N⁶-trimethyl-L-lysine

Other name(s):

Systematic name:

S-adenosyl-L-methionine:[fructose-bisphosphate aldolase]-lysine N⁶-methyltransferase

Comments:

The enzyme methylates a conserved lysine in the C-terminal part of higher plant fructose-bisphosphate aldolase (EC 4.1.2.13). The enzyme from pea (Pisum sativum) also methylates Lys-14 in the large subunits of hexadecameric higher plant ribulose-bisphosphate-carboxylase (EC 4.1.1.39) [2], but that from Arabidopsis thaliana does not.

Links to other databases:

References:

1.	Magnani, R., Nayak, N.R., Mazarei, M., Dirk, L.M. and Houtz, R.L. Polypeptide substrate specificity of PsLSMT. A set domain protein methyltransferase. J. Biol. Chem. 282 (2007) 27857–27864. [DOI] [PMID: 17635932]
2.	Mininno, M., Brugiere, S., Pautre, V., Gilgen, A., Ma, S., Ferro, M., Tardif, M., Alban, C. and Ravanel, S. Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as lysine-methylated proteins in plants. J. Biol. Chem. 287 (2012) 21034–21044. [DOI] [PMID: 22547063]

[EC 2.1.1.259 created 2012]

2.1.1.260

Accepted name:

rRNA small subunit pseudouridine methyltransferase Nep1

Reaction:

S-adenosyl-L-methionine + pseudouridine¹¹⁹¹ in yeast 18S rRNA = S-adenosyl-L-homocysteine + N¹-methylpseudouridine¹¹⁹¹ in yeast 18S rRNA

Other name(s):

Nep1; nucleolar essential protein 1

Systematic name:

S-adenosyl-L-methionine:18S rRNA (pseudouridine¹¹⁹¹-N¹)-methyltransferase

Comments:

This enzyme, which occurs in both prokaryotes and eukaryotes, recognizes specific pseudouridine residues (Ψ) in small subunits of ribosomal RNA based on the local RNA structure. It recognizes Ψ⁹¹⁴ in 16S rRNA from the archaeon Methanocaldococcus jannaschii, Ψ¹¹⁹¹ in yeast 18S rRNA, and Ψ¹²⁴⁸ in human 18S rRNA.

Links to other databases:

References:

1.	Taylor, A.B., Meyer, B., Leal, B.Z., Kötter, P., Schirf, V., Demeler, B., Hart, P.J., Entian, K.-D. and Wöhnert, J. The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site. Nucleic Acids Res. 36 (2008) 1542–1554. [DOI] [PMID: 18208838]
2.	Wurm, J.P., Meyer, B., Bahr, U., Held, M., Frolow, O., Kötter, P., Engels, J.W., Heckel, A., Karas, M., Entian, K.-D. and Wöhnert, J. The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N¹-specific methyltransferase. Nucleic Acids Res. 38 (2010) 2387–2398. [DOI] [PMID: 20047967]
3.	Meyer, B., Wurm, J.P., Kötter, P., Leisegang, M.S., Schilling, V., Buchhaupt, M., Held, M., Bahr, U., Karas, M., Heckel, A., Bohnsack, M.T., Wöhnert, J. and Entian, K.-D. The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Ψ¹¹⁹¹ in yeast 18S rRNA. Nucleic Acids Res. 39 (2011) 1526–1537. [DOI] [PMID: 20972225]

[EC 2.1.1.260 created 2012]

2.1.1.261

Accepted name:

4-dimethylallyltryptophan N-methyltransferase

Reaction:

S-adenosyl-L-methionine + 4-prenyl-L-tryptophan = S-adenosyl-L-homocysteine + 4-prenyl-L-abrine

For diagram of ergot alkaloid biosynthesis, click here

Glossary:

4-prenyl-L-tryptophan = 4-(3-methylbut-2-enyl)-L-tryptophan = 4-dimethylallyl-L-tryptophan (ambiguous);
4-prenyl-L-abrine = 4-(3-methylbut-2-enyl)-L-abrine = 4-dimethylallyl-L-abrine (ambiguous)

Other name(s):

fgaMT (gene name); easF (gene name)

Systematic name:

S-adenosyl-L-methionine:4-(3-methylbut-2-enyl)-L-tryptophan N-methyltransferase

Comments:

The enzyme catalyses a step in the pathway leading to biosynthesis of ergot alkaloids in certain fungi.

Links to other databases:

References:

1.	Rigbers, O. and Li, S.M. Ergot alkaloid biosynthesis in Aspergillus fumigatus. Overproduction and biochemical characterization of a 4-dimethylallyltryptophan N-methyltransferase. J. Biol. Chem. 283 (2008) 26859–26868. [DOI] [PMID: 18678866]

[EC 2.1.1.261 created 2012]

2.1.1.262

Accepted name:

squalene methyltransferase

Reaction:

2 S-adenosyl-L-methionine + squalene = 2 S-adenosyl-L-homocysteine + 3,22-dimethyl-1,2,23,24-tetradehydro-2,3,22,23-tetrahydrosqualene (overall reaction)
(1a) S-adenosyl-L-methionine + squalene = S-adenosyl-L-homocysteine + 3-methyl-1,2-didehydro-2,3-dihydrosqualene
(1b) S-adenosyl-L-methionine + 3-methyl-1,2-didehydro-2,3-dihydrosqualene = S-adenosyl-L-homocysteine + 3,22-dimethyl-1,2,23,24-tetradehydro-2,3,22,23-tetrahydrosqualene

For diagram of botryococcus braunii BOT22 squalene and botrycoccene biosynthesis, click here

Other name(s):

TMT-1; TMT-2

Systematic name:

S-adenosyl-L-methionine:squalene C-methyltransferase

Comments:

Two isoforms differing in their specificity were isolated from the green alga Botryococcus braunii BOT22. TMT-1 gave more of the dimethylated form whereas TMT2 gave more of the monomethylated form.

Links to other databases:

References:

1.	Niehaus, T.D., Kinison, S., Okada, S., Yeo, Y.S., Bell, S.A., Cui, P., Devarenne, T.P. and Chappell, J. Functional identification of triterpene methyltransferases from Botryococcus braunii race B. J. Biol. Chem. 287 (2012) 8163–8173. [DOI] [PMID: 22241476]

[EC 2.1.1.262 created 2012]

2.1.1.263

Accepted name:

botryococcene C-methyltransferase

Reaction:

2 S-adenosyl-L-methionine + C₃₀ botryococcene = 2 S-adenosyl-L-homocysteine + 3,20-dimethyl-1,2,21,22-tetradehydro-2,3,20,21-tetrahydrobotryococcene (overall reaction)
(1a) S-adenosyl-L-methionine + C₃₀ botryococcene = S-adenosyl-L-homocysteine + 3-methyl-1,2-didehydro-2,3-dihydrobotryococcene
(1b) S-adenosyl-L-methionine + 3-methyl-1,2-didehydro-2,3-dihydrobotryococcene = S-adenosyl-L-homocysteine + 3,20-dimethyl-1,2,21,22-tetradehydro-2,3,20,21-tetrahydrobotryococcene
(2a) S-adenosyl-L-methionine + C₃₀ botryococcene = S-adenosyl-L-homocysteine + 20-methyl-21,22-didehydro-20,21-dihydrobotryococcene
(2b) S-adenosyl-L-methionine + 20-methyl-21,22-didehydro-20,21-dihydrobotryococcene = S-adenosyl-L-homocysteine + 3,20-dimethyl-1,2,21,22-tetradehydro-2,3,20,21-tetrahydrobotryococcene

For diagram of botryococcus braunii BOT22 squalene and botrycoccene biosynthesis, click here

Glossary:

C₃₀ botryococcene = (10S,13R)-10-ethenyl-2,6,10,13,17,21-hexamethyldocosa-2,5,11,16,20-pentaene
3-methyl-1,2-didehydro-2,3-dihydrobotryococcene = showacene
20-methyl-21,22-didehydro-20,21-dihydrobotryococcene = isoshowacene

Other name(s):

TMT-3

Systematic name:

S-adenosyl-L-methionine:botryococcene C-methyltransferase

Comments:

Isolated from the green alga Botryococcus braunii BOT22. Shows a very weak activity with squalene.

Links to other databases:

References:

1.	Niehaus, T.D., Kinison, S., Okada, S., Yeo, Y.S., Bell, S.A., Cui, P., Devarenne, T.P. and Chappell, J. Functional identification of triterpene methyltransferases from Botryococcus braunii race B. J. Biol. Chem. 287 (2012) 8163–8173. [DOI] [PMID: 22241476]

[EC 2.1.1.263 created 2012]

2.1.1.264

Accepted name:

23S rRNA (guanine²⁰⁶⁹-N⁷)-methyltransferase

Reaction:

S-adenosyl-L-methionine + guanine²⁰⁶⁹ in 23S rRNA = S-adenosyl-L-homocysteine + N⁷-methylguanine²⁰⁶⁹ in 23S rRNA

Other name(s):

rlmK (gene name); 23S rRNA m⁷G²⁰⁶⁹ methyltransferase

Systematic name:

S-adenosyl-L-methionine:23S rRNA (guanine²⁰⁶⁹-N⁷)-methyltransferase

Comments:

The enzyme specifically methylates guanine²⁰⁶⁹ at position N7 in 23S rRNA. In γ-proteobacteria the enzyme also catalyses EC 2.1.1.173, 23S rRNA (guanine²⁴⁴⁵-N²)-methyltransferase, while in β-proteobacteria the activities are carried out by separate proteins [1]. The enzyme from the γ-proteobacterium Escherichia coli has RNA unwinding activity as well [1].

Links to other databases:

References:

1.	Kimura, S., Ikeuchi, Y., Kitahara, K., Sakaguchi, Y., Suzuki, T. and Suzuki, T. Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity. Nucleic Acids Res. 40 (2012) 4071–4085. [DOI] [PMID: 22210896]

[EC 2.1.1.264 created 2012]

2.1.1.265

Accepted name:

tellurite methyltransferase

Reaction:

S-adenosyl-L-methionine + tellurite = S-adenosyl-L-homocysteine + methanetelluronate

Other name(s):

TehB

Systematic name:

S-adenosyl-L-methionine:tellurite methyltransferase

Comments:

The enzyme is involved in the detoxification of tellurite. It can also methylate selenite and selenium dioxide.

Links to other databases:

References:

1.	Liu, M., Turner, R.J., Winstone, T.L., Saetre, A., Dyllick-Brenzinger, M., Jickling, G., Tari, L.W., Weiner, J.H. and Taylor, D.E. Escherichia coli TehB requires S-adenosylmethionine as a cofactor to mediate tellurite resistance. J. Bacteriol. 182 (2000) 6509–6513. [DOI] [PMID: 11053398]
2.	Choudhury, H.G., Cameron, A.D., Iwata, S. and Beis, K. Structure and mechanism of the chalcogen-detoxifying protein TehB from Escherichia coli. Biochem. J. 435 (2011) 85–91. [DOI] [PMID: 21244361]

[EC 2.1.1.265 created 2012]

*EC

2.3.1.177

Accepted name:

3,5-dihydroxybiphenyl synthase

Reaction:

3 malonyl-CoA + benzoyl-CoA = 4 CoA + 3,5-dihydroxybiphenyl + 4 CO₂

For diagram of polyketides biosynthesis, click here

Other name(s):

BIS1; biphenyl synthase (ambiguous)

Systematic name:

malonyl-CoA:benzoyl-CoA malonyltransferase

Comments:

A polyketide synthase that is involved in the production of the phytoalexin aucuparin. 2-Hydroxybenzoyl-CoA can also act as substrate but it leads to the derailment product 4-hydroxycoumarin (cf. EC 2.3.1.208, 4-hydroxycoumarin synthase) [2]. This enzyme uses the same starter substrate as EC 2.3.1.151, benzophenone synthase.

Links to other databases:

BRENDA, EXPASY, KEGG, PDB, CAS registry number: 1217551-24-0

References:

1.	Liu, B., Beuerle, T., Klundt, T. and Beerhues, L. Biphenyl synthase from yeast-extract-treated cell cultures of Sorbus aucuparia. Planta 218 (2004) 492–496. [DOI] [PMID: 14595561]
2.	Liu, B., Raeth, T., Beuerle, T. and Beerhues, L. Biphenyl synthase, a novel type III polyketide synthase. Planta 225 (2007) 1495–1503. [DOI] [PMID: 17109150]

[EC 2.3.1.177 created 2006, modified 2012]

2.3.1.199

Accepted name:

very-long-chain 3-oxoacyl-CoA synthase

Reaction:

a very-long-chain acyl-CoA + malonyl-CoA = a very-long-chain 3-oxoacyl-CoA + CO₂ + CoA

Glossary:

a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.

Other name(s):

very-long-chain 3-ketoacyl-CoA synthase; very-long-chain β-ketoacyl-CoA synthase; condensing enzyme (ambiguous); CUT1 (gene name); CER6 (gene name); FAE1 (gene name); KCS (gene name); ELO (gene name)

Systematic name:

malonyl-CoA:very-long-chain acyl-CoA malonyltransferase (decarboxylating and thioester-hydrolysing)

Comments:

This is the first component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long-chain acyl CoAs. Multiple forms exist with differing preferences for the substrate, and thus the specific form expressed determines the local composition of very-long-chain fatty acids [6,7]. For example, the FAE1 form from the plant Arabidopsis thaliana accepts only 16 and 18 carbon substrates, with oleoyl-CoA (18:1) being the preferred substrate [5], while CER6 from the same plant prefers substrates with chain length of C₂₂ to C₃₂ [4,8]. cf. EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, EC 4.2.1.134, very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase

Links to other databases:

References:

1.	Toke, D.A. and Martin, C.E. Isolation and characterization of a gene affecting fatty acid elongation in Saccharomyces cerevisiae. J. Biol. Chem. 271 (1996) 18413–18422. [DOI] [PMID: 8702485]
2.	Oh, C.S., Toke, D.A., Mandala, S. and Martin, C.E. ELO₂ and ELO3, homologues of the Saccharomyces cerevisiae ELO1 gene, function in fatty acid elongation and are required for sphingolipid formation. J. Biol. Chem. 272 (1997) 17376–17384. [DOI] [PMID: 9211877]
3.	Dittrich, F., Zajonc, D., Huhne, K., Hoja, U., Ekici, A., Greiner, E., Klein, H., Hofmann, J., Bessoule, J.J., Sperling, P. and Schweizer, E. Fatty acid elongation in yeast^--biochemical characteristics of the enzyme system and isolation of elongation-defective mutants. Eur. J. Biochem. 252 (1998) 477–485. [DOI] [PMID: 9546663]
4.	Millar, A.A., Clemens, S., Zachgo, S., Giblin, E.M., Taylor, D.C. and Kunst, L. CUT1, an Arabidopsis gene required for cuticular wax biosynthesis and pollen fertility, encodes a very-long-chain fatty acid condensing enzyme. Plant Cell 11 (1999) 825–838. [PMID: 10330468]
5.	Ghanevati, M. and Jaworski, J.G. Engineering and mechanistic studies of the Arabidopsis FAE1 β-ketoacyl-CoA synthase, FAE1 KCS. Eur. J. Biochem. 269 (2002) 3531–3539. [DOI] [PMID: 12135493]
6.	Blacklock, B.J. and Jaworski, J.G. Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases. Biochem. Biophys. Res. Commun. 346 (2006) 583–590. [DOI] [PMID: 16765910]
7.	Denic, V. and Weissman, J.S. A molecular caliper mechanism for determining very long-chain fatty acid length. Cell 130 (2007) 663–677. [DOI] [PMID: 17719544]
8.	Tresch, S., Heilmann, M., Christiansen, N., Looser, R. and Grossmann, K. Inhibition of saturated very-long-chain fatty acid biosynthesis by mefluidide and perfluidone, selective inhibitors of 3-ketoacyl-CoA synthases. Phytochemistry 76 (2012) 162–171. [DOI] [PMID: 22284369]

[EC 2.3.1.199 created 2012]

2.3.1.200

Accepted name:

lipoyl amidotransferase

Reaction:

[glycine cleavage system H]-N⁶-lipoyl-L-lysine + a [lipoyl-carrier protein] = glycine cleavage system H + a [lipoyl-carrier protein]-N⁶-lipoyl-L-lysine

Glossary:

lipoic acid = 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid

Other name(s):

LipL (gene name, ambiguous)

Systematic name:

[glycine cleavage system H]-N⁶-lipoyl-L-lysine:[lipoyl-carrier protein]-N⁶-L-lysine lipoyltransferase

Comments:

In the bacterium Listeria monocytogenes the enzyme takes part in a pathway for scavenging of lipoic acid. The enzyme is bound to 2-oxo-acid dehydrogenases such as the pyruvate dehydrogenase complex, where it transfers the lipoyl moiety from lipoyl-[glycine cleavage system H] to the E2 subunits of the complexes.

Links to other databases:

References:

1.	Christensen, Q.H., Hagar, J.A., O'Riordan, M.X. and Cronan, J.E. A complex lipoate utilization pathway in Listeria monocytogenes. J. Biol. Chem. 286 (2011) 31447–31456. [DOI] [PMID: 21768091]

[EC 2.3.1.200 created 2012]

2.3.1.201

Accepted name:

UDP-2-acetamido-3-amino-2,3-dideoxy-glucuronate N-acetyltransferase

Reaction:

acetyl-CoA + UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucuronate = CoA + UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronate

For diagram of UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronate biosynthesis, click here

Other name(s):

WbpD; WlbB

Systematic name:

acetyl-CoA:UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucuronate N-acetyltransferase

Comments:

This enzyme participates in the biosynthetic pathway for UDP-α-D-ManNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronic acid), an important precursor of B-band lipopolysaccharide.

Links to other databases:

References:

1.	Westman, E.L., McNally, D.J., Charchoglyan, A., Brewer, D., Field, R.A. and Lam, J.S. Characterization of WbpB, WbpE, and WbpD and reconstitution of a pathway for the biosynthesis of UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronic acid in Pseudomonas aeruginosa. J. Biol. Chem. 284 (2009) 11854–11862. [DOI] [PMID: 19282284]
2.	Larkin, A. and Imperiali, B. Biosynthesis of UDP-GlcNAc(3NAc)A by WbpB, WbpE, and WbpD: enzymes in the Wbp pathway responsible for O-antigen assembly in Pseudomonas aeruginosa PAO1. Biochemistry 48 (2009) 5446–5455. [DOI] [PMID: 19348502]

[EC 2.3.1.201 created 2012]

2.3.1.202

Accepted name:

UDP-4-amino-4,6-dideoxy-N-acetyl-β-L-altrosamine N-acetyltransferase

Reaction:

acetyl-CoA + UDP-4-amino-4,6-dideoxy-N-acetyl-β-L-altrosamine = CoA + UDP-2,4-diacetamido-2,4,6-trideoxy-β-L-altropyranose

Other name(s):

PseH

Systematic name:

acetyl-CoA:UDP-4-amino-4,6-dideoxy-N-acetyl-β-L-altrosamine N-acetyltransferase

Comments:

Isolated from Helicobacter pylori. The enzyme is involved in the biosynthesis of pseudaminic acid.

Links to other databases:

References:

1.	Schoenhofen, I.C., McNally, D.J., Brisson, J.R. and Logan, S.M. Elucidation of the CMP-pseudaminic acid pathway in Helicobacter pylori: synthesis from UDP-N-acetylglucosamine by a single enzymatic reaction. Glycobiology 16 (2006) 8C–14C. [DOI] [PMID: 16751642]

[EC 2.3.1.202 created 2012]

2.3.1.203

Accepted name:

UDP-N-acetylbacillosamine N-acetyltransferase

Reaction:

acetyl-CoA + UDP-N-acetylbacillosamine = CoA + UDP-N,N′-diacetylbacillosamine

For diagram of legionaminic acid biosynthesis, click here

Glossary:

UDP-N-acetylbacillosamine = UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine
UDP-N,N′-diacetylbacillosamine = UDP-2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose

Other name(s):

UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine N-acetyltransferase; pglD (gene name)

Systematic name:

acetyl-CoA:UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine N-acetyltransferase

Comments:

The product, UDP-N,N′-diacetylbacillosamine, is an intermediate in protein glycosylation pathways in several bacterial species, including N-linked glycosylation of certain L-asparagine residues in Campylobacter species [1,2] and O-linked glycosylation of certain L-serine residues in Neisseria species [3].

Links to other databases:

References:

1.	Olivier, N.B., Chen, M.M., Behr, J.R. and Imperiali, B. In vitro biosynthesis of UDP-N,N′-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system. Biochemistry 45 (2006) 13659–13669. [DOI] [PMID: 17087520]
2.	Rangarajan, E.S., Ruane, K.M., Sulea, T., Watson, D.C., Proteau, A., Leclerc, S., Cygler, M., Matte, A. and Young, N.M. Structure and active site residues of PglD, an N-acetyltransferase from the bacillosamine synthetic pathway required for N-glycan synthesis in Campylobacter jejuni. Biochemistry 47 (2008) 1827–1836. [DOI] [PMID: 18198901]
3.	Hartley, M.D., Morrison, M.J., Aas, F.E., Borud, B., Koomey, M. and Imperiali, B. Biochemical characterization of the O-linked glycosylation pathway in Neisseria gonorrhoeae responsible for biosynthesis of protein glycans containing N,N′-diacetylbacillosamine. Biochemistry 50 (2011) 4936–4948. [DOI] [PMID: 21542610]

[EC 2.3.1.203 created 2012, modified 2013]

2.3.1.204

Accepted name:

octanoyl-[GcvH]:protein N-octanoyltransferase

Reaction:

[glycine cleavage system H]-N⁶-octanoyl-L-lysine + a [lipoyl-carrier protein] = glycine cleavage system H + a [lipoyl-carrier protein]-N⁶-octanoyl-L-lysine

Glossary:

GcvH = glycine cleavage system H]

Other name(s):

LipL; octanoyl-[GcvH]:E2 amidotransferase; ywfL (gene name)

Systematic name:

[glycine cleavage system H]-N⁶-octanoyl-L-lysine:[lipoyl-carrier protein]-N⁶-L-lysine octanoyltransferase

Comments:

In the bacterium Bacillus subtilis it has been shown that the enzyme catalyses the amidotransfer of the octanoyl moiety from [glycine cleavage system H]-N⁶-octanoyl-L-lysine (i.e. octanoyl-GcvH) to the E2 subunit (dihydrolipoamide acetyltransferase) of pyruvate dehydrogenase.

Links to other databases:

References:

1.	Christensen, Q.H., Martin, N., Mansilla, M.C., de Mendoza, D. and Cronan, J.E. A novel amidotransferase required for lipoic acid cofactor assembly in Bacillus subtilis. Mol. Microbiol. 80 (2011) 350–363. [DOI] [PMID: 21338421]
2.	Martin, N., Christensen, Q.H., Mansilla, M.C., Cronan, J.E. and de Mendoza, D. A novel two-gene requirement for the octanoyltransfer reaction of Bacillus subtilis lipoic acid biosynthesis. Mol. Microbiol. 80 (2011) 335–349. [DOI] [PMID: 21338420]

[EC 2.3.1.204 created 2012]

2.3.1.205

Accepted name:

fumigaclavine B O-acetyltransferase

Reaction:

acetyl-CoA + fumigaclavine B = CoA + fumigaclavine A

For diagram of fumigaclavin alkaloid biosynthesis, click here

Glossary:

fumigaclavine B = 6,8β-dimethylergolin-9-ol;
fumigaclavine A = 6,8β-dimethylergolin-9β-yl acetate

Other name(s):

FgaAT

Systematic name:

acetyl-CoA:fumigaclavine B O-acetyltransferase

Comments:

The enzyme participates in the biosynthesis of fumigaclavine C, an ergot alkaloid produced by some fungi of the Trichocomaceae family.

Links to other databases:

References:

1.	Liu, X., Wang, L., Steffan, N., Yin, W.B. and Li, S.M. Ergot alkaloid biosynthesis in Aspergillus fumigatus: FgaAT catalyses the acetylation of fumigaclavine B. ChemBioChem 10 (2009) 2325–2328. [DOI] [PMID: 19672909]

[EC 2.3.1.205 created 2012]

2.3.1.206

Accepted name:

3,5,7-trioxododecanoyl-CoA synthase

Reaction:

3 malonyl-CoA + hexanoyl-CoA = 3 CoA + 3,5,7-trioxododecanoyl-CoA + 3 CO₂

For diagram of cannabinoid biosynthesis, click here

Other name(s):

TKS (ambiguous); olivetol synthase (incorrect)

Systematic name:

malonyl-CoA:hexanoyl-CoA malonyltransferase (3,5,7-trioxododecanoyl-CoA-forming)

Comments:

A polyketide synthase catalysing the first committed step in the cannabinoids biosynthetic pathway of the plant Cannabis sativa. The enzyme was previously thought to also function as a cyclase, but the cyclization is now known to be catalysed by EC 4.4.1.26, olivetolic acid cyclase.

Links to other databases:

References:

1.	Taura, F., Tanaka, S., Taguchi, C., Fukamizu, T., Tanaka, H., Shoyama, Y. and Morimoto, S. Characterization of olivetol synthase, a polyketide synthase putatively involved in cannabinoid biosynthetic pathway. FEBS Lett. 583 (2009) 2061–2066. [DOI] [PMID: 19454282]
2.	Gagne, S.J., Stout, J.M., Liu, E., Boubakir, Z., Clark, S.M. and Page, J.E. Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides. Proc. Natl. Acad. Sci. USA 109 (2012) 12811–12816. [DOI] [PMID: 22802619]

[EC 2.3.1.206 created 2012]

2.3.1.207

Accepted name:

β-ketodecanoyl-[acyl-carrier-protein] synthase

Reaction:

octanoyl-CoA + a malonyl-[acyl-carrier protein] = a 3-oxodecanoyl-[acyl-carrier protein] + CoA + CO₂

Glossary:

[acyl-carrier protein] = [acp]

Systematic name:

octanoyl-CoA:malonyl-[acyl-carrier protein] C-heptanoylltransferase (decarboxylating, CoA-forming)

Comments:

This enzyme, which has been characterized from the bacterium Pseudomonas aeruginosa PAO1, catalyses the condensation of octanoyl-CoA, obtained from exogenously supplied fatty acids via β-oxidation, with malonyl-[acp], forming 3-oxodecanoyl-[acp], an intermediate of the fatty acid elongation cycle. The enzyme provides a shunt for β-oxidation degradation intermediates into de novo fatty acid biosynthesis.

Links to other databases:

References:

1.	Yuan, Y., Leeds, J.A. and Meredith, T.C. Pseudomonas aeruginosa directly shunts β-oxidation degradation intermediates into de novo fatty acid biosynthesis. J. Bacteriol. 194 (2012) 5185–5196. [DOI] [PMID: 22753057]

[EC 2.3.1.207 created 2012]

2.3.1.208

Accepted name:

4-hydroxycoumarin synthase

Reaction:

malonyl-CoA + 2-hydroxybenzoyl-CoA = 2 CoA + 4-hydroxycoumarin + CO₂

For diagram of polyketides biosynthesis, click here

Glossary:

2-hydroxybenzoyl-CoA = salicyloyl-CoA

Other name(s):

BIS2; BIS3

Systematic name:

malonyl-CoA:2-hydroxybenzoyl-CoA malonyltransferase

Comments:

The enzyme, a polyketide synthase, can also accept benzoyl-CoA as substrate, which it condenses with 3 malonyl-CoA molecules to form 3,5-dihydroxybiphenyl (cf. EC 2.3.1.177, biphenyl synthase) [1].

Links to other databases:

References:

1.	Liu, B., Raeth, T., Beuerle, T. and Beerhues, L. A novel 4-hydroxycoumarin biosynthetic pathway. Plant Mol. Biol. 72 (2010) 17–25. [DOI] [PMID: 19757094]

[EC 2.3.1.208 created 2012]

2.3.1.209

Accepted name:

dTDP-4-amino-4,6-dideoxy-D-glucose acyltransferase

Reaction:

acetyl-CoA + dTDP-4-amino-4,6-dideoxy-α-D-glucose = CoA + dTDP-4-acetamido-4,6-dideoxy-α-D-glucose

Other name(s):

VioB

Systematic name:

acetyl-CoA:dTDP-4-amino-4,6-dideoxy-α-D-glucose N-acetyltransferase

Comments:

The non-activated product, 4-acetamido-4,6-dideoxy-α-D-glucose, is part of the O antigens of Shigella dysenteriae type 7 and Escherichia coli O7.

Links to other databases:

References:

1.	Wang, Y., Xu, Y., Perepelov, A.V., Qi, Y., Knirel, Y.A., Wang, L. and Feng, L. Biochemical characterization of dTDP-D-Qui4N and dTDP-D-Qui4NAc biosynthetic pathways in Shigella dysenteriae type 7 and Escherichia coli O7. J. Bacteriol. 189 (2007) 8626–8635. [DOI] [PMID: 17905981]

[EC 2.3.1.209 created 2012]

2.3.1.210

Accepted name:

dTDP-4-amino-4,6-dideoxy-D-galactose acyltransferase

Reaction:

acetyl-CoA + dTDP-4-amino-4,6-dideoxy-α-D-galactose = CoA + dTDP-4-acetamido-4,6-dideoxy-α-D-galactose

For diagram of dTDP-Fuc3NAc and dTDP-Fuc4NAc biosynthesis, click here

Glossary:

dTDP-4-amino-4,6-dideoxy-α-D-galactose = dTDP-α-D-fucosamine

Other name(s):

TDP-fucosamine acetyltransferase; WecD; RffC

Systematic name:

acetyl-CoA:dTDP-4-amino-4,6-dideoxy-α-D-galactose N-acetyltransferase

Comments:

The product, TDP-4-acetamido-4,6-dideoxy-D-galactose, is utilized in the biosynthesis of enterobacterial common antigen (ECA).

Links to other databases:

References:

1.	Hung, M.N., Rangarajan, E., Munger, C., Nadeau, G., Sulea, T. and Matte, A. Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthesis. J. Bacteriol. 188 (2006) 5606–5617. [DOI] [PMID: 16855251]

[EC 2.3.1.210 created 2012]

2.3.2.19

Accepted name:

ribostamycin:4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoyl-[BtrI acyl-carrier protein] 4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoate transferase

Reaction:

4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoyl-[BtrI acyl-carrier protein] + ribostamycin = γ-L-glutamyl-butirosin B + BtrI acyl-carrier protein

Other name(s):

btrH (gene name)

Systematic name:

ribostamycin:4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoyl-[BtrI acyl-carrier protein] 4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoate transferase

Comments:

The enzyme attaches the side chain of the aminoglycoside antibiotics of the butirosin family. The side chain confers resistance against several aminoglycoside-modifying enzymes.

Links to other databases:

References:

1.	Llewellyn, N.M., Li, Y. and Spencer, J.B. Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain. Chem. Biol. 14 (2007) 379–386. [DOI] [PMID: 17462573]

[EC 2.3.2.19 created 2012]

*EC

2.4.1.60

Accepted name:

CDP-abequose:α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und α-1,3-abequosyltransferase

Reaction:

CDP-α-D-abequose + α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und = CDP + α-D-Abe-(1→3)-α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und

Glossary:

D-abequose = 3,6-deoxy-D-xylo-hexose = 3,6-deoxy-D-galactose = 3-deoxy-D-fucose
α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und = α-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
α-D-Abe-(1→3)-α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und = α-D-abequopyranosyl-(1→3)-α-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol

Other name(s):

wbaV (gene name); rfbV (gene name); trihexose diphospholipid abequosyltransferase; abequosyltransferase (ambiguous); CDP-α-D-abequose:Man(α1→4)Rha(α1→3)Gal(β-1)-diphospholipid D-abequosyltransferase

Systematic name:

CDP-α-D-abequose:α-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol 3^III-α-abequosyltransferase (configuration retaining)

Comments:

The enzyme from Salmonella participates in the biosynthesis of the repeat unit of O antigens produced by strains that belong to the A, B and D1-D3 groups. The enzyme is able to transfer abequose, paratose, or tyvelose, depending on the availability of the specific dideoxyhexose in a particular strain.

Links to other databases:

BRENDA, EXPASY, KEGG, CAS registry number: 37277-67-1

References:

1.	Osborn, M.J. and Weiner, I.M. Biosynthesis of a bacterial lipopolysaccharide. VI. Mechanism of incorporation of abequose into the O-antigen of Salmonella typhimurium. J. Biol. Chem. 243 (1968) 2631–2639. [PMID: 4297268]
2.	Liu, D., Lindqvist, L. and Reeves, P.R. Transferases of O-antigen biosynthesis in Salmonella enterica: dideoxyhexosyltransferases of groups B and C2 and acetyltransferase of group C2. J. Bacteriol. 177 (1995) 4084–4088. [DOI] [PMID: 7541787]

[EC 2.4.1.60 created 1972, modified 2012, modified 2021]

2.4.1.119

Transferred entry:

dolichyl-diphosphooligosaccharideprotein glycotransferase. As the enzyme transfers more than one hexosyl group, it has been transferred to EC 2.4.99.18, dolichyl-diphosphooligosaccharideprotein glycotransferase

[EC 2.4.1.119 created 1984, deleted 2012]

*EC

2.4.1.131

Accepted name:

GDP-Man:Man₃GlcNAc₂-PP-dolichol α-1,2-mannosyltransferase

Reaction:

2 GDP-α-D-mannose + α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = 2 GDP + α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol

For diagram of dolichyltetradecasaccharide biosynthesis, click here

Other name(s):

ALG11; ALG11 mannosyltransferase; LEW3 (gene name); At2G40190 (gene name); gmd3 (gene name); galactomannan deficiency protein 3; GDP-mannose:glycolipid 1,2-α-D-mannosyltransferase; glycolipid 2-α-mannosyltransferase; GDP-mannose:glycolipid 2-α-D-mannosyltransferase; GDP-Man:Man₃GlcNAc₂-PP-Dol α-1,2-mannosyltransferase; GDP-α-D-mannose:D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol 2-α-D-mannosyltransferase

Systematic name:

GDP-α-D-mannose:α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 2-α-D-mannosyltransferase (configuration-retaining)

Comments:

The biosynthesis of asparagine-linked glycoproteins (N-linked protein glycosylation) utilizes a dolichyl diphosphate-linked glycosyl donor, which is assembled by the series of membrane-bound glycosyltransferases that comprise the dolichol pathway. ALG11 mannosyltransferase from Saccharomyces cerevisiae carries out two sequential steps in the formation of the lipid-linked core oligosaccharide, adding two mannose residues in α(1→2) linkages to the nascent oligosaccharide.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 74506-43-7

References:

1.	O'Reilly, M.K., Zhang, G. and Imperiali, B. In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis. Biochemistry 45 (2006) 9593–9603. [DOI] [PMID: 16878994]
2.	Absmanner, B., Schmeiser, V., Kampf, M. and Lehle, L. Biochemical characterization, membrane association and identification of amino acids essential for the function of Alg11 from Saccharomyces cerevisiae, an α1,2-mannosyltransferase catalysing two sequential glycosylation steps in the formation of the lipid-linked core oligosaccharide. Biochem. J. 426 (2010) 205–217. [DOI] [PMID: 19929855]
3.	Schutzbach, J.S., Springfield, J.D. and Jensen, J.W. The biosynthesis of oligosaccharide-lipids. Formation of an α-1,2-mannosyl-mannose linkage. J. Biol. Chem. 255 (1980) 4170–4175. [PMID: 6154707]

[EC 2.4.1.131 created 1984, modified 2011, modified 2012]

*EC

2.4.1.202

Accepted name:

2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one 2-D-glucosyltransferase

Reaction:

(1) UDP-α-D-glucose + 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one = UDP + (2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside
(2) UDP-α-D-glucose + 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one = UDP + (2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside

For diagram of benzoxazinone biosynthesis, click here

Glossary:

2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one = DIBOA
2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one = DIMBOA
(2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = DIBOA β-D-glucoside
(2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = DIMBOA β-D-glucoside

Other name(s):

uridine diphosphoglucose-2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one 2-glucosyltransferase; BX8; BX9; benzoxazinoid glucosyltransferase; DIMBOA glucosyltransferase

Systematic name:

UDP-α-D-glucose:2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one 2-β-D-glucosyltransferase

Comments:

The enzyme is involved in the detoxification of the benzoxazinoids DIBOA (2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one) and DIMBOA (2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one) which are stored as the respective non-toxic glucosides in the vacuoles in some plants, most commonly from the family of Poaceae (grasses). Benzoxazinoids are known to exhibit antimicrobial, antifeedant, and antiinsecticidal effects and are involved in the interaction of plants with other plants, insects, or microorganisms.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, CAS registry number: 122544-56-3

References:

1.	Bailey, B.A. and Larson, R.L. Hydroxamic acid glucosyltransferases from maize seedlings. Plant Physiol. 90 (1989) 1071–1076. [PMID: 16666853]
2.	von Rad, U., Huttl, R., Lottspeich, F., Gierl, A. and Frey, M. Two glucosyltransferases are involved in detoxification of benzoxazinoids in maize. Plant J. 28 (2001) 633–642. [DOI] [PMID: 11851909]

[EC 2.4.1.202 created 1992, modified 2012]

*EC

2.4.1.256

Accepted name:

dolichyl-P-Glc:Glc₂Man₉GlcNAc₂-PP-dolichol α-1,2-glucosyltransferase

Reaction:

dolichyl β-D-glucosyl phosphate + α-D-Glc-(1→3)-α-D-Glc-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = dolichyl phosphate + α-D-Glc-(1→2)-α-D-Glc-(1→3)-α-D-Glc-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol

For diagram of dolichyltetradecasaccharide biosynthesis, click here

Other name(s):

ALG10; Dol-P-Glc:Glc₂Man₉GlcNAc₂-PP-Dol α-1,2-glucosyltransferase; dolichyl β-D-glucosyl phosphate:D-Glc-α-(1→3)-D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol 2-α-D-glucosyltransferase

Systematic name:

dolichyl β-D-glucosyl-phosphate:α-D-Glc-(1→3)-α-D-Glc-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol α-1,2-glucosyltransferase (configuration-retaining)

Comments:

This eukaryotic enzyme performs the final step in the synthesis of the lipid-linked oligosaccharide, attaching D-glucose in an α-1,2-linkage to the outermost D-glucose in the long branch. The lipid-linked oligosaccharide is involved in N-linked protein glycosylation of selected asparagine residues of nascent polypeptide chains in eukaryotic cells.

Links to other databases:

References:

1.	Burda, P. and Aebi, M. The ALG10 locus of Saccharomyces cerevisiae encodes the α-1,2 glucosyltransferase of the endoplasmic reticulum: the terminal glucose of the lipid-linked oligosaccharide is required for efficient N-linked glycosylation. Glycobiology 8 (1998) 455–462. [DOI] [PMID: 9597543]

[EC 2.4.1.256 created 2011, modified 2012]

*EC

2.4.1.257

Accepted name:

GDP-Man:Man₂GlcNAc₂-PP-dolichol α-1,6-mannosyltransferase

Reaction:

GDP-α-D-mannose + α-D-Man-(1→3)-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = GDP + α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol

For diagram of dolichyltetradecasaccharide biosynthesis, click here

Other name(s):

GDP-Man:Man₂GlcNAc₂-PP-Dol α-1,6-mannosyltransferase; Alg2 mannosyltransferase (ambiguous); ALG2 (gene name, ambiguous); GDP-Man:Man₁GlcNAc₂-PP-dolichol mannosyltransferase (ambiguous); GDP-D-mannose:D-Man-α-(1→3)-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-6-mannosyltransferase

Systematic name:

GDP-α-D-mannose:α-D-Man-(1→3)-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 6-α-D-mannosyltransferase (configuration-retaining)

Comments:

The biosynthesis of asparagine-linked glycoproteins utilizes a dolichyl diphosphate-linked glycosyl donor, which is assembled by the series of membrane-bound glycosyltransferases that comprise the dolichol pathway. Alg2 mannosyltransferase from Saccharomyces cerevisiae carries out an α1,3-mannosylation (cf. EC 2.4.1.132) of β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol, followed by an α1,6-mannosylation, to form the first branched pentasaccharide intermediate of the dolichol pathway [1,2].

Links to other databases:

References:

1.	Kampf, M., Absmanner, B., Schwarz, M. and Lehle, L. Biochemical characterization and membrane topology of Alg2 from Saccharomyces cerevisiae as a bifunctional α1,3- and 1,6-mannosyltransferase involved in lipid-linked oligosaccharide biosynthesis. J. Biol. Chem. 284 (2009) 11900–11912. [DOI] [PMID: 19282279]
2.	O'Reilly, M.K., Zhang, G. and Imperiali, B. In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis. Biochemistry 45 (2006) 9593–9603. [DOI] [PMID: 16878994]

[EC 2.4.1.257 created 2011, modified 2012]

*EC

2.4.1.261

Accepted name:

dolichyl-P-Man:Man₈GlcNAc₂-PP-dolichol α-1,2-mannosyltransferase

Reaction:

dolichyl β-D-mannosyl phosphate + α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol + dolichyl phosphate

For diagram of dolichyltetradecasaccharide biosynthesis, click here

Other name(s):

ALG9; ALG9 α1,2 mannosyltransferase; dolichylphosphomannose-dependent ALG9 mannosyltransferase; ALG9 mannosyltransferase; Dol-P-Man:Man₈GlcNAc₂-PP-Dol α-1,2-mannosyltransferase; dolichyl β-D-mannosyl phosphate:D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol 2-α-D-mannosyltransferase

Systematic name:

dolichyl β-D-mannosyl-phosphate:α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 2-α-D-mannosyltransferase (configuration-inverting)

Comments:

The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc₃Man₉GlcNAc₂ core-oligosaccharide on the lipid carrier dolichyl diphosphate. Early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man₅GlcNAc₂-PP-Dol to Man₉Glc-NAc₂-PP-Dol on the lumenal side use dolichyl β-D-mannosyl phosphate. ALG9 mannosyltransferase catalyses the addition of two different α-1,2-mannose residues: the addition of α-1,2-mannose to Man₆GlcNAc₂-PP-Dol (EC 2.4.1.259) and the addition of α-1,2-mannose to Man₈GlcNAc₂-PP-Dol (EC 2.4.1.261).

Links to other databases:

References:

1.	Vleugels, W., Keldermans, L., Jaeken, J., Butters, T.D., Michalski, J.C., Matthijs, G. and Foulquier, F. Quality control of glycoproteins bearing truncated glycans in an ALG9-defective (CDG-IL) patient. Glycobiology 19 (2009) 910–917. [DOI] [PMID: 19451548]
2.	Frank, C.G. and Aebi, M. ALG9 mannosyltransferase is involved in two different steps of lipid-linked oligosaccharide biosynthesis. Glycobiology 15 (2005) 1156–1163. [DOI] [PMID: 15987956]

[EC 2.4.1.261 created 1976 as EC 2.4.1.130, part transferred 2011 to EC 2.4.1.261, modified 2012]

2.4.1.282

Accepted name:

3-O-α-D-glucosyl-L-rhamnose phosphorylase

Reaction:

3-O-α-D-glucopyranosyl-L-rhamnopyranose + phosphate = L-rhamnopyranose + β-D-glucose 1-phosphate

Other name(s):

cphy1019 (gene name)

Systematic name:

3-O-α-D-glucopyranosyl-L-rhamnopyranose:phosphate β-D-glucosyltransferase

Comments:

The enzyme does not phosphorylate α,α-trehalose, kojibiose, nigerose, or maltose. In the reverse phosphorolysis reaction the enzyme is specific for L-rhamnose as acceptor and β-D-glucose 1-phosphate as donor.

Links to other databases:

References:

1.	Nihira, T., Nakai, H. and Kitaoka, M. 3-O-α-D-glucopyranosyl-L-rhamnose phosphorylase from Clostridium phytofermentans. Carbohydr. Res. 350 (2012) 94–97. [DOI] [PMID: 22277537]

[EC 2.4.1.282 created 2012]

2.4.1.283

Accepted name:

2-deoxystreptamine N-acetyl-D-glucosaminyltransferase

Reaction:

UDP-N-acetyl-α-D-glucosamine + 2-deoxystreptamine = UDP + 2′-N-acetylparomamine

For diagram of paromamine biosynthesis, click here

Other name(s):

btrM (gene name); neoD (gene name); kanF (gene name)

Systematic name:

UDP-N-acetyl-α-D-glucosamine:2-deoxystreptamine N-acetyl-D-glucosaminyltransferase

Comments:

Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin, butirosin, neomycin and ribostamycin. Unlike the enzyme from the bacterium Streptomyces kanamyceticus, which can also accept UDP-D-glucose [2] (cf. EC 2.4.1.284, 2-deoxystreptamine glucosyltransferase), the enzyme from Bacillus circulans can only accept UDP-N-acetyl-α-D-glucosamine [1].

Links to other databases:

References:

1.	Yokoyama, K., Yamamoto, Y., Kudo, F. and Eguchi, T. Involvement of two distinct N-acetylglucosaminyltransferases and a dual-function deacetylase in neomycin biosynthesis. ChemBioChem 9 (2008) 865–869. [DOI] [PMID: 18311744]
2.	Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843–852. [DOI] [PMID: 21983602]

[EC 2.4.1.283 created 2012]

2.4.1.284

Accepted name:

2-deoxystreptamine glucosyltransferase

Reaction:

UDP-α-D-glucose + 2-deoxystreptamine = UDP + 2′-deamino-2′-hydroxyparomamine

Glossary:

2′-deamino-2′-hydroxyparomamine = 4-O-α-D-glucopyranosyl-2-deoxy-D-streptamine

Other name(s):

kanF (gene name)

Systematic name:

UDP-α-D-glucose:2-deoxystreptamine 6-α-D-glucosyltransferase

Comments:

Involved in the biosynthesis of kanamycin B and kanamycin C. Also catalyses EC 2.4.1.283, 2-deoxystreptamine N-acetyl-D-glucosaminyltransferase, but activity is only one fifth of that with UDP-α-D-glucose.

Links to other databases:

References:

1.	Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843–852. [DOI] [PMID: 21983602]

[EC 2.4.1.284 created 2012]

2.4.1.285

Accepted name:

UDP-GlcNAc:ribostamycin N-acetylglucosaminyltransferase

Reaction:

UDP-N-acetyl-α-D-glucosamine + ribostamycin = UDP + 2′′′-acetyl-6′′′-hydroxyneomycin C

Other name(s):

neoK (gene name)

Systematic name:

UDP-N-acetyl-α-D-glucosamine:ribostamycin N-acetylglucosaminyltransferase

Comments:

Involved in biosynthesis of the aminoglycoside antibiotic neomycin. Requires a divalent metal ion, optimally Mg²⁺, Mn²⁺ or Co²⁺.

Links to other databases:

References:

1.	Yokoyama, K., Yamamoto, Y., Kudo, F. and Eguchi, T. Involvement of two distinct N-acetylglucosaminyltransferases and a dual-function deacetylase in neomycin biosynthesis. ChemBioChem 9 (2008) 865–869. [DOI] [PMID: 18311744]

[EC 2.4.1.285 created 2012]

2.4.1.286

Accepted name:

chalcone 4′-O-glucosyltransferase

Reaction:

(1) UDP-α-D-glucose + naringenin chalcone = UDP + 2′,4,4′,6′-tetrahydroxychalcone 4′-O-β-D-glucoside
(2) UDP-α-D-glucose + 2′,3,4,4′,6′-pentahydroxychalcone = UDP + 2′,3,4,4′,6′-pentahydroxychalcone 4′-O-β-D-glucoside

For diagram of aureusidin biosynthesis, click here

Glossary:

naringenin chalcone = 2′,4,4′,6′-tetrahydroxychalcone = 3-(4-hydroxyphemyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one

Other name(s):

4′CGT

Systematic name:

UDP-α-D-glucose:2′,4,4′,6′-tetrahydroxychalcone 4′-O-β-D-glucosyltransferase

Comments:

Isolated from the plant Antirrhinum majus (snapdragon). Involved in the biosynthesis of aurones, plant flavonoids that provide yellow color to the flowers.

Links to other databases:

References:

Ono, E., Fukuchi-Mizutani, M., Nakamura, N., Fukui, Y., Yonekura-Sakakibara, K., Yamaguchi, M., Nakayama, T., Tanaka, T., Kusumi, T. and Tanaka, Y. Yellow flowers generated by expression of the aurone biosynthetic pathway. Proc. Natl. Acad. Sci. USA 103 (2006) 11075–11080. [DOI] [PMID: 16832053]

[EC 2.4.1.286 created 2012]

2.4.1.287

Accepted name:

rhamnopyranosyl-N-acetylglucosaminyl-diphospho-decaprenol β-1,4/1,5-galactofuranosyltransferase

Reaction:

2 UDP-α-D-galactofuranose + α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol = 2 UDP + β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol (overall reaction)
(1a) UDP-α-D-galactofuranose + α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol = UDP + β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol
(1b) UDP-α-D-galactofuranose + β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol = UDP + β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol

For diagram of galactofuranan biosynthesis, click here

Other name(s):

arabinogalactan galactofuranosyl transferase 1; GlfT1

Systematic name:

UDP-α-D-galactofuranose:α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol 4-β/4-β-galactofuranosyltransferase (configuration-inverting)

Comments:

Isolated from the bacteria Mycobacterium tuberculosis and M. smegmatis, the enzyme has dual β-(1→4) and β-(1→5) transferase action. Involved in the formation of the cell wall in mycobacteria.

Links to other databases:

References:

1.	Mikusová, K., Belánová, M., Korduláková, J., Honda, K., McNeil, M.R., Mahapatra, S., Crick, D.C. and Brennan, P.J. Identification of a novel galactosyl transferase involved in biosynthesis of the mycobacterial cell wall. J. Bacteriol. 188 (2006) 6592–6598. [DOI] [PMID: 16952951]
2.	Belánová, M., Dianisková, P., Brennan, P.J., Completo, G.C., Rose, N.L., Lowary, T.L. and Mikusová, K. Galactosyl transferases in mycobacterial cell wall synthesis. J. Bacteriol. 190 (2008) 1141–1145. [DOI] [PMID: 18055597]

[EC 2.4.1.287 created 2012, modified 2017]

2.4.1.288

Accepted name:

galactofuranosylgalactofuranosylrhamnosyl-N-acetylglucosaminyl-diphospho-decaprenol β-1,5/1,6-galactofuranosyltransferase

Reaction:

28 UDP-α-D-galactofuranose + β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol = 28 UDP + [β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→6)]₁₄-β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol

For diagram of arabinofuranogalactofuranan biosynthesis, click here

Other name(s):

GlfT2

Systematic name:

UDP-α-D-galactofuranose:β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol 4-β/5-β-D-galactofuranosyltransferase

Comments:

Isolated from Mycobacterium tuberculosis. The enzyme adds approximately twenty-eight galactofuranosyl residues with alternating 1→5 and 1→6 links forming a galactan domain with approximately thirty galactofuranosyl residues. Involved in the formation of the cell wall in mycobacteria.

Links to other databases:

References:

1.	Rose, N.L., Zheng, R.B., Pearcey, J., Zhou, R., Completo, G.C. and Lowary, T.L. Development of a coupled spectrophotometric assay for GlfT2, a bifunctional mycobacterial galactofuranosyltransferase. Carbohydr. Res. 343 (2008) 2130–2139. [DOI] [PMID: 18423586]
2.	May, J.F., Splain, R.A., Brotschi, C. and Kiessling, L.L. A tethering mechanism for length control in a processive carbohydrate polymerization. Proc. Natl. Acad. Sci. USA 106 (2009) 11851–11856. [DOI] [PMID: 19571009]
3.	Wheatley, R.W., Zheng, R.B., Richards, M.R., Lowary, T.L. and Ng, K.K. Tetrameric structure of the GlfT2 galactofuranosyltransferase reveals a scaffold for the assembly of mycobacterial Arabinogalactan. J. Biol. Chem. 287 (2012) 28132–28143. [DOI] [PMID: 22707726]

[EC 2.4.1.288 created 2012]

2.4.1.289

Accepted name:

N-acetylglucosaminyl-diphospho-decaprenol L-rhamnosyltransferase

Reaction:

dTDP-6-deoxy-β-L-mannose + N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol = dTDP + α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol

For diagram of galactofuranan biosynthesis, click here

Glossary:

dTDP-6-deoxy-β-L-mannose = dTDP-4-β-L-rhamnose

Other name(s):

WbbL

Systematic name:

dTDP-6-deoxy-β-L-mannose:N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol 3-α-L-rhamnosyltransferase

Comments:

Requires Mn²⁺ or Mg²⁺. Isolated from Mycobacterium smegmatis [1] and Mycobacterium tuberculosis [2]. The enzyme catalyses the addition of a rhamnosyl unit to N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol, completing the synthesis of the linkage unit that attaches the arabinogalactan moiety to the peptidoglycan moiety in Mycobacterial cell wall.

Links to other databases:

References:

1.	Mills, J.A., Motichka, K., Jucker, M., Wu, H.P., Uhlik, B.C., Stern, R.J., Scherman, M.S., Vissa, V.D., Pan, F., Kundu, M., Ma, Y.F. and McNeil, M. Inactivation of the mycobacterial rhamnosyltransferase, which is needed for the formation of the arabinogalactan-peptidoglycan linker, leads to irreversible loss of viability. J. Biol. Chem. 279 (2004) 43540–43546. [DOI] [PMID: 15294902]
2.	Grzegorzewicz, A.E., Ma, Y., Jones, V., Crick, D., Liav, A. and McNeil, M.R. Development of a microtitre plate-based assay for lipid-linked glycosyltransferase products using the mycobacterial cell wall rhamnosyltransferase WbbL. Microbiology 154 (2008) 3724–3730. [DOI] [PMID: 19047740]

[EC 2.4.1.289 created 2012]

2.4.1.290

Accepted name:

N,N′-diacetylbacillosaminyl-diphospho-undecaprenol α-1,3-N-acetylgalactosaminyltransferase

Reaction:

UDP-N-acetyl-α-D-galactosamine + N,N′-diacetyl-α-D-bacillosaminyl-diphospho-tritrans,heptacis-undecaprenol = UDP + N-acetyl-D-galactosaminyl-α-(1→3)-N,N′-diacetyl-α-D-bacillosaminyl-diphospho-tritrans,heptacis-undecaprenol

For diagram of undecaprenyldiphosphoheptasaccharide biosynthesis, click here

Glossary:

N,N′-diacetyl-D-bacillosamine = 2,4-diacetamido-2,4,6-trideoxy-D-glucopyranose

Other name(s):

PglA

Systematic name:

UDP-N-acetyl-α-D-galactosamine:N,N′-diacetyl-α-D-bacillosaminyl-diphospho-tritrans,heptacis-undecaprenol 3-α-N-acetyl-D-galactosaminyltransferase

Comments:

Isolated from Campylobacter jejuni. Part of a bacterial N-linked glycosylation pathway.

Links to other databases:

References:

1.	Glover, K.J., Weerapana, E. and Imperiali, B. In vitro assembly of the undecaprenylpyrophosphate-linked heptasaccharide for prokaryotic N-linked glycosylation. Proc. Natl. Acad. Sci. USA 102 (2005) 14255–14259. [DOI] [PMID: 16186480]

[EC 2.4.1.290 created 2012]

2.4.1.291

Accepted name:

N-acetylgalactosamine-N,N′-diacetylbacillosaminyl-diphospho-undecaprenol 4-α-N-acetylgalactosaminyltransferase

Reaction:

UDP-N-acetyl-α-D-galactosamine + N-acetyl-D-galactosaminyl-α-(1→3)-N,N′-diacetyl-α-D-bacillosaminyl-diphospho-tritrans,heptacis-undecaprenol = UDP + N-acetyl-D-galactosaminyl-α-(1→4)-N-acetyl-D-galactosaminyl-α-(1→3)-N,N′-diacetyl-α-D-bacillosaminyl-diphospho-tritrans,heptacis-undecaprenol

For diagram of undecaprenyldiphosphoheptasaccharide biosynthesis, click here

Glossary:

N,N′-diacetyl-D-bacillosamine = 2,4-diacetamido-2,4,6-trideoxy-D-glucopyranose

Other name(s):

PglJ

Systematic name:

UDP-N-acetyl-α-D-galactosamine:N-acetylgalactosaminyl-α-(1→3)-N,N′-diacetyl-α-D-bacillosaminyl-diphospho-tritrans,heptacis-undecaprenol 3-α-N-acetyl-D-galactosaminyltransferase

Comments:

Isolated from Campylobacter jejuni. Part of a bacterial N-linked glycosylation pathway.

Links to other databases:

References:

1.	Glover, K.J., Weerapana, E. and Imperiali, B. In vitro assembly of the undecaprenylpyrophosphate-linked heptasaccharide for prokaryotic N-linked glycosylation. Proc. Natl. Acad. Sci. USA 102 (2005) 14255–14259. [DOI] [PMID: 16186480]
2.	Chen, M.M., Weerapana, E., Ciepichal, E., Stupak, J., Reid, C.W., Swiezewska, E. and Imperiali, B. Polyisoprenol specificity in the Campylobacter jejuni N-linked glycosylation pathway. Biochemistry 46 (2007) 14342–14348. [DOI] [PMID: 18034500]

[EC 2.4.1.291 created 2012]

2.4.1.292

Accepted name:

GalNAc-α-(1→4)-GalNAc-α-(1→3)-diNAcBac-PP-undecaprenol α-1,4-N-acetyl-D-galactosaminyltransferase

Reaction:

3 UDP-N-acetyl-α-D-galactosamine + GalNAc-α-(1→4)-GalNAc-α-(1→3)-diNAcBac-PP-tritrans,heptacis-undecaprenol = 3 UDP + [GalNAc-α-(1→4)]₄-GalNAc-α-(1→3)-diNAcBac-PP-tritrans,heptacis-undecaprenol

For diagram of undecaprenyldiphosphoheptasaccharide biosynthesis, click here

Glossary:

diNAcBac = N,N′-diacetyl-D-bacillosamine = 2,4-diacetamido-2,4,6-trideoxy-D-glucopyranose

Other name(s):

PglH

Systematic name:

UDP-N-acetyl-α-D-galactosamine:GalNAc-α-(1→4)-GalNAc-α-(1→3)-diNAcBac-PP-tritrans,heptacis-undecaprenol 4-α-N-acetyl-D-galactosaminyltransferase

Comments:

Isolated from Campylobacter jejuni. Part of a bacterial N-linked glycosylation pathway.

Links to other databases:

References:

1.	Glover, K.J., Weerapana, E. and Imperiali, B. In vitro assembly of the undecaprenylpyrophosphate-linked heptasaccharide for prokaryotic N-linked glycosylation. Proc. Natl. Acad. Sci. USA 102 (2005) 14255–14259. [DOI] [PMID: 16186480]
2.	Troutman, J.M. and Imperiali, B. Campylobacter jejuni PglH is a single active site processive polymerase that utilizes product inhibition to limit sequential glycosyl transfer reactions. Biochemistry 48 (2009) 2807–2816. [DOI] [PMID: 19159314]
3.	Borud, B., Viburiene, R., Hartley, M.D., Paulsen, B.S., Egge-Jacobsen, W., Imperiali, B. and Koomey, M. Genetic and molecular analyses reveal an evolutionary trajectory for glycan synthesis in a bacterial protein glycosylation system. Proc. Natl. Acad. Sci. USA 108 (2011) 9643–9648. [DOI] [PMID: 21606362]

[EC 2.4.1.292 created 2012]

2.4.1.293

Accepted name:

GalNAc₅-diNAcBac-PP-undecaprenol β-1,3-glucosyltransferase

Reaction:

UDP-α-D-glucose + [GalNAc-α-(1→4)]₄-GalNAc-α-(1→3)-diNAcBac-diphospho-tritrans,heptacis-undecaprenol = UDP + [GalNAc-α-(1→4)]₂-[Glc-β-(1→3)]-[GalNAc-α-(1→4)]₂-GalNAc-α-(1→3)-diNAcBac-diphospho-tritrans,heptacis-undecaprenol

For diagram of undecaprenyldiphosphoheptasaccharide biosynthesis, click here

Glossary:

diNAcBac = N,N′-diacetyl-D-bacillosamine = 2,4-diacetamido-2,4,6-trideoxy-D-glucopyranose

Other name(s):

PglI

Systematic name:

UDP-α-D-glucose:[GalNAc-α-(1→4)]4-GalNAc-α-(1→3)-diNAcBac-diphospho-tritrans,heptacis-undecaprenol 3-β-D-glucosyltransferase

Comments:

Isolated from the bacterium Campylobacter jejuni. Part of a bacterial N-linked glycosylation pathway.

Links to other databases:

References:

1.	Glover, K.J., Weerapana, E. and Imperiali, B. In vitro assembly of the undecaprenylpyrophosphate-linked heptasaccharide for prokaryotic N-linked glycosylation. Proc. Natl. Acad. Sci. USA 102 (2005) 14255–14259. [DOI] [PMID: 16186480]
2.	Kelly, J., Jarrell, H., Millar, L., Tessier, L., Fiori, L.M., Lau, P.C., Allan, B. and Szymanski, C.M. Biosynthesis of the N-linked glycan in Campylobacter jejuni and addition onto protein through block transfer. J. Bacteriol. 188 (2006) 2427–2434. [DOI] [PMID: 16547029]

[EC 2.4.1.293 created 2012]

2.4.2.45

Accepted name:

decaprenyl-phosphate phosphoribosyltransferase

Reaction:

trans,octacis-decaprenyl phosphate + 5-phospho-α-D-ribose 1-diphosphate = trans,octacis-decaprenylphospho-β-D-ribofuranose 5-phosphate + diphosphate

For diagram of decaprenylphosphoarabinofuranose biosynthesis, click here

Other name(s):

5-phospho-α-D-ribose-1-diphosphate:decaprenyl-phosphate 5-phosphoribosyltransferase; 5-phospho-α-D-ribose 1-pyrophosphate:decaprenyl phosphate 5-phosphoribosyltransferase; DPPR synthase; Rv3806

Systematic name:

trans,octacis-decaprenylphospho-β-D-ribofuranose 5-phosphate:diphosphate phospho-α-D-ribosyltransferase

Comments:

Requires Mg²⁺. Isolated from Mycobacterium tuberculosis. Has some activity with other polyprenyl phosphates.

Links to other databases:

References:

Huang, H., Scherman, M.S., D'Haeze, W., Vereecke, D., Holsters, M., Crick, D.C. and McNeil, M.R. Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-α-D-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-D-arabinose synthesis. J. Biol. Chem. 280 (2005) 24539–24543. [DOI] [PMID: 15878857]

[EC 2.4.2.45 created 2012]

2.4.2.46

Accepted name:

galactan 5-O-arabinofuranosyltransferase

Reaction:

Adds an α-D-arabinofuranosyl group from trans,octacis-decaprenylphospho-β-D-arabinofuranose at the 5-O-position of the eighth, tenth and twelfth galactofuranose unit of the galactofuranan chain of [β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→6)]₁₄-β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol

For diagram of arabinofuranogalactofuranan biosynthesis, click here

Other name(s):

AftA; Rv3792

Systematic name:

galactofuranan:trans,octacis-decaprenylphospho-β-D-arabinofuranose 5-O-α-D-arabinofuranosyltransferase

Comments:

Isolated from Mycobacterium tuberculosis and Corynebacterium glutamicum. These arabinofuranosyl groups form the start of an arabinofuranan chain as part of the of the cell wall in mycobacteria.

Links to other databases:

References:

1.	Alderwick, L.J., Seidel, M., Sahm, H., Besra, G.S. and Eggeling, L. Identification of a novel arabinofuranosyltransferase (AftA) involved in cell wall arabinan biosynthesis in Mycobacterium tuberculosis. J. Biol. Chem. 281 (2006) 15653–15661. [DOI] [PMID: 16595677]

[EC 2.4.2.46 created 2012]

2.4.2.47

Accepted name:

arabinofuranan 3-O-arabinosyltransferase

Reaction:

Adds an α-D-arabinofuranosyl group from trans,octacis-decaprenylphospho-β-D-arabinofuranose at the 3-O-position of an α-(1→5)-arabinofuranan chain attached to a β-(1→5)-galactofuranan chain

For diagram of arabinofuranogalactofuranan biosynthesis, click here

Other name(s):

AftC

Systematic name:

α-(1→5)-arabinofuranan:trans,octacis-decaprenylphospho-β-D-arabinofuranose 3-O-α-D-arabinofuranosyltransferase

Comments:

Isolated from Mycobacterium smegmatis. Involved in the formation of the cell wall in mycobacteria.

Links to other databases:

References:

1.	Birch, H.L., Alderwick, L.J., Bhatt, A., Rittmann, D., Krumbach, K., Singh, A., Bai, Y., Lowary, T.L., Eggeling, L. and Besra, G.S. Biosynthesis of mycobacterial arabinogalactan: identification of a novel α(1-→3) arabinofuranosyltransferase. Mol. Microbiol. 69 (2008) 1191–1206. [DOI] [PMID: 18627460]
2.	Zhang, J., Angala, S.K., Pramanik, P.K., Li, K., Crick, D.C., Liav, A., Jozwiak, A., Swiezewska, E., Jackson, M. and Chatterjee, D. Reconstitution of functional mycobacterial arabinosyltransferase AftC proteoliposome and assessment of decaprenylphosphorylarabinose analogues as arabinofuranosyl donors. ACS Chem. Biol. 6 (2011) 819–828. [DOI] [PMID: 21595486]

[EC 2.4.2.47 created 2012]

2.4.2.48

Accepted name:

tRNA-guanine¹⁵ transglycosylase

Reaction:

guanine¹⁵ in tRNA + 7-cyano-7-carbaguanine = 7-cyano-7-carbaguanine¹⁵ in tRNA + guanine

Glossary:

7-cyano-7-carbaguanine = preQ₀ = 7-cyano-7-deazaguanine
archaeosine = G* = 7-amidino-7-deazaguanosine

Other name(s):

tRNA transglycosylase (ambiguous); transfer ribonucleate glycosyltransferase (ambiguous); tRNA guanine¹⁵ transglycosidase; TGT (ambiguous); transfer ribonucleic acid guanine¹⁵ transglycosylase

Systematic name:

tRNA-guanine¹⁵:7-cyano-7-carbaguanine tRNA-D-ribosyltransferase

Comments:

Archaeal tRNAs contain the modified nucleoside archaeosine at position 15. This archaeal enzyme catalyses the exchange of guanine at position 15 of tRNA with the base preQ₀, which is ultimately modified to form the nucleoside archaeosine (cf. EC 2.6.1.97) [1].

Links to other databases:

References:

1.	Bai, Y., Fox, D.T., Lacy, J.A., Van Lanen, S.G. and Iwata-Reuyl, D. Hypermodification of tRNA in thermophilic archaea. Cloning, overexpression, and characterization of tRNA-guanine transglycosylase from Methanococcus jannaschii. J. Biol. Chem. 275 (2000) 28731–28738. [DOI] [PMID: 10862614]

[EC 2.4.2.48 created 2012]

2.4.99.17

Accepted name:

S-adenosylmethionine:tRNA ribosyltransferase-isomerase

Reaction:

S-adenosyl-L-methionine + 7-aminomethyl-7-carbaguanosine³⁴ in tRNA = L-methionine + adenine + epoxyqueuosine³⁴ in tRNA

For diagram of queuine biosynthesis, click here

Glossary:

7-aminomethyl-7-carbaguanine = preQ₁ = 7-aminomethyl-7-deazaguanine
epoxyqueosine = oQ

Other name(s):

QueA enzyme; queuosine biosynthesis protein QueA

Systematic name:

S-adenosyl-L-methionine:7-aminomethyl-7-deazaguanosine ribosyltransferase (ribosyl isomerizing; L-methionine, adenine releasing)

Comments:

The reaction is a combined transfer and isomerization of the ribose moiety of S-adenosyl-L-methionine to the modified guanosine base in the wobble position in tRNAs specific for Tyr, His, Asp or Asn. It is part of the queuosine biosynthesis pathway.

Links to other databases:

References:

1.	Slany, R.K., Bosl, M., Crain, P.F. and Kersten, H. A new function of S-adenosylmethionine: the ribosyl moiety of AdoMet is the precursor of the cyclopentenediol moiety of the tRNA wobble base queuine. Biochemistry 32 (1993) 7811–7817. [PMID: 8347586]
2.	Slany, R.K., Bosl, M. and Kersten, H. Transfer and isomerization of the ribose moiety of AdoMet during the biosynthesis of queuosine tRNAs, a new unique reaction catalyzed by the QueA protein from Escherichia coli. Biochimie 76 (1994) 389–393. [DOI] [PMID: 7849103]
3.	Kinzie, S.D., Thern, B. and Iwata-Reuyl, D. Mechanistic studies of the tRNA-modifying enzyme QueA: a chemical imperative for the use of AdoMet as a "ribosyl" donor. Org. Lett. 2 (2000) 1307–1310. [PMID: 10810734]
4.	Van Lanen, S.G. and Iwata-Reuyl, D. Kinetic mechanism of the tRNA-modifying enzyme S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). Biochemistry 42 (2003) 5312–5320. [DOI] [PMID: 12731872]
5.	Mathews, I., Schwarzenbacher, R., McMullan, D., Abdubek, P., Ambing, E., Axelrod, H., Biorac, T., Canaves, J.M., Chiu, H.J., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Hornsby, M., Jaroszewski, L., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., Miller, M.D., Moy, K., Nigoghossian, E., Ouyang, J., Paulsen, J., Quijano, K., Reyes, R., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J. and Wilson, I.A. Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 Å resolution reveals a new fold. Proteins 59 (2005) 869–874. [DOI] [PMID: 15822125]
6.	Grimm, C., Ficner, R., Sgraja, T., Haebel, P., Klebe, G. and Reuter, K. Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase. Biochem. Biophys. Res. Commun. 351 (2006) 695–701. [DOI] [PMID: 17083917]

[EC 2.4.99.17 created 2012]

2.4.99.18

Accepted name:

dolichyl-diphosphooligosaccharide—protein glycotransferase

Reaction:

dolichyl diphosphooligosaccharide + [protein]-L-asparagine = dolichyl diphosphate + a glycoprotein with the oligosaccharide chain attached by N-β-D-glycosyl linkage to a protein L-asparagine

For diagram of glycoprotein biosynthesis, click here

Other name(s):

dolichyldiphosphooligosaccharide-protein glycosyltransferase; asparagine N-glycosyltransferase; dolichyldiphosphooligosaccharide-protein oligosaccharyltransferase; dolichylpyrophosphodiacetylchitobiose-protein glycosyltransferase; oligomannosyltransferase; oligosaccharide transferase; dolichyldiphosphoryloligosaccharide-protein oligosaccharyltransferase; dolichyl-diphosphooligosaccharide:protein-L-asparagine oligopolysaccharidotransferase; STT3

Systematic name:

dolichyl-diphosphooligosaccharide:protein-L-asparagine N-β-D-oligopolysaccharidotransferase

Comments:

Occurs in eukaryotes that form a glycoprotein by the transfer of a glucosyl-mannosyl-glucosamine polysaccharide to the side-chain of an L-asparagine residue in the sequence -Asn-Xaa-Ser- or -Asn-Xaa-Thr- (Xaa not Pro) in nascent polypeptide chains. The basic oligosaccharide is the tetradecasaccharide Glc₃Man₉GlcNAc₂ (for diagram click here). However, smaller oligosaccharides derived from it and oligosaccharides with additional monosaccharide units attached may be involved. See ref [2] for a review of N-glycoproteins in eukaryotes. Man₃GlcNAc₂ seems to be common for all of the oligosaccharides involved with the terminal N-acetylglucosamine linked to the protein L-asparagine. Occurs on the cytosolic face of the endoplasmic reticulum. The dolichol involved normally has 14-21 isoprenoid units with two trans double-bonds at the ω end, and the rest of the double-bonds in cis form.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 75302-32-8

References:

1.	Das, R.C. and Heath, E.C. Dolichyldiphosphoryloligosaccharide-protein oligosaccharyltransferase; solubilization, purification, and properties. Proc. Natl. Acad. Sci. USA 77 (1980) 3811–3815. [DOI] [PMID: 6933437]
2.	Song, W., Henquet, M.G., Mentink, R.A., van Dijk, A.J., Cordewener, J.H., Bosch, D., America, A.H. and van der Krol, A.R. N-glycoproteomics in plants: perspectives and challenges. J Proteomics 74 (2011) 1463–1474. [DOI] [PMID: 21605711]

[EC 2.4.99.18 created 1984 as EC 2.4.1.119, transferred 2012 to EC 2.4.99.18]

2.4.99.19

Accepted name:

undecaprenyl-diphosphooligosaccharide—protein glycotransferase

Reaction:

tritrans,heptacis-undecaprenyl diphosphooligosaccharide + [protein]-L-asparagine = tritrans,heptacis-undecaprenyl diphosphate + a glycoprotein with the oligosaccharide chain attached by N-β-D-glycosyl linkage to protein L-asparagine

Other name(s):

PglB

Systematic name:

tritrans,heptacis-undecaprenyl-diphosphooligosaccharide:protein-L-asparagine N-β-D-oligosaccharidotransferase

Comments:

A bacterial enzyme that has been isolated from Campylobacter jejuni [1] and Campylobacter lari [2]. It forms a glycoprotein by the transfer of a glucosyl-N-acetylgalactosaminyl-N,N′-diacetylbacillosamine (GalNAc₂(Glc)GalNAc₃diNAcBac) polysaccharide and related oligosaccharides to the side-chain of an L-asparagine residue in the sequence -Asp/Glu-Xaa-Asn-Xaa’-Ser/Thr- (Xaa and Xaa’ not Pro) in nascent polypeptide chains. Requires Mn²⁺ or Mg²⁺. Occurs on the external face of the plasma membrane. The polyprenol involved is normally tritrans,heptacis-undecaprenol but a decaprenol is used by some species.

Links to other databases:

References:

1.	Maita, N., Nyirenda, J., Igura, M., Kamishikiryo, J. and Kohda, D. Comparative structural biology of eubacterial and archaeal oligosaccharyltransferases. J. Biol. Chem. 285 (2010) 4941–4950. [DOI] [PMID: 20007322]
2.	Lizak, C., Gerber, S., Numao, S., Aebi, M. and Locher, K.P. X-ray structure of a bacterial oligosaccharyltransferase. Nature 474 (2011) 350–355. [DOI] [PMID: 21677752]

[EC 2.4.99.19 created 2012]

*EC

2.5.1.21

Accepted name:

squalene synthase

Reaction:

2 (2E,6E)-farnesyl diphosphate + NAD(P)H + H⁺ = squalene + 2 diphosphate + NAD(P)⁺ (overall reaction)
(1a) 2 (2E,6E)-farnesyl diphosphate = diphosphate + presqualene diphosphate
(1b) presqualene diphosphate + NAD(P)H + H⁺ = squalene + diphosphate + NAD(P)⁺

For diagram of squalene, phytoene and 4,4′-diapophytoene biosynthesis, click here

Other name(s):

farnesyltransferase; presqualene-diphosphate synthase; presqualene synthase; squalene synthetase; farnesyl-diphosphate farnesyltransferase; SQS

Systematic name:

(2E,6E)-farnesyl-diphosphate:(2E,6E)-farnesyl-diphosphate farnesyltransferase

Comments:

This microsomal enzyme catalyses the first committed step in the biosynthesis of sterols. The enzyme from yeast requires either Mg²⁺ or Mn²⁺ for activity. In the absence of NAD(P)H, presqualene diphosphate (PSPP) is accumulated. When NAD(P)H is present, presqualene diphosphate does not dissociate from the enzyme during the synthesis of squalene from farnesyl diphosphate (FPP) [8]. High concentrations of FPP inhibit the production of squalene but not of PSPP [8].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9077-14-9

References:

1.	Kuswick-Rabiega, G. and Rilling, H.C. Squalene synthetase. Solubilization and partial purification of squalene synthetase, copurification of presqualene pyrophosphate and squalene synthetase activities. J. Biol. Chem. 262 (1987) 1505–1509. [PMID: 3805037]
2.	Ericsson, J., Appelkvist, E.L., Thelin, A., Chojnacki, T. and Dallner, G. Isoprenoid biosynthesis in rat liver peroxisomes. Characterization of cis-prenyltransferase and squalene synthetase. J. Biol. Chem. 267 (1992) 18708–18714. [PMID: 1527001]
3.	Tansey, T.R. and Shechter, I. Structure and regulation of mammalian squalene synthase. Biochim. Biophys. Acta 1529 (2000) 49–62. [DOI] [PMID: 11111077]
4.	LoGrasso, P.V., Soltis, D.A. and Boettcher, B.R. Overexpression, purification, and kinetic characterization of a carboxyl-terminal-truncated yeast squalene synthetase. Arch. Biochem. Biophys. 307 (1993) 193–199. [DOI] [PMID: 8239656]
5.	Shechter, I., Klinger, E., Rucker, M.L., Engstrom, R.G., Spirito, J.A., Islam, M.A., Boettcher, B.R. and Weinstein, D.B. Solubilization, purification, and characterization of a truncated form of rat hepatic squalene synthetase. J. Biol. Chem. 267 (1992) 8628–8635. [PMID: 1569107]
6.	Agnew, W.S. and Popják, G. Squalene synthetase. Stoichiometry and kinetics of presqualene pyrophosphate and squalene synthesis by yeast microsomes. J. Biol. Chem. 253 (1978) 4566–4573. [PMID: 26684]
7.	Pandit, J., Danley, D.E., Schulte, G.K., Mazzalupo, S., Pauly, T.A., Hayward, C.M., Hamanaka, E.S., Thompson, J.F. and Harwood, H.J., Jr. Crystal structure of human squalene synthase. A key enzyme in cholesterol biosynthesis. J. Biol. Chem. 275 (2000) 30610–30617. [DOI] [PMID: 10896663]
8.	Radisky, E.S. and Poulter, C.D. Squalene synthase: steady-state, pre-steady-state, and isotope-trapping studies. Biochemistry 39 (2000) 1748–1760. [DOI] [PMID: 10677224]

[EC 2.5.1.21 created 1976, modified 2005, modified 2012]

*EC

2.5.1.32

Accepted name:

15-cis-phytoene synthase

Reaction:

2 geranylgeranyl diphosphate = 15-cis-phytoene + 2 diphosphate (overall reaction)
(1a) 2 geranylgeranyl diphosphate = diphosphate + prephytoene diphosphate
(1b) prephytoene diphosphate = 15-cis-phytoene + diphosphate

For diagram of squalene, phytoene and 4,4′-diapophytoene biosynthesis, click here

Other name(s):

PSY (gene name); crtB (gene name); prephytoene-diphosphate synthase; phytoene synthetase; PSase; geranylgeranyl-diphosphate geranylgeranyltransferase

Systematic name:

geranylgeranyl-diphosphate:geranylgeranyl-diphosphate geranylgeranyltransferase (15-cis-phytoene-forming)

Comments:

Requires Mn²⁺ for activity. The enzyme condenses two molecules of geranylgeranyl diphosphate to give prephytoene diphosphate, followed by rearrangement of the cyclopropylcarbinyl intermediate to 15-cis-phytoene.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 50936-61-3

References:

1.	Chamovitz, D., Misawa, N., Sandmann, G. and Hirschberg, J. Molecular cloning and expression in Escherichia coli of a cyanobacterial gene coding for phytoene synthase, a carotenoid biosynthesis enzyme. FEBS Lett. 296 (1992) 305–310. [DOI] [PMID: 1537409]
2.	Sandmann, G. and Misawa, N. New functional assignment of the carotenogenic genes crtB and crtE with constructs of these genes from Erwinia species. FEMS Microbiol. Lett. 69 (1992) 253–257. [PMID: 1555761]
3.	Scolnik, P.A. and Bartley, G.E. Nucleotide sequence of an Arabidopsis cDNA for phytoene synthase. Plant Physiol. 104 (1994) 1471–1472. [PMID: 8016277]
4.	Misawa, N., Truesdale, M.R., Sandmann, G., Fraser, P.D., Bird, C., Schuch, W. and Bramley, P.M. Expression of a tomato cDNA coding for phytoene synthase in Escherichia coli, phytoene formation in vivo and in vitro, and functional analysis of the various truncated gene products. J. Biochem. (Tokyo) 116 (1994) 980–985. [PMID: 7896759]
5.	Schledz, M., al-Babili, S., von Lintig, J., Haubruck, H., Rabbani, S., Kleinig, H. and Beyer, P. Phytoene synthase from Narcissus pseudonarcissus: functional expression, galactolipid requirement, topological distribution in chromoplasts and induction during flowering. Plant J. 10 (1996) 781–792. [DOI] [PMID: 8953242]

[EC 2.5.1.32 created 1984, modified 2005, modified 2012]

2.5.1.99

Deleted entry:

all-trans-phytoene synthase. The activity was an artifact caused by photoisomerization of the product of EC 2.5.1.32, 15-cis-phytoene synthase.

[EC 2.5.1.99 created 2012, deleted 2018]

2.5.1.100

Accepted name:

fumigaclavine A dimethylallyltransferase

Reaction:

fumigaclavine A + prenyl diphosphate = fumigaclavine C + diphosphate

For diagram of fumigaclavin alkaloid biosynthesis, click here

Glossary:

fumigaclavine A = 6,8β-dimethylergolin-9β-yl acetate;
fumigaclavine C = 6,8β-dimethyl-2-(2-methylbut-3-en-2-yl)ergolin-9β-yl acetate

Other name(s):

FgaPT1; dimethylallyl-diphosphate:fumigaclavine A dimethylallyltransferase

Systematic name:

prenyl-diphosphate:fumigaclavine A prenyltransferase

Comments:

Fumigaclavine C is an ergot alkaloid produced by some fungi of the Trichocomaceae family. Activity does not require any metal ions.

Links to other databases:

References:

1.	Unsöld, I.A. and Li, S.M. Reverse prenyltransferase in the biosynthesis of fumigaclavine C in Aspergillus fumigatus: gene expression, purification, and characterization of fumigaclavine C synthase FGAPT1. ChemBioChem 7 (2006) 158–164. [DOI] [PMID: 16397874]

[EC 2.5.1.100 created 2012]

2.5.1.101

Accepted name:

N,N′-diacetyllegionaminate synthase

Reaction:

2,4-diacetamido-2,4,6-trideoxy-α-D-mannopyranose + phosphoenolpyruvate + H₂O = N,N′-diacetyllegionaminate + phosphate

For diagram of legionaminic acid biosynthesis, click here

Glossary:

legionaminate = 5,7-diamino-3,5,7,9-tetradeoxy-D-glycero-D-galacto-non-2-ulosonate

Other name(s):

neuB (gene name); legI (gene name)

Systematic name:

phosphoenolpyruvate:2,4-diacetamido-2,4,6-trideoxy-α-D-mannopyranose 1-(2-carboxy-2-oxoethyl)transferase

Comments:

Requires a divalent metal such as Mn²⁺. Isolated from the bacteria Legionella pneumophila and Campylobacter jejuni, where it is involved in the biosynthesis of legionaminic acid, a virulence-associated, cell surface sialic acid-like derivative.

Links to other databases:

References:

1.	Glaze, P.A., Watson, D.C., Young, N.M. and Tanner, M.E. Biosynthesis of CMP-N,N′-diacetyllegionaminic acid from UDP-N,N′-diacetylbacillosamine in Legionella pneumophila. Biochemistry 47 (2008) 3272–3282. [DOI] [PMID: 18275154]
2.	Schoenhofen, I.C., Vinogradov, E., Whitfield, D.M., Brisson, J.R. and Logan, S.M. The CMP-legionaminic acid pathway in Campylobacter: biosynthesis involving novel GDP-linked precursors. Glycobiology 19 (2009) 715–725. [DOI] [PMID: 19282391]

[EC 2.5.1.101 created 2012]

2.5.1.102

Accepted name:

geranyl-pyrophosphate—olivetolic acid geranyltransferase

Reaction:

geranyl diphosphate + 2,4-dihydroxy-6-pentylbenzoate = diphosphate + cannabigerolate

For diagram of cannabinoid biosynthesis, click here

Glossary:

2,4-dihydroxy-6-pentylbenzoate = olivetolate
cannabigerolate = CBGA = 3-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-2,4-dihydroxy-6-pentylbenzoate
cannabinerolate = 3-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-2,4-dihydroxy-6-pentylbenzoate

Other name(s):

GOT (ambiguous)

Systematic name:

geranyl-diphosphate:olivetolate geranyltransferase

Comments:

Part of the cannabinoids biosynthetic pathway of the plant Cannabis sativa. The enzyme can also use neryl diphosphate as substrate, forming cannabinerolate.

Links to other databases:

References:

1.	Fellermeier, M. and Zenk, M.H. Prenylation of olivetolate by a hemp transferase yields cannabigerolic acid, the precursor of tetrahydrocannabinol. FEBS Lett. 427 (1998) 283–285. [DOI] [PMID: 9607329]

[EC 2.5.1.102 created 2012]

2.5.1.103

Accepted name:

presqualene diphosphate synthase

Reaction:

2 (2E,6E)-farnesyl diphosphate = presqualene diphosphate + diphosphate

For diagram of botryococcus braunii BOT22 squalene and botrycoccene biosynthesis, click here

Other name(s):

SSL-1 (gene name); hpnD (gene name)

Systematic name:

(2E,6E)-farnesyl-diphosphate:(2E,6E)-farnesyl-diphosphate farnesyltransferase (presqualene diphosphate-forming)

Comments:

Isolated from the green alga Botryococcus braunii BOT22. Unlike EC 2.5.1.21, squalene synthase, where squalene is formed in one step from farnesyl diphosphate, in this alga the intermediate presqualene diphosphate is generated and released by this enzyme. This compound is then converted into either squalene (by EC 1.3.1.96, Botryococcus squalene synthase) or botryococcene (EC 1.3.1.97, botryococcene synthase).

Links to other databases:

References:

1.	Niehaus, T.D., Okada, S., Devarenne, T.P., Watt, D.S., Sviripa, V. and Chappell, J. Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii. Proc. Natl. Acad. Sci. USA 108 (2011) 12260–12265. [DOI] [PMID: 21746901]
2.	Pan, J.J., Solbiati, J.O., Ramamoorthy, G., Hillerich, B.S., Seidel, R.D., Cronan, J.E., Almo, S.C. and Poulter, C.D. Biosynthesis of squalene from farnesyl diphosphate in bacteria: three steps catalyzed by three enzymes. ACS Cent. Sci. 1 (2015) 77–82. [DOI] [PMID: 26258173]

[EC 2.5.1.103 created 2012]

*EC

2.6.1.19

Accepted name:

4-aminobutyrate—2-oxoglutarate transaminase

Reaction:

4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate

For diagram of arginine catabolism, click here

Glossary:

4-aminobutanoate = γ-aminobutyrate = GABA

Other name(s):

β-alanine-oxoglutarate transaminase; aminobutyrate aminotransferase (ambiguous); β-alanine aminotransferase; β-alanine-oxoglutarate aminotransferase; γ-aminobutyrate aminotransaminase (ambiguous); γ-aminobutyrate transaminase (ambiguous); γ-aminobutyrate-α-ketoglutarate aminotransferase; γ-aminobutyrate-α-ketoglutarate transaminase; γ-aminobutyrate:α-oxoglutarate aminotransferase; γ-aminobutyric acid aminotransferase (ambiguous); γ-aminobutyric acid transaminase (ambiguous); γ-aminobutyric acid-α-ketoglutarate transaminase; γ-aminobutyric acid-α-ketoglutaric acid aminotransferase; γ-aminobutyric acid-2-oxoglutarate transaminase; γ-aminobutyric transaminase (ambiguous); 4-aminobutyrate aminotransferase (ambiguous); 4-aminobutyrate-2-ketoglutarate aminotransferase; 4-aminobutyrate-2-oxoglutarate aminotransferase; 4-aminobutyrate-2-oxoglutarate transaminase; 4-aminobutyric acid 2-ketoglutaric acid aminotransferase; 4-aminobutyric acid aminotransferase (ambiguous); aminobutyrate transaminase (ambiguous); GABA aminotransferase (ambiguous); GABA transaminase (ambiguous); GABA transferase (ambiguous); GABA-α-ketoglutarate aminotransferase; GABA-α-ketoglutarate transaminase; GABA-α-ketoglutaric acid transaminase; GABA-α-oxoglutarate aminotransferase; GABA-2-oxoglutarate aminotransferase; GABA-2-oxoglutarate transaminase; GABA-oxoglutarate aminotransferase; GABA-oxoglutarate transaminase; glutamate-succinic semialdehyde transaminase; GabT

Systematic name:

4-aminobutanoate:2-oxoglutarate aminotransferase

Comments:

Requires pyridoxal phosphate. Some preparations also act on β-alanine, 5-aminopentanoate and (R,S)-3-amino-2-methylpropanoate. cf. EC 2.6.1.120, β-alanine—2-oxoglutarate transaminase.

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9037-67-6

References:

1.	Scott, E.M. and Jakoby, W.B. Soluble γ-aminobutyric-glutamic transaminase from Pseudomonas fluorescens. J. Biol. Chem. 234 (1959) 932–936. [PMID: 13654294]
2.	Aurich, H. Über die β-Alanin-α-Ketoglutarat-Transaminase aus Neurospora crassa. Hoppe-Seyler's Z. Physiol. Chem. 326 (1961) 25–33. [PMID: 13863304]
3.	Schausboe, A., Wu, J.-Y. and Roberts, E. Purification and characterization of the 4-aminobutyrate-2-ketoglutarate transaminase from mouse brain. Biochemistry 12 (1973) 2868–2873. [PMID: 4719123]
4.	Bartsch, K., von Johnn-Marteville, A. and Schulz, A. Molecular analysis of two genes of the Escherichia coli gab cluster: nucleotide sequence of the glutamate:succinic semialdehyde transaminase gene (gabT) and characterization of the succinic semialdehyde dehydrogenase gene (gabD). J. Bacteriol. 172 (1990) 7035–7042. [DOI] [PMID: 2254272]

[EC 2.6.1.19 created 1965, modified 1982, modified 2012, modified 2021]

2.6.1.93

Accepted name:

neamine transaminase

Reaction:

neamine + 2-oxoglutarate = 6′-dehydroparomamine + L-glutamate

For diagram of neamine and ribostamycin biosynthesis, click here

Other name(s):

glutamate—6′-dehydroparomamine aminotransferase; btrB (gene name); neoN (gene name); kacL (gene name)

Systematic name:

neamine:2-oxoglutarate aminotransferase

Comments:

The reaction occurs in vivo in the opposite direction. Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin B, butirosin, neomycin and ribostamycin. Works in combination with EC 1.1.3.43, paromamine 6-oxidase, to replace the 6′-hydroxy group of paromamine with an amino group. The enzyme from the bacterium Streptomyces kanamyceticus can also catalyse EC 2.6.1.94, 2′-deamino-2′-hydroxyneamine transaminase, which leads to production of kanamycin A [3]. The enzyme from the bacterium Streptomyces fradiae can also catalyse EC 2.6.1.95, leading to production of neomycin C [2].

Links to other databases:

References:

1.	Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem 8 (2007) 283–288. [DOI] [PMID: 17206729]
2.	Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6′-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642–651. [DOI] [PMID: 21689223]
3.	Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843–852. [DOI] [PMID: 21983602]

[EC 2.6.1.93 created 2012]

2.6.1.94

Accepted name:

2′-deamino-2′-hydroxyneamine transaminase

Reaction:

2′-deamino-2′-hydroxyneamine + 2-oxoglutarate = 2′-deamino-2′-hydroxy-6′-dehydroparomamine + L-glutamate

Other name(s):

kacL (gene name)

Systematic name:

2′-deamino-2′-hydroxyneamine:2-oxoglutarate aminotransferase

Comments:

The reaction occurs in vivo in the opposite direction. Involved in the biosynthetic pathway of kanamycin A and kanamycin D. The enzyme, characterized from the bacterium Streptomyces kanamyceticus, can also catalyse EC 2.6.1.93, neamine transaminase.

Links to other databases:

References:

1.	Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843–852. [DOI] [PMID: 21983602]

[EC 2.6.1.94 created 2012]

2.6.1.95

Accepted name:

neomycin C transaminase

Reaction:

neomycin C + 2-oxoglutarate = 6′′′-deamino-6′′′-oxoneomycin C + L-glutamate

Other name(s):

neoN (gene name)

Systematic name:

2-oxoglutarate:neomycin C aminotransferase

Comments:

The reaction occurs in vivo in the opposite direction. Involved in the biosynthetic pathway of aminoglycoside antibiotics of the neomycin family. Works in combination with EC 1.1.3.44, 6′′′-hydroxyneomycin C oxidase, to replace the 6′′′-hydroxy group of 6′′′-deamino-6′′′-hydroxyneomycin C with an amino group. The enzyme, characterized from the bacterium Streptomyces fradiae, can also catalyse EC 2.6.1.93, neamine transaminase.

Links to other databases:

References:

1.	Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem 8 (2007) 283–288. [DOI] [PMID: 17206729]
2.	Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6′-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642–651. [DOI] [PMID: 21689223]

[EC 2.6.1.95 created 2012]

2.6.1.96

Accepted name:

4-aminobutyrate—pyruvate transaminase

Reaction:

(1) 4-aminobutanoate + pyruvate = succinate semialdehyde + L-alanine
(2) 4-aminobutanoate + glyoxylate = succinate semialdehyde + glycine

Other name(s):

aminobutyrate aminotransferase (ambiguous); γ-aminobutyrate aminotransaminase (ambiguous); γ-aminobutyrate transaminase (ambiguous); γ-aminobutyric acid aminotransferase (ambiguous); γ-aminobutyric acid pyruvate transaminase; γ-aminobutyric acid transaminase (ambiguous); γ-aminobutyric transaminase (ambiguous); 4-aminobutyrate aminotransferase (ambiguous); 4-aminobutyric acid aminotransferase (ambiguous); aminobutyrate transaminase (ambiguous); GABA aminotransferase (ambiguous); GABA transaminase (ambiguous); GABA transferase (ambiguous); POP2 (gene name)

Systematic name:

4-aminobutanoate:pyruvate aminotransferase

Comments:

Requires pyridoxal 5′-phosphate. The enzyme is found in plants that do not have the 2-oxoglutarate dependent enzyme (cf. EC 2.6.1.19). The reaction with pyruvate is reversible while the reaction with glyoxylate only takes place in the forward direction.

Links to other databases:

References:

1.	Van Cauwenberghe, O.R. and Shelp, B.J. Biochemical characterization of partially purified gaba:pyruvate transaminase from Nicotiana tabacum. Phytochemistry 52 (1999) 575–581.
2.	Palanivelu, R., Brass, L., Edlund, A.F. and Preuss, D. Pollen tube growth and guidance is regulated by POP2, an Arabidopsis gene that controls GABA levels. Cell 114 (2003) 47–59. [DOI] [PMID: 12859897]
3.	Clark, S.M., Di Leo, R., Dhanoa, P.K., Van Cauwenberghe, O.R., Mullen, R.T. and Shelp, B.J. Biochemical characterization, mitochondrial localization, expression, and potential functions for an Arabidopsis γ-aminobutyrate transaminase that utilizes both pyruvate and glyoxylate. J. Exp. Bot. 60 (2009) 1743–1757. [DOI] [PMID: 19264755]
4.	Clark, S.M., Di Leo, R., Van Cauwenberghe, O.R., Mullen, R.T. and Shelp, B.J. Subcellular localization and expression of multiple tomato γ-aminobutyrate transaminases that utilize both pyruvate and glyoxylate. J. Exp. Bot. 60 (2009) 3255–3267. [DOI] [PMID: 19470656]

[EC 2.6.1.96 created 2012]

2.6.1.97

Accepted name:

archaeosine synthase

Reaction:

L-glutamine + 7-cyano-7-carbaguanine¹⁵ in tRNA + H₂O = L-glutamate + archaeine¹⁵ in tRNA

Glossary:

7-cyano-7-carbaguanine = preQ₀ = 7-cyano-7-deazaguanine
archaeine = 7-deaza-7-carbamidoylguanine = base G*
archaeosine = G* = 7-amidino-7-deazaguanosine

Other name(s):

ArcS; TgtA2; MJ1022 (gene name); glutamine:preQ₀-tRNA amidinotransferase (incorrect)

Systematic name:

L-glutamine:7-cyano-7-carbaguanine aminotransferase

Comments:

In Euryarchaeota the reaction is catalysed by ArcS [1,2]. In Crenarchaeota, which do not have an ArcS homologue, the reaction is catalysed either by a homologue of EC 6.3.4.20, 7-cyano-7-deazaguanine synthase that includes a glutaminase domain (cf. EC 3.5.1.2), or by a homologue of EC 1.7.1.13, preQ₁ synthase [2]. The enzyme from the Euryarchaeon Methanocaldococcus jannaschii can also use arginine and ammonium as amino donors.

Links to other databases:

References:

1.	Phillips, G., Chikwana, V.M., Maxwell, A., El-Yacoubi, B., Swairjo, M.A., Iwata-Reuyl, D. and de Crecy-Lagard, V. Discovery and characterization of an amidinotransferase involved in the modification of archaeal tRNA. J. Biol. Chem. 285 (2010) 12706–12713. [DOI] [PMID: 20129918]
2.	Phillips, G., Swairjo, M.A., Gaston, K.W., Bailly, M., Limbach, P.A., Iwata-Reuyl, D. and de Crecy-Lagard, V. Diversity of archaeosine synthesis in crenarchaeota. ACS Chem. Biol. 7 (2012) 300–305. [DOI] [PMID: 22032275]

[EC 2.6.1.97 created 2012]

2.6.1.98

Accepted name:

UDP-2-acetamido-2-deoxy-ribo-hexuluronate aminotransferase

Reaction:

UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucuronate + 2-oxoglutarate = UDP-2-acetamido-2-deoxy-α-D-ribo-hex-3-uluronate + L-glutamate

For diagram of UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronate biosynthesis, click here

Other name(s):

WbpE; WlbC

Systematic name:

UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucuronate:2-oxoglutarate aminotransferase

Comments:

A pyridoxal 5′-phosphate protein. This enzyme participates in the biosynthetic pathway for UDP-α-D-ManNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronic acid), an important precursor of B-band lipopolysaccharide. The enzymes from Pseudomonas aeruginosa serotype O5 and Thermus thermophilus form a complex with the previous enzyme in the pathway, EC 1.1.1.335 (UDP-N-acetyl-2-amino-2-deoxyglucuronate oxidase).

Links to other databases:

References:

1.	Westman, E.L., McNally, D.J., Charchoglyan, A., Brewer, D., Field, R.A. and Lam, J.S. Characterization of WbpB, WbpE, and WbpD and reconstitution of a pathway for the biosynthesis of UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronic acid in Pseudomonas aeruginosa. J. Biol. Chem. 284 (2009) 11854–11862. [DOI] [PMID: 19282284]
2.	Larkin, A. and Imperiali, B. Biosynthesis of UDP-GlcNAc(3NAc)A by WbpB, WbpE, and WbpD: enzymes in the Wbp pathway responsible for O-antigen assembly in Pseudomonas aeruginosa PAO1. Biochemistry 48 (2009) 5446–5455. [DOI] [PMID: 19348502]
3.	Larkin, A., Olivier, N.B. and Imperiali, B. Structural analysis of WbpE from Pseudomonas aeruginosa PAO1: a nucleotide sugar aminotransferase involved in O-antigen assembly. Biochemistry 49 (2010) 7227–7237. [DOI] [PMID: 20604544]

[EC 2.6.1.98 created 2012]

2.6.1.99

Accepted name:

L-tryptophan—pyruvate aminotransferase

Reaction:

L-tryptophan + pyruvate = indole-3-pyruvate + L-alanine

For diagram of indoleacetic acid biosynthesis, click here

Other name(s):

TAA1 (gene name); vt2 (gene name)

Systematic name:

L-tryptophan:pyruvate aminotransferase

Comments:

This plant enzyme, along with EC 1.14.13.168, indole-3-pyruvate monooxygenase, is responsible for the biosynthesis of the plant hormone indole-3-acetate from L-tryptophan.

Links to other databases:

References:

1.	Tao, Y., Ferrer, J.L., Ljung, K., Pojer, F., Hong, F., Long, J.A., Li, L., Moreno, J.E., Bowman, M.E., Ivans, L.J., Cheng, Y., Lim, J., Zhao, Y., Ballare, C.L., Sandberg, G., Noel, J.P. and Chory, J. Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell 133 (2008) 164–176. [DOI] [PMID: 18394996]
2.	Mashiguchi, K., Tanaka, K., Sakai, T., Sugawara, S., Kawaide, H., Natsume, M., Hanada, A., Yaeno, T., Shirasu, K., Yao, H., McSteen, P., Zhao, Y., Hayashi, K., Kamiya, Y. and Kasahara, H. The main auxin biosynthesis pathway in Arabidopsis. Proc. Natl. Acad. Sci. USA 108 (2011) 18512–18517. [DOI] [PMID: 22025724]
3.	Phillips, K.A., Skirpan, A.L., Liu, X., Christensen, A., Slewinski, T.L., Hudson, C., Barazesh, S., Cohen, J.D., Malcomber, S. and McSteen, P. vanishing tassel2 encodes a grass-specific tryptophan aminotransferase required for vegetative and reproductive development in maize. Plant Cell 23 (2011) 550–566. [DOI] [PMID: 21335375]
4.	Zhao, Y. Auxin biosynthesis: a simple two-step pathway converts tryptophan to indole-3-acetic acid in plants. Mol. Plant 5 (2012) 334–338. [DOI] [PMID: 22155950]

[EC 2.6.1.99 created 2012]

*EC

2.7.1.31

Accepted name:

glycerate 3-kinase

Reaction:

ATP + D-glycerate = ADP + 3-phospho-D-glycerate

Other name(s):

glycerate kinase (phosphorylating) (ambiguous); D-glycerate 3-kinase; D-glycerate kinase (ambiguous); glycerate-kinase (ambiguous); GK (ambiguous); D-glyceric acid kinase (ambiguous); ATP:(R)-glycerate 3-phosphotransferase

Systematic name:

ATP:D-glycerate 3-phosphotransferase

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9026-61-3

References:

1.	Doughty, C.C., Hayashi, J.A. and Guenther, H.L. Purification and properties of D-glycerate 3-kinase from Escherichia coli. J. Biol. Chem. 241 (1966) 568–572. [PMID: 5325263]
2.	Ichihara, A. and Greenberg, D.M. Studies on the purification and properties of D-glyceric acid kinase of liver. J. Biol. Chem. 225 (1957) 949–958. [PMID: 13416296]

[EC 2.7.1.31 created 1961, modified 2012]

2.7.1.177

Accepted name:

L-threonine kinase

Reaction:

ATP + L-threonine = ADP + O-phospho-L-threonine

For diagram of corrin biosynthesis (part 6), click here

Other name(s):

PduX

Systematic name:

ATP:L-threonine O³-phosphotransferase

Comments:

The enzyme is involved in the de novo synthesis of adenosylcobalamin. It is specific for ATP and free L-threonine. In the bacterium Salmonella enterica the activity with CTP, GTP, or UTP is 6, 11, and 3% of the activity with ATP.

Links to other databases:

References:

1.	Fan, C. and Bobik, T.A. The PduX enzyme of Salmonella enterica is an L-threonine kinase used for coenzyme B₁₂ synthesis. J. Biol. Chem. 283 (2008) 11322–11329. [DOI] [PMID: 18308727]
2.	Fan, C., Fromm, H.J. and Bobik, T.A. Kinetic and functional analysis of L-threonine kinase, the PduX enzyme of Salmonella enterica. J. Biol. Chem. 284 (2009) 20240–20248. [DOI] [PMID: 19509296]

[EC 2.7.1.177 created 2012]

2.7.4.26

Accepted name:

isopentenyl phosphate kinase

Reaction:

ATP + 3-methylbut-3-en-1-yl phosphate = ADP + 3-methylbut-3-en-1-yl diphosphate

For diagram of the archaeal mevalonate pathway, click here

Other name(s):

ATP:isopentenyl phosphate phosphotransferase

Systematic name:

ATP:3-methylbut-3-en-1-yl-phosphate phosphotransferase

Comments:

The enzyme is involved in the mevalonate pathway in Archaea [1]. The activity has also been identified in the plant Mentha piperita (peppermint) [2]. It is strictly specific for ATP but can use other phosphate acceptors such as prenyl phosphate, geranyl phosphate, or fosfomycin.

Links to other databases:

References:

1.	Grochowski, L.L., Xu, H. and White, R.H. Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate. J. Bacteriol. 188 (2006) 3192–3198. [DOI] [PMID: 16621811]
2.	Lange, B.M. and Croteau, R. Isopentenyl diphosphate biosynthesis via a mevalonate-independent pathway: isopentenyl monophosphate kinase catalyzes the terminal enzymatic step. Proc. Natl. Acad. Sci. USA 96 (1999) 13714–13719. [DOI] [PMID: 10570138]
3.	Chen, M. and Poulter, C.D. Characterization of thermophilic archaeal isopentenyl phosphate kinases. Biochemistry 49 (2010) 207–217. [DOI] [PMID: 19928876]
4.	Mabanglo, M.F., Schubert, H.L., Chen, M., Hill, C.P. and Poulter, C.D. X-ray structures of isopentenyl phosphate kinase. ACS Chem. Biol. 5 (2010) 517–527. [DOI] [PMID: 20402538]

[EC 2.7.4.26 created 2012]

2.7.4.27

Accepted name:

[pyruvate, phosphate dikinase]-phosphate phosphotransferase

Reaction:

[pyruvate, phosphate dikinase] phosphate + phosphate = [pyruvate, phosphate dikinase] + diphosphate

Other name(s):

PPDK regulatory protein (ambiguous); pyruvate, phosphate dikinase regulatory protein (ambiguous); bifunctional dikinase regulatory protein (ambiguous); PDRP1 (gene name)

Systematic name:

[pyruvate, phosphate dikinase]-phosphate:phosphate phosphotransferase

Comments:

The enzyme from the plants maize and Arabidopsis is bifunctional and also catalyses the phosphorylation of pyruvate, phosphate dikinase (EC 2.7.9.1), cf. EC 2.7.11.32, [pyruvate, phosphate dikinase] kinase [2-5].

Links to other databases:

References:

1.	Burnell, J.N. and Hatch, M.D. Regulation of C₄ photosynthesis: identification of a catalytically important histidine residue and its role in the regulation of pyruvate,P_i dikinase. Arch. Biochem. Biophys. 231 (1984) 175–182. [DOI] [PMID: 6326674]
2.	Burnell, J.N. and Hatch, M.D. Regulation of C₄ photosynthesis: purification and properties of the protein catalyzing ADP-mediated inactivation and P_i-mediated activation of pyruvate,P_i dikinase. Arch. Biochem. Biophys. 237 (1985) 490–503. [DOI] [PMID: 2983615]
3.	Chastain, C.J., Botschner, M., Harrington, G.E., Thompson, B.J., Mills, S.E., Sarath, G. and Chollet, R. Further analysis of maize C₄ pyruvate,orthophosphate dikinase phosphorylation by its bifunctional regulatory protein using selective substitutions of the regulatory Thr-456 and catalytic His-458 residues. Arch. Biochem. Biophys. 375 (2000) 165–170. [DOI] [PMID: 10683263]
4.	Burnell, J.N. and Chastain, C.J. Cloning and expression of maize-leaf pyruvate, P_i dikinase regulatory protein gene. Biochem. Biophys. Res. Commun. 345 (2006) 675–680. [DOI] [PMID: 16696949]
5.	Chastain, C.J., Xu, W., Parsley, K., Sarath, G., Hibberd, J.M. and Chollet, R. The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented Ser/Thr protein kinase primary structure. Plant J. 53 (2008) 854–863. [DOI] [PMID: 17996018]

[EC 2.7.4.27 created 2012]

2.7.4.28

Accepted name:

[pyruvate, water dikinase]-phosphate phosphotransferase

Reaction:

[pyruvate, water dikinase] phosphate + phosphate = [pyruvate, water dikinase] + diphosphate

Other name(s):

PSRP (ambiguous)

Systematic name:

[pyruvate, water dikinase]-phosphate:phosphate phosphotransferase

Comments:

Links to other databases:

References:

1.	Burnell, J.N. Cloning and characterization of Escherichia coli DUF299: a bifunctional ADP-dependent kinase—P_i-dependent pyrophosphorylase from bacteria. BMC Biochem. 11:1 (2010). [DOI] [PMID: 20044937]

[EC 2.7.4.28 created 2012]

*EC

2.7.7.23

Accepted name:

UDP-N-acetylglucosamine diphosphorylase

Reaction:

UTP + N-acetyl-α-D-glucosamine 1-phosphate = diphosphate + UDP-N-acetyl-α-D-glucosamine

For diagram of UDP-N-acetylglucosamine biosynthesis, click here

Other name(s):

UDP-N-acetylglucosamine pyrophosphorylase; uridine diphosphoacetylglucosamine pyrophosphorylase; UTP:2-acetamido-2-deoxy-α-D-glucose-1-phosphate uridylyltransferase; UDP-GlcNAc pyrophosphorylase; GlmU uridylyltransferase; Acetylglucosamine 1-phosphate uridylyltransferase; UDP-acetylglucosamine pyrophosphorylase; uridine diphosphate-N-acetylglucosamine pyrophosphorylase; uridine diphosphoacetylglucosamine phosphorylase; acetylglucosamine 1-phosphate uridylyltransferase

Systematic name:

UTP:N-acetyl-α-D-glucosamine-1-phosphate uridylyltransferase

Comments:

Part of the pathway for acetamido sugar biosynthesis in bacteria and archaea. The enzyme from several bacteria (e.g., Escherichia coli, Bacillus subtilis and Haemophilus influenzae) has been shown to be bifunctional and also to possess the activity of EC 2.3.1.157, glucosamine-1-phosphate N-acetyltransferase [3,4,6]. The enzyme from plants and animals is also active toward N-acetyl-α-D-galactosamine 1-phosphate (cf. EC 2.7.7.83, UDP-N-acetylgalactosamine diphosphorylase) [5,7], while the bacterial enzyme shows low activity toward that substrate [4].

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9023-06-7

References:

1.	Pattabiramin, T.N. and Bachhawat, B.K. Purification of uridine diphosphoacetylglucosamine pyrophosphorylase from sheep brain. Biochim. Biophys. Acta 50 (1961) 129–134. [DOI] [PMID: 13733356]
2.	Strominger, J.L. and Smith, M.S. Uridine diphosphoacetylglucosamine pyrophosphorylase. J. Biol. Chem. 234 (1959) 1822–1827. [PMID: 13672971]
3.	Mengin-Lecreulx, D. and van Heijenoort, J. Copurification of glucosamine-1-phosphate acetyltransferase and N-acetylglucosamine-1-phosphate uridyltransferase activities of Escherichia coli: characterization of the glmU gene product as a bifunctional enzyme catalyzing two subsequent steps in the pathway for UDP-N-acetylglucosamine synthesis. J. Bacteriol. 176 (1994) 5788–5795. [DOI] [PMID: 8083170]
4.	Gehring, A.M., Lees, W.J., Mindiola, D.J., Walsh, C.T. and Brown, E.D. Acetyltransfer precedes uridylyltransfer in the formation of UDP-N-acetylglucosamine in separable active sites of the bifunctional GlmU protein of Escherichia coli. Biochemistry 35 (1996) 579–585. [DOI] [PMID: 8555230]
5.	Wang-Gillam, A., Pastuszak, I. and Elbein, A.D. A 17-amino acid insert changes UDP-N-acetylhexosamine pyrophosphorylase specificity from UDP-GalNAc to UDP-GlcNAc. J. Biol. Chem. 273 (1998) 27055–27057. [DOI] [PMID: 9765219]
6.	Olsen, L.R. and Roderick, S.L. Structure of the Escherichia coli GlmU pyrophosphorylase and acetyltransferase active sites. Biochemistry 40 (2001) 1913–1921. [DOI] [PMID: 11329257]
7.	Peneff, C., Ferrari, P., Charrier, V., Taburet, Y., Monnier, C., Zamboni, V., Winter, J., Harnois, M., Fassy, F. and Bourne, Y. Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture. EMBO J. 20 (2001) 6191–6202. [DOI] [PMID: 11707391]

[EC 2.7.7.23 created 1965, modified 2012]

2.7.7.82

Accepted name:

CMP-N,N′-diacetyllegionaminic acid synthase

Reaction:

CTP + N,N′-diacetyllegionaminate = CMP-N,N′-diacetyllegionaminate + diphosphate

For diagram of legionaminic acid biosynthesis, click here

Glossary:

legionaminate = 5,7-diamino-3,5,7,9-tetradeoxy-D-glycero-D-galacto-non-2-ulosonate

Other name(s):

CMP-N,N′-diacetyllegionaminic acid synthetase; neuA (gene name); legF (gene name)

Systematic name:

CTP:N,N′-diacetyllegionaminate cytidylyltransferase

Comments:

Isolated from the bacteria Legionella pneumophila and Campylobacter jejuni. Involved in biosynthesis of legionaminic acid, a sialic acid-like derivative that is incorporated into virulence-associated cell surface glycoconjugates which may include lipopolysaccharide (LPS), capsular polysaccharide, pili and flagella.

Links to other databases:

References:

1.	Glaze, P.A., Watson, D.C., Young, N.M. and Tanner, M.E. Biosynthesis of CMP-N,N′-diacetyllegionaminic acid from UDP-N,N′-diacetylbacillosamine in Legionella pneumophila. Biochemistry 47 (2008) 3272–3282. [DOI] [PMID: 18275154]
2.	Schoenhofen, I.C., Vinogradov, E., Whitfield, D.M., Brisson, J.R. and Logan, S.M. The CMP-legionaminic acid pathway in Campylobacter: biosynthesis involving novel GDP-linked precursors. Glycobiology 19 (2009) 715–725. [DOI] [PMID: 19282391]

[EC 2.7.7.82 created 2012]

2.7.7.83

Accepted name:

UDP-N-acetylgalactosamine diphosphorylase

Reaction:

UTP + N-acetyl-α-D-galactosamine 1-phosphate = diphosphate + UDP-N-acetyl-α-D-galactosamine

Systematic name:

UTP:N-acetyl-α-D-galactosamine-1-phosphate uridylyltransferase

Comments:

The enzyme from plants and animals also has activity toward N-acetyl-α-D-glucosamine 1-phosphate (cf. EC 2.7.7.23, UDP-N-acetylglucosamine diphosphorylase) [1,2].

Links to other databases:

References:

1.	Wang-Gillam, A., Pastuszak, I. and Elbein, A.D. A 17-amino acid insert changes UDP-N-acetylhexosamine pyrophosphorylase specificity from UDP-GalNAc to UDP-GlcNAc. J. Biol. Chem. 273 (1998) 27055–27057. [DOI] [PMID: 9765219]
2.	Peneff, C., Ferrari, P., Charrier, V., Taburet, Y., Monnier, C., Zamboni, V., Winter, J., Harnois, M., Fassy, F. and Bourne, Y. Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture. EMBO J. 20 (2001) 6191–6202. [DOI] [PMID: 11707391]

[EC 2.7.7.83 created 2012]

2.7.8.35

Accepted name:

UDP-N-acetylglucosamine—decaprenyl-phosphate N-acetylglucosaminephosphotransferase

Reaction:

UDP-N-acetyl-α-D-glucosamine + trans,octacis-decaprenyl phosphate = UMP + N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol

For diagram of galactofuranan biosynthesis, click here

Other name(s):

GlcNAc-1-phosphate transferase; UDP-GlcNAc:undecaprenyl phosphate GlcNAc-1-phosphate transferase; WecA; WecA transferase

Systematic name:

UDP-N-acetyl-α-D-glucosamine:trans,octacis-decaprenyl-phosphate N-acetylglucosaminephosphotransferase

Comments:

Isolated from Mycobacterium tuberculosis and Mycobacterium smegmatis. This enzyme catalyses the synthesis of monotrans,octacis-decaprenyl-N-acetyl-α-D-glucosaminyl diphosphate (mycobacterial lipid I), an essential lipid intermediate for the biosynthesis of various bacterial cell envelope components. cf. EC 2.7.8.33, UDP-GlcNAc:undecaprenyl-phosphate GlcNAc-1-phosphate transferase.

Links to other databases:

References:

1.	Jin, Y., Xin, Y., Zhang, W. and Ma, Y. Mycobacterium tuberculosis Rv1302 and Mycobacterium smegmatis MSMEG_4947 have WecA function and MSMEG_4947 is required for the growth of M. smegmatis. FEMS Microbiol. Lett. 310 (2010) 54–61. [DOI] [PMID: 20637039]

[EC 2.7.8.35 created 2012]

2.7.8.36

Accepted name:

undecaprenyl phosphate N,N′-diacetylbacillosamine 1-phosphate transferase

Reaction:

UDP-N,N′-diacetylbacillosamine + tritrans,heptacis-undecaprenyl phosphate = UMP + N,N′-diacetyl-α-D-bacillosaminyl-diphospho-tritrans,heptacis-undecaprenol

For diagram of undecaprenyldiphosphoheptasaccharide biosynthesis, click here

Glossary:

UDP-N,N′-diacetylbacillosamine = UDP-2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose

Other name(s):

PglC

Systematic name:

UDP-N,N′-diacetylbacillosamine:tritrans,heptacis-undecaprenyl-phosphate N,N′-diacetylbacillosamine transferase

Comments:

Isolated from Campylobacter jejuni. Part of a bacterial N-linked glycosylation pathway.

Links to other databases:

References:

Glover, K.J., Weerapana, E., Chen, M.M. and Imperiali, B. Direct biochemical evidence for the utilization of UDP-bacillosamine by PglC, an essential glycosyl-1-phosphate transferase in the Campylobacter jejuni N-linked glycosylation pathway. Biochemistry 45 (2006) 5343–5350. [DOI] [PMID: 16618123]

[EC 2.7.8.36 created 2012]

2.7.8.37

Accepted name:

α-D-ribose 1-methylphosphonate 5-triphosphate synthase

Reaction:

ATP + methylphosphonate = α-D-ribose 1-methylphosphonate 5-triphosphate + adenine

For diagram of phosphonate metabolism, click here

Systematic name:

ATP:methylphosphonate 5-triphosphoribosyltransferase

Comments:

Isolated from the bacterium Escherichia coli.

Links to other databases:

References:

1.	Kamat, S.S., Williams, H.J. and Raushel, F.M. Intermediates in the transformation of phosphonates to phosphate by bacteria. Nature 480 (2011) 570–573. [DOI] [PMID: 22089136]

[EC 2.7.8.37 created 2012]

2.7.11.32

Accepted name:

[pyruvate, phosphate dikinase] kinase

Reaction:

ADP + [pyruvate, phosphate dikinase] = AMP + [pyruvate, phosphate dikinase] phosphate

Other name(s):

PPDK regulatory protein (ambiguous); pyruvate; phosphate dikinase regulatory protein (ambiguous); bifunctional dikinase regulatory protein (ambiguous)

Systematic name:

ADP:[pyruvate, phosphate dikinase] phosphotransferase

Comments:

The enzymes from the plants Zea mays (maize) and Arabidopsis thaliana are bifunctional and catalyse both the phosphorylation and dephosphorylation of EC 2.7.9.1 (pyruvate, phosphate dikinase). cf. EC 2.7.4.27, [pyruvate, phosphate dikinase]-phosphate phosphotransferase [2-5]. The enzyme is specific for a reaction intermediate form of EC 2.7.9.1, and phosphorylates a threonine located adjacent to the catalytic histidine. The phosphorylation only takes place if the histidine is already phosphorylated [3-5].

Links to other databases:

References:

1.	Burnell, J.N. and Hatch, M.D. Regulation of C₄ photosynthesis: identification of a catalytically important histidine residue and its role in the regulation of pyruvate,P_i dikinase. Arch. Biochem. Biophys. 231 (1984) 175–182. [DOI] [PMID: 6326674]
2.	Burnell, J.N. and Hatch, M.D. Regulation of C₄ photosynthesis: purification and properties of the protein catalyzing ADP-mediated inactivation and P_i-mediated activation of pyruvate,P_i dikinase. Arch. Biochem. Biophys. 237 (1985) 490–503. [DOI] [PMID: 2983615]
3.	Chastain, C.J., Botschner, M., Harrington, G.E., Thompson, B.J., Mills, S.E., Sarath, G. and Chollet, R. Further analysis of maize C₄ pyruvate,orthophosphate dikinase phosphorylation by its bifunctional regulatory protein using selective substitutions of the regulatory Thr-456 and catalytic His-458 residues. Arch. Biochem. Biophys. 375 (2000) 165–170. [DOI] [PMID: 10683263]
4.	Burnell, J.N. and Chastain, C.J. Cloning and expression of maize-leaf pyruvate, P_i dikinase regulatory protein gene. Biochem. Biophys. Res. Commun. 345 (2006) 675–680. [DOI] [PMID: 16696949]
5.	Chastain, C.J., Xu, W., Parsley, K., Sarath, G., Hibberd, J.M. and Chollet, R. The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented Ser/Thr protein kinase primary structure. Plant J. 53 (2008) 854–863. [DOI] [PMID: 17996018]

[EC 2.7.11.32 created 2012]

2.7.11.33

Accepted name:

[pyruvate, water dikinase] kinase

Reaction:

ADP + [pyruvate, water dikinase] = AMP + [pyruvate, water dikinase] phosphate

Other name(s):

PSRP (ambiguous); PEPS kinase

Systematic name:

ADP:[pyruvate, water dikinase] phosphotransferase

Comments:

The enzyme from the bacterium Escherichia coli is bifunctional and catalyses both the phosphorylation and dephosphorylation of EC 2.7.9.2, pyruvate, water dikinase. cf. EC 2.7.4.28, ([pyruvate, water dikinase] phosphate) phosphotransferase [1]. The enzyme is specific for a reaction intermediate form of EC 2.7.9.2, where it phosphorylates an active site histidine [1]. It has no activity toward EC 2.7.9.1 pyruvate, phosphate dikinase (cf. EC 2.7.11.32, [pyruvate, phosphate dikinase] kinase).

Links to other databases:

References:

1.	Burnell, J.N. Cloning and characterization of Escherichia coli DUF299: a bifunctional ADP-dependent kinase—P_i-dependent pyrophosphorylase from bacteria. BMC Biochem. 11:1 (2010). [DOI] [PMID: 20044937]

[EC 2.7.11.33 created 2012]

3.1.1.91

Accepted name:

2-oxo-3-(5-oxofuran-2-ylidene)propanoate lactonase

Reaction:

2-oxo-3-(5-oxofuran-2-ylidene)propanoate + H₂O = maleylpyruvate

Other name(s):

naaC (gene name)

Systematic name:

2-oxo-3-(5-oxofuran-2-ylidene)propanoate lactonohydrolase

Comments:

This enzyme, characterized from the soil bacterium Bradyrhizobium sp. JS329, is involved in the pathway of 5-nitroanthranilate degradation.

Links to other databases:

References:

1.	Qu, Y. and Spain, J.C. Molecular and biochemical characterization of the 5-nitroanthranilic acid degradation pathway in Bradyrhizobium sp. strain JS329. J. Bacteriol. 193 (2011) 3057–3063. [DOI] [PMID: 21498645]

[EC 3.1.1.91 created 2012]

3.1.1.92

Accepted name:

4-sulfomuconolactone hydrolase

Reaction:

4-sulfomuconolactone + H₂O = maleylacetate + sulfite

Glossary:

4-sulfomuconolactone = 4-carboxymethylen-4-sulfobut-2-en-olide = 2-(5-oxo-2-sulfo-2,5-dihydrofuran-2-yl)acetic acid
maleylacetate = (2Z)-4-oxohex-2-enedioate

Systematic name:

4-sulfomuconolactone sulfohydrolase

Comments:

The enzyme was isolated from the bacteria Hydrogenophaga intermedia and Agrobacterium radiobacter S2. It catalyses a step in the degradation of 4-sulfocatechol.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, KEGG

References:

1.	Halak, S., Basta, T., Burger, S., Contzen, M., Wray, V., Pieper, D.H. and Stolz, A. 4-sulfomuconolactone hydrolases from Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2. J. Bacteriol. 189 (2007) 6998–7006. [DOI] [PMID: 17660282]

[EC 3.1.1.92 created 2012]

3.1.1.93

Accepted name:

mycophenolic acid acyl-glucuronide esterase

Reaction:

mycophenolic acid O-acyl-glucuronide + H₂O = mycophenolate + D-glucuronate

Glossary:

mycophenolate = (4E)-6-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)-4-methylhex-4-enoate
mycophenolic acid O-acyl-glucuronide = 1-O-[(4E)-6-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)-4-methylhex-4-enoyl]-β-D-glucopyranuronic acid

Other name(s):

mycophenolic acid acyl-glucuronide deglucuronidase; AcMPAG deglucuronidase

Systematic name:

mycophenolic acid O-acyl-glucuronide-ester hydrolase

Comments:

This liver enzyme deglucuronidates mycophenolic acid O-acyl-glucuronide, a metabolite of the immunosuppressant drug mycophenolate that is thought to be immunotoxic.

Links to other databases:

References:

1.	Iwamura, A., Fukami, T., Higuchi, R., Nakajima, M. and Yokoi, T. Human α/β hydrolase domain containing 10 (ABHD10) is responsible enzyme for deglucuronidation of mycophenolic acid acyl-glucuronide in liver. J. Biol. Chem. 287 (2012) 9240–9249. [DOI] [PMID: 22294686]

[EC 3.1.1.93 created 2012]

3.1.3.88

Accepted name:

5′′-phosphoribostamycin phosphatase

Reaction:

5′′-phosphoribostamycin + H₂O = ribostamycin + phosphate

For diagram of neamine and ribostamycin biosynthesis, click here

Other name(s):

btrP (gene name); neoI (gene name)

Systematic name:

5′′-phosphoribostamycin phosphohydrolase

Comments:

Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including ribostamycin, neomycin and butirosin. No metal is required for activity.

Links to other databases:

References:

1.	Kudo, F., Fujii, T., Kinoshita, S. and Eguchi, T. Unique O-ribosylation in the biosynthesis of butirosin. Bioorg. Med. Chem. 15 (2007) 4360–4368. [DOI] [PMID: 17482823]

[EC 3.1.3.88 created 2012]

*EC

3.2.1.89

Accepted name:

arabinogalactan endo-β-1,4-galactanase

Reaction:

The enzyme specifically hydrolyses (1→4)-β-D-galactosidic linkages in type I arabinogalactans.

Other name(s):

endo-1,4-β-galactanase; galactanase (ambiguous); arabinogalactanase; ganB (gene name)

Systematic name:

arabinogalactan 4-β-D-galactanohydrolase

Comments:

This enzyme, isolated from the bacterium Bacillus subtilis, hydrolyses the β(1→4) bonds found in type I plant arabinogalactans, which are a component of the primary cell walls of dicots. The predominant product is a tetrasaccharide. cf. EC 3.2.1.181, galactan endo-β-1,3-galactanase.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 58182-40-4

References:

1.	Emi, S. and Yamamoto, T. Purification and properties of several galactanases of Bacillus subtilis var. amylosacchariticus. Agric. Biol. Chem. 36 (1972) 1945–1954.
2.	Labavitch, J.M., Freeman, L.E. and Albersheim, P. Structure of plant cell walls. Purification and characterization of a β-1,4-galactanase which degrades a structural component of the primary cell walls of dicots. J. Biol. Chem. 251 (1976) 5904–5910. [PMID: 823153]
3.	Shipkowski, S. and Brenchley, J.E. Bioinformatic, genetic, and biochemical evidence that some glycoside hydrolase family 42 β-galactosidases are arabinogalactan type I oligomer hydrolases. Appl. Environ. Microbiol. 72 (2006) 7730–7738. [DOI] [PMID: 17056685]

[EC 3.2.1.89 created 1976, modified 2012]

3.2.1.181

Accepted name:

galactan endo-β-1,3-galactanase

Reaction:

The enzyme specifically hydrolyses β-1,3-galactan and β-1,3-galactooligosaccharides

Other name(s):

endo-β-1,3-galactanase

Systematic name:

arabinogalactan 3-β-D-galactanohydrolase

Comments:

The enzyme from the fungus Flammulina velutipes (winter mushroom) hydrolyses the β(1→3) bonds found in type II plant arabinogalactans, which occur in cell walls of dicots and cereals. The enzyme is an endohydrolase, and requires at least 3 contiguous β-1,3-residues. cf. EC 3.2.1.89, arabinogalactan endo-β-1,4-galactanase and EC 3.2.1.145, galactan 1,3-β-galactosidase.

Links to other databases:

References:

1.	Kotake, T., Hirata, N., Degi, Y., Ishiguro, M., Kitazawa, K., Takata, R., Ichinose, H., Kaneko, S., Igarashi, K., Samejima, M. and Tsumuraya, Y. Endo-β-1,3-galactanase from winter mushroom Flammulina velutipes. J. Biol. Chem. 286 (2011) 27848–27854. [DOI] [PMID: 21653698]

[EC 3.2.1.181 created 2012]

3.2.1.182

Accepted name:

4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside β-D-glucosidase

Reaction:

(1) (2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside + H₂O = 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one + D-glucose
(2) (2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside + H₂O = 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one + D-glucose

Glossary:

DIMBOA glucoside = (2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside
DIBOA glucoside = (2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside

Other name(s):

DIMBOAGlc hydrolase; DIMBOA glucosidase

Systematic name:

(2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside β-D-glucosidase

Comments:

The enzyme from Triticum aestivum (wheat) has a higher affinity for DIMBOA glucoside than DIBOA glucoside. With Secale cereale (rye) the preference is reversed.

Links to other databases:

References:

1.	Sue, M., Ishihara, A. and Iwamura, H. Purification and characterization of a hydroxamic acid glucoside β-glucosidase from wheat (Triticum aestivum L.) seedlings. Planta 210 (2000) 432–438. [PMID: 10750901]
2.	Sue, M., Ishihara, A. and Iwamura, H. Purification and characterization of a β-glucosidase from rye (Secale cereale L.) seedlings. Plant Sci. 155 (2000) 67–74. [DOI] [PMID: 10773341]
3.	Czjzek, M., Cicek, M., Zamboni, V., Bevan, D.R., Henrissat, B. and Esen, A. The mechanism of substrate (aglycone) specificity in β-glucosidases is revealed by crystal structures of mutant maize β-glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes. Proc. Natl. Acad. Sci. USA 97 (2000) 13555–13560. [DOI] [PMID: 11106394]
4.	Nikus, J., Esen, A. and Jonsson, L.M.V. Cloning of a plastidic rye (Secale cereale) β-glucosidase cDNA and its expression in Escherichia coli. Physiol. Plantarum 118 (2003) 337–348.
5.	Sue, M., Yamazaki, K., Yajima, S., Nomura, T., Matsukawa, T., Iwamura, H. and Miyamoto, T. Molecular and structural characterization of hexameric β-D-glucosidases in wheat and rye. Plant Physiol. 141 (2006) 1237–1247. [DOI] [PMID: 16751439]
6.	Sue, M., Nakamura, C., Miyamoto, T. and Yajima, S. Active-site architecture of benzoxazinone-glucoside β-D-glucosidases in Triticeae. Plant Sci. 180 (2011) 268–275. [DOI] [PMID: 21421370]

[EC 3.2.1.182 created 2012]

3.2.1.183

Accepted name:

UDP-N-acetylglucosamine 2-epimerase (hydrolysing)

Reaction:

UDP-N-acetyl-α-D-glucosamine + H₂O = N-acetyl-D-mannosamine + UDP

For diagram of N-acetylneuraminic acid biosynthesis, click here, and for mechanism, click here

Other name(s):

UDP-N-acetylglucosamine 2-epimerase (ambiguous); GNE (gene name); siaA (gene name); neuC (gene name)

Systematic name:

UDP-N-acetyl-α-D-glucosamine hydrolase (2-epimerising)

Comments:

The enzyme is found in mammalian liver, as well as in some pathogenic bacteria including Neisseria meningitidis and Staphylococcus aureus. It catalyses the first step of sialic acid (N-acetylneuraminic acid) biosynthesis. The initial product formed is the α anomer, which rapidly mutarotates to a mixture of anomers [2]. The mammalian enzyme is bifunctional and also catalyses EC 2.7.1.60, N-acetylmannosamine kinase. cf. EC 5.1.3.14, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing).

Links to other databases:

References:

1.	Stasche, R., Hinderlich, S., Weise, C., Effertz, K., Lucka, L., Moormann, P. and Reutter, W. A bifunctional enzyme catalyzes the first two steps in N-acetylneuraminic acid biosynthesis of rat liver. Molecular cloning and functional expression of UDP-N-acetyl-glucosamine 2-epimerase/N-acetylmannosamine kinase. J. Biol. Chem. 272 (1997) 24319–24324. [DOI] [PMID: 9305888]
2.	Chou, W.K., Hinderlich, S., Reutter, W. and Tanner, M.E. Sialic acid biosynthesis: stereochemistry and mechanism of the reaction catalyzed by the mammalian UDP-N-acetylglucosamine 2-epimerase. J. Am. Chem. Soc. 125 (2003) 2455–2461. [DOI] [PMID: 12603133]
3.	Blume, A., Ghaderi, D., Liebich, V., Hinderlich, S., Donner, P., Reutter, W. and Lucka, L. UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase, functionally expressed in and purified from Escherichia coli, yeast, and insect cells. Protein Expr. Purif. 35 (2004) 387–396. [DOI] [PMID: 15135418]
4.	Murkin, A.S., Chou, W.K., Wakarchuk, W.W. and Tanner, M.E. Identification and mechanism of a bacterial hydrolyzing UDP-N-acetylglucosamine 2-epimerase. Biochemistry 43 (2004) 14290–14298. [DOI] [PMID: 15518580]

[EC 3.2.1.183 created 2012]

3.2.1.184

Accepted name:

UDP-N,N′-diacetylbacillosamine 2-epimerase (hydrolysing)

Reaction:

UDP-N,N′-diacetylbacillosamine + H₂O = UDP + 2,4-diacetamido-2,4,6-trideoxy-D-mannopyranose

For diagram of legionaminic acid biosynthesis, click here, and for mechanism, click here

Glossary:

UDP-N,N′-diacetylbacillosamine = UDP-2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose

Other name(s):

UDP-Bac2Ac₄Ac 2-epimerase; NeuC

Systematic name:

UDP-N,N′-diacetylbacillosamine hydrolase (2-epimerising)

Comments:

Requires Mg²⁺. Involved in biosynthesis of legionaminic acid, a nonulosonate derivative that is incorporated by some bacteria into assorted virulence-associated cell surface glycoconjugates. The initial product formed by the enzyme from Legionella pneumophila, which incorporates legionaminic acid into the O-antigen moiety of its lipopolysaccharide, is 2,4-diacetamido-2,4,6-trideoxy-α-D-mannopyranose, which rapidly mutarotates to a mixture of anomers [1]. The enzyme from Campylobacter jejuni, which incorporates legionaminic acid into flagellin, prefers GDP-N,N′-diacetylbacillosamine [2].

Links to other databases:

References:

1.	Glaze, P.A., Watson, D.C., Young, N.M. and Tanner, M.E. Biosynthesis of CMP-N,N′-diacetyllegionaminic acid from UDP-N,N′-diacetylbacillosamine in Legionella pneumophila. Biochemistry 47 (2008) 3272–3282. [DOI] [PMID: 18275154]
2.	Schoenhofen, I.C., Vinogradov, E., Whitfield, D.M., Brisson, J.R. and Logan, S.M. The CMP-legionaminic acid pathway in Campylobacter: biosynthesis involving novel GDP-linked precursors. Glycobiology 19 (2009) 715–725. [DOI] [PMID: 19282391]

[EC 3.2.1.184 created 2012]

3.5.1.111

Accepted name:

2-oxoglutaramate amidase

Reaction:

2-oxoglutaramate + H₂O = 2-oxoglutarate + NH₃

Glossary:

2-oxoglutaramate = 2-ketoglutaramate = 5-amino-2,5-dioxopentanoate

Other name(s):

ω-amidase (ambiguous)

Systematic name:

5-amino-2,5-dioxopentanoate amidohydrolase

Comments:

The enzyme, which is highly specific for its substrate, participates in the nicotine degradation pathway of several Gram-positive bacteria.

Links to other databases:

References:

1.	Cobzaru, C., Ganas, P., Mihasan, M., Schleberger, P. and Brandsch, R. Homologous gene clusters of nicotine catabolism, including a new ω-amidase for α-ketoglutaramate, in species of three genera of Gram-positive bacteria. Res. Microbiol. 162 (2011) 285–291. [DOI] [PMID: 21288482]

[EC 3.5.1.111 created 2012]

3.5.1.112

Accepted name:

2′-N-acetylparomamine deacetylase

Reaction:

2′-N-acetylparomamine + H₂O = paromamine + acetate

For diagram of paromamine biosynthesis, click here

Glossary:

paromamine = (1R)-O⁴-(2-amino-2-deoxy-α-D-glucopyranosyl)-2-deoxy-streptamine

Other name(s):

btrD (gene name); neoL (gene name); kanN (gene name)

Systematic name:

2′-N-acetylparomamine hydrolase (acetate-forming)

Comments:

Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin, butirosin, neomycin and ribostamycin. The enzyme from the bacterium Streptomyces fradiae can also accept 2′′′-acetyl-6′′′-hydroxyneomycin C as substrate, cf. EC 3.5.1.113, 2′′′-acetyl-6′′′-hydroxyneomycin C deacetylase [2].

Links to other databases:

References:

1.	Truman, A.W., Huang, F., Llewellyn, N.M. and Spencer, J.B. Characterization of the enzyme BtrD from Bacillus circulans and revision of its functional assignment in the biosynthesis of butirosin. Angew. Chem. Int. Ed. Engl. 46 (2007) 1462–1464. [DOI] [PMID: 17226887]
2.	Yokoyama, K., Yamamoto, Y., Kudo, F. and Eguchi, T. Involvement of two distinct N-acetylglucosaminyltransferases and a dual-function deacetylase in neomycin biosynthesis. ChemBioChem 9 (2008) 865–869. [DOI] [PMID: 18311744]

[EC 3.5.1.112 created 2012]

3.5.1.113

Accepted name:

2′′′-acetyl-6′′′-hydroxyneomycin C deacetylase

Reaction:

2′′′-acetyl-6′′′-deamino-6′′′-hydroxyneomycin C + H₂O = 6′′′-deamino-6′′′-hydroxyneomycin C + acetate

Other name(s):

neoL (gene name)

Systematic name:

2′′′-acetyl-6′′′-hydroxyneomycin C hydrolase (acetate-forming)

Comments:

Involved in the biosynthetic pathway of aminoglycoside antibiotics of the neomycin family. The enzyme from the bacterium Streptomyces fradiae also catalyses EC 3.5.1.112, 2′-N-acetylparomamine deacetylase.

Links to other databases:

References:

1.	Yokoyama, K., Yamamoto, Y., Kudo, F. and Eguchi, T. Involvement of two distinct N-acetylglucosaminyltransferases and a dual-function deacetylase in neomycin biosynthesis. ChemBioChem 9 (2008) 865–869. [DOI] [PMID: 18311744]

[EC 3.5.1.113 created 2012]

*EC

3.5.99.5

Accepted name:

2-aminomuconate deaminase

Reaction:

2-aminomuconate + H₂O = (3E)-2-oxohex-3-enedioate + NH₃

Other name(s):

amnD (gene name); nbaF (gene name)

Systematic name:

2-aminomuconate aminohydrolase

Comments:

2-Aminomuconate is an intermediate in the bacterial biodegradation of nitrobenzene. The enzyme has been isolated from several species, including Pseudomonas pseudocaligenes JS45, Pseudomonas fluorescens KU-7, Pseudomonas sp. AP3 and Burkholderia cenocepacia J2315. The reaction is spontaneous in acid conditions.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 201098-29-5

References:

1.	He, Z and Spain, J.C. Studies of the catabolic pathway of degradation of nitrobenzene by Pseudomonas pseudoalcaligenes JS45: removal of the amino group from 2-aminomuconic semialdehyde. Appl. Environ. Microbiol. 63 (1997) 4839–4843. [PMID: 9471964]
2.	He, Z. and Spain, J.C. A novel 2-aminomuconate deaminase in the nitrobenzene degradation pathway of Pseudomonas pseudoalcaligenes JS45. J. Bacteriol. 180 (1998) 2502–2506. [PMID: 9573204]
3.	Takenaka, S., Murakami, S., Kim, Y.J. and Aoki, K. Complete nucleotide sequence and functional analysis of the genes for 2-aminophenol metabolism from Pseudomonas sp. AP-3. Arch. Microbiol. 174 (2000) 265–272. [PMID: 11081795]
4.	Muraki, T., Taki, M., Hasegawa, Y., Iwaki, H. and Lau, P.C. Prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of Pseudomonas fluorescens strain KU-7. Appl. Environ. Microbiol. 69 (2003) 1564–1572. [DOI] [PMID: 12620844]

[EC 3.5.99.5 created 2000, modified 2012]

3.5.99.9

Accepted name:

2-nitroimidazole nitrohydrolase

Reaction:

2-nitroimidazole + H₂O = imidazol-2-one + nitrite

Other name(s):

NnhA; 2NI nitrohydrolase; 2NI denitrase

Systematic name:

2-nitroimidazole nitrohydrolase

Comments:

The enzyme catalyses the initial step in the biodegradation of 2-nitroimidazole by the soil bacterium Mycobacterium sp. JS330

Links to other databases:

References:

1.	Qu, Y. and Spain, J.C. Catabolic pathway for 2-nitroimidazole involves a novel nitrohydrolase that also confers drug resistance. Environ. Microbiol. 13 (2011) 1010–1017. [DOI] [PMID: 21244596]

[EC 3.5.99.9 created 2012]

*EC

3.6.1.27

Accepted name:

undecaprenyl-diphosphate phosphatase

Reaction:

ditrans,octacis-undecaprenyl diphosphate + H₂O = ditrans,octacis-undecaprenyl phosphate + phosphate

For diagram of peptidoglycan biosynthesis (part 3), click here and for diagram of xanthan biosynthesis, click here

Other name(s):

C₅₅-isoprenyl diphosphatase; C₅₅-isoprenyl pyrophosphatase; isoprenyl pyrophosphatase (ambiguous); undecaprenyl pyrophosphate phosphatase; undecaprenyl pyrophosphate pyrophosphatase; UPP phosphatase; Und-PP pyrophosphatase; UppP (ambiguous); BacA; undecaprenyl-diphosphate phosphohydrolase; undecaprenyl-diphosphatase

Systematic name:

ditrans,octacis-undecaprenyl-diphosphate phosphohydrolase

Comments:

Isolated from the bacteria Micrococcus lysodeikticus [1], Escherichia coli [2,3,5,6] and Bacillus subtilis [4]. The product of the reaction, ditrans,octacis-undecaprenyl phosphate, is essential for cell wall polysaccharide biosynthesis in these strains.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9077-80-9

References:

1.	Goldman, R. and Strominger, J.L. Purification and properties of C₅₅-isoprenylpyrophosphate phosphatase from Micrococcus lysodeikticus. J. Biol. Chem. 247 (1972) 5116–5122. [PMID: 4341539]
2.	El Ghachi, M., Bouhss, A., Blanot, D. and Mengin-Lecreulx, D. The bacA gene of Escherichia coli encodes an undecaprenyl pyrophosphate phosphatase activity. J. Biol. Chem. 279 (2004) 30106–30113. [DOI] [PMID: 15138271]
3.	El Ghachi, M., Derbise, A., Bouhss, A. and Mengin-Lecreulx, D. Identification of multiple genes encoding membrane proteins with undecaprenyl pyrophosphate phosphatase (UppP) activity in Escherichia coli. J. Biol. Chem. 280 (2005) 18689–18695. [DOI] [PMID: 15778224]
4.	Bernard, R., El Ghachi, M., Mengin-Lecreulx, D., Chippaux, M. and Denizot, F. BcrC from Bacillus subtilis acts as an undecaprenyl pyrophosphate phosphatase in bacitracin resistance. J. Biol. Chem. 280 (2005) 28852–28857. [DOI] [PMID: 15946938]
5.	Tatar, L.D., Marolda, C.L., Polischuk, A.N., van Leeuwen, D. and Valvano, M.A. An Escherichia coli undecaprenyl-pyrophosphate phosphatase implicated in undecaprenyl phosphate recycling. Microbiology 153 (2007) 2518–2529. [DOI] [PMID: 17660416]
6.	Touze, T., Blanot, D. and Mengin-Lecreulx, D. Substrate specificity and membrane topology of Escherichia coli PgpB, an undecaprenyl pyrophosphate phosphatase. J. Biol. Chem. 283 (2008) 16573–16583. [DOI] [PMID: 18411271]

[EC 3.6.1.27 created 1978, modified 2002, modified 2012]

3.6.1.63

Accepted name:

α-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase

Reaction:

α-D-ribose 1-methylphosphonate 5-triphosphate + H₂O = α-D-ribose 1-methylphosphonate 5-phosphate + diphosphate

For diagram of phosphonate metabolism, click here

Other name(s):

phnM (gene name)

Systematic name:

α-D-ribose-1-methylphosphonate-5-triphosphate diphosphohydrolase

Comments:

Isolated from the bacterium Escherichia coli.

Links to other databases:

References:

1.	Kamat, S.S., Williams, H.J. and Raushel, F.M. Intermediates in the transformation of phosphonates to phosphate by bacteria. Nature 480 (2011) 570–573. [DOI] [PMID: 22089136]

[EC 3.6.1.63 created 2012]

*EC

3.7.1.14

Accepted name:

2-hydroxy-6-oxonona-2,4-dienedioate hydrolase

Reaction:

(1) (2Z,4E)-2-hydroxy-6-oxonona-2,4-diene-1,9-dioate + H₂O = (2Z)-2-hydroxypenta-2,4-dienoate + succinate
(2) (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioate + H₂O = (2Z)-2-hydroxypenta-2,4-dienoate + fumarate

For diagram of 3-phenylpropanoate catabolism, click here and for diagram of cinnamate catabolism, click here

Other name(s):

mhpC (gene name)

Systematic name:

(2Z,4E)-2-hydroxy-6-oxona-2,4-dienedioate succinylhydrolase

Comments:

This enzyme catalyses a step in a pathway of phenylpropanoid compounds degradation. The first step of the enzyme mechanism involves a reversible keto-enol tautomerization [4].

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB

References:

1.	Burlingame, R. and Chapman, P.J. Catabolism of phenylpropionic acid and its 3-hydroxy derivative by Escherichia coli. J. Bacteriol. 155 (1983) 113–121. [PMID: 6345502]
2.	Burlingame, R.P., Wyman, L. and Chapman, P.J. Isolation and characterization of Escherichia coli mutants defective for phenylpropionate degradation. J. Bacteriol. 168 (1986) 55–64. [DOI] [PMID: 3531186]
3.	Lam, W. W. Y and Bugg, T. D. H. Chemistry of extradiol aromatic ring cleavage: isolation of a stable dienol ring fission intermediate and stereochemistry of its enzymatic hydrolytic clevage. J. Chem. Soc., Chem. Commun. 10 (1994) 1163–1164.
4.	Lam, W.W. and Bugg, T.D. Purification, characterization, and stereochemical analysis of a C-C hydrolase: 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase. Biochemistry 36 (1997) 12242–12251. [DOI] [PMID: 9315862]
5.	Ferrández, A., García, J.L. and Díaz, E. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12. J. Bacteriol. 179 (1997) 2573–2581. [DOI] [PMID: 9098055]
6.	Díaz, E., Ferrández, A. and García, J.L. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180 (1998) 2915–2923. [PMID: 9603882]

[EC 3.7.1.14 created 2011, modified 2012]

3.7.1.19

Accepted name:

2,6-dihydroxypseudooxynicotine hydrolase

Reaction:

1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one + H₂O = 2,6-dihydroxypyridine + 4-methylaminobutanoate

For diagram of nicotine catabolism by arthrobacter, click here

Glossary:

1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one = 2,6-dihydroxypseudooxynicotine

Systematic name:

1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one hydrolase

Comments:

The enzyme, characterized from the soil bacterium Arthrobacter nicotinovorans, participates in nicotine degradation.

Links to other databases:

References:

1.	Gherna, R.L., Richardson, S.H. and Rittenberg, S.C. The bacterial oxidation of nicotine. VI. The metabolism of 2,6-dihydroxypseudooxynicotine. J. Biol. Chem. 240 (1965) 3669–3674. [PMID: 5835946]
2.	Sachelaru, P., Schiltz, E., Igloi, G.L. and Brandsch, R. An α/β-fold C—C bond hydrolase is involved in a central step of nicotine catabolism by Arthrobacter nicotinovorans. J. Bacteriol. 187 (2005) 8516–8519. [DOI] [PMID: 16321959]

[EC 3.7.1.19 created 2012]

3.7.1.20

Accepted name:

3-fumarylpyruvate hydrolase

Reaction:

3-fumarylpyruvate + H₂O = fumarate + pyruvate

Other name(s):

nagK (gene name); naaD (gene name)

Systematic name:

3-fumarylpyruvate hydrolase

Comments:

The enzyme is involved in bacterial degradation of 5-substituted salicylates, including gentisate (5-hydroxysalicylate), 5-nitrosalicylate and 5-halosalicylates.

Links to other databases:

References:

1.	Zhou, N.Y., Fuenmayor, S.L. and Williams, P.A. nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism. J. Bacteriol. 183 (2001) 700–708. [DOI] [PMID: 11133965]
2.	Qu, Y. and Spain, J.C. Molecular and biochemical characterization of the 5-nitroanthranilic acid degradation pathway in Bradyrhizobium sp. strain JS329. J. Bacteriol. 193 (2011) 3057–3063. [DOI] [PMID: 21498645]

[EC 3.7.1.20 created 2012]

*EC

4.1.1.77

Accepted name:

2-oxo-3-hexenedioate decarboxylase

Reaction:

(3E)-2-oxohex-3-enedioate = 2-oxopent-4-enoate + CO₂

For diagram of catechol catabolism (meta ring cleavage), click here

Other name(s):

4-oxalocrotonate carboxy-lyase (misleading); 4-oxalocrotonate decarboxylase (misleading); cnbF (gene name); praD (gene name); amnE (gene name); nbaG (gene name); xylI (gene name)

Systematic name:

(3E)-2-oxohex-3-enedioate carboxy-lyase (2-oxopent-4-enoate-forming)

Comments:

Involved in the meta-cleavage pathway for the degradation of phenols, modified phenols and catechols. The enzyme has been reported to accept multiple tautomeric forms [1-4]. However, careful analysis of the stability of the different tautomers, as well as characterization of the enzyme that produces its substrate, EC 5.3.2.6, 2-hydroxymuconate tautomerase, showed that the actual substrate for the enzyme is (3E)-2-oxohex-3-enedioate [4].

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 37325-55-6

References:

1.	Shingler, V., Marklund, U., Powlowski, J. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J. Bacteriol. 174 (1992) 711–724. [DOI] [PMID: 1732207]
2.	Takenaka, S., Murakami, S., Shinke, R. and Aoki, K. Metabolism of 2-aminophenol by Pseudomonas sp. AP-3: modified meta-cleavage pathway. Arch. Microbiol. 170 (1998) 132–137. [PMID: 9683650]
3.	Stanley, T.M., Johnson, W.H., Jr., Burks, E.A., Whitman, C.P., Hwang, C.C. and Cook, P.F. Expression and stereochemical and isotope effect studies of active 4-oxalocrotonate decarboxylase. Biochemistry 39 (2000) 718–726. [DOI] [PMID: 10651637]
4.	Wang, S.C., Johnson, W.H., Jr., Czerwinski, R.M., Stamps, S.L. and Whitman, C.P. Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions. Biochemistry 46 (2007) 11919–11929. [DOI] [PMID: 17902707]
5.	Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758–6768. [DOI] [PMID: 19717587]

[EC 4.1.1.77 created 1999, modified 2011, modified 2012]

4.1.1.95

Accepted name:

L-glutamyl-[BtrI acyl-carrier protein] decarboxylase

Reaction:

L-glutamyl-[BtrI acyl-carrier protein] = 4-amino butanoyl-[BtrI acyl-carrier protein] + CO₂

Other name(s):

btrK (gene name)

Systematic name:

L-glutamyl-[BtrI acyl-carrier protein] carboxy-lyase

Comments:

Binds pyridoxal 5′-phosphate. Catalyses a step in the biosynthesis of the side chain of the aminoglycoside antibiotics of the butirosin family. Has very low activity with substrates not bound to an acyl-carrier protein.

Links to other databases:

References:

1.	Li, Y., Llewellyn, N.M., Giri, R., Huang, F. and Spencer, J.B. Biosynthesis of the unique amino acid side chain of butirosin: possible protective-group chemistry in an acyl carrier protein-mediated pathway. Chem. Biol. 12 (2005) 665–675. [DOI] [PMID: 15975512]

[EC 4.1.1.95 created 2012]

4.1.1.96

Accepted name:

carboxynorspermidine decarboxylase

Reaction:

(1) carboxynorspermidine = bis(3-aminopropyl)amine + CO₂
(2) carboxyspermidine = spermidine + CO₂

Glossary:

bis(3-aminopropyl)amine = norspermidine

Other name(s):

carboxyspermidine decarboxylase; CANSDC; VC1623 (gene name)

Systematic name:

carboxynorspermidine carboxy-lyase (bis(3-aminopropyl)amine-forming)

Comments:

A pyridoxal 5′-phosphate enzyme. Part of a bacterial polyamine biosynthesis pathway. The enzyme is essential for biofilm formation in the bacterium Vibrio cholerae [1]. The enzyme from Campylobacter jejuni only produces spermidine in vivo even though it shows activity with carboxynorspermidine in vitro [3].

Links to other databases:

References:

1.	Lee, J., Sperandio, V., Frantz, D.E., Longgood, J., Camilli, A., Phillips, M.A. and Michael, A.J. An alternative polyamine biosynthetic pathway is widespread in bacteria and essential for biofilm formation in Vibrio cholerae. J. Biol. Chem. 284 (2009) 9899–9907. [DOI] [PMID: 19196710]
2.	Deng, X., Lee, J., Michael, A.J., Tomchick, D.R., Goldsmith, E.J. and Phillips, M.A. Evolution of substrate specificity within a diverse family of β/α-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine. J. Biol. Chem. 285 (2010) 25708–25719. [DOI] [PMID: 20534592]
3.	Hanfrey, C.C., Pearson, B.M., Hazeldine, S., Lee, J., Gaskin, D.J., Woster, P.M., Phillips, M.A. and Michael, A.J. Alternative spermidine biosynthetic route is critical for growth of Campylobacter jejuni and is the dominant polyamine pathway in human gut microbiota. J. Biol. Chem. 286 (2011) 43301–43312. [DOI] [PMID: 22025614]

[EC 4.1.1.96 created 2012]

*EC

4.1.3.17

Accepted name:

4-hydroxy-4-methyl-2-oxoglutarate aldolase

Reaction:

(1) 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate
(2) 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = oxaloacetate + pyruvate

For diagram of the protocatechuate 3,4-cleavage pathway, click here

Other name(s):

pyruvate aldolase; γ-methyl-γ-hydroxy-α-ketoglutaric aldolase; 4-hydroxy-4-methyl-2-ketoglutarate aldolase; 4-hydroxy-4-methyl-2-oxoglutarate pyruvate-lyase; HMG aldolase; CHA aldolase; 4-carboxy-4-hydroxy-2-oxoadipate aldolase

Systematic name:

4-hydroxy-4-methyl-2-oxoglutarate pyruvate-lyase (pyruvate-forming)

Comments:

Requires a divalent metal ion [3]. This enzyme participates in the degradation of 3,4-dihydroxybenzoate (via the meta-cleavage pathway), phthalate, syringate and 3,4,5-trihydroxybenzoate [1-3]. The enzyme from Pseudomonas straminea can also catalyse the activity of EC 4.1.3.16, 4-hydroxy-2-oxoglutarate aldolase, and the decarboxylation of oxaloacetate [3].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37290-65-6

References:

1.	Tack, B.F., Chapman, P.J. and Dagley, S. Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase. J. Biol. Chem. 247 (1972) 6444–6449. [PMID: 5076765]
2.	Wood, W.A. 2-Keto-3-deoxy-6-phosphogluconic and related aldolases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 281–302.
3.	Maruyama, K. Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae grown on phthalate. J. Biochem. 108 (1990) 327–333. [PMID: 2229032]
4.	Nogales, J., Canales, A., Jiménez-Barbero, J., Serra B., Pingarrón, J. M., García, J. L. and Díaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359–374. [DOI] [PMID: 21219457]

[EC 4.1.3.17 created 1972, modified 2012]

*EC

4.2.1.33

Accepted name:

3-isopropylmalate dehydratase

Reaction:

(2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate (overall reaction)
(1a) (2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H₂O
(1b) 2-isopropylmaleate + H₂O = (2S)-2-isopropylmalate

For diagram of leucine biosynthesis, click here

Glossary:

α-isopropylmalate = (2S)-2-isopropylmalate
β-isopropylmalate = (2R,3S)-3-isopropylmalate

Other name(s):

(2R,3S)-3-isopropylmalate hydro-lyase; β-isopropylmalate dehydratase; isopropylmalate isomerase; α-isopropylmalate isomerase; 3-isopropylmalate hydro-lyase

Systematic name:

(2R,3S)-3-isopropylmalate hydro-lyase (2-isopropylmaleate-forming)

Comments:

Forms part of the leucine biosynthesis pathway. The enzyme brings about the interconversion of the two isomers of isopropylmalate. It contains an iron-sulfur cluster.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37290-72-5

References:

1.	Gross, S.R., Burns, R.O. and Umbarger, H.E. The biosynthesis of leucine. II. The enzymic isomerization of β-carboxy-β-hydroxyisocaproate and α-hydroxy-β-carboxyisocaproate. Biochemistry 2 (1963) 1046–1052. [PMID: 14087357]
2.	Calvo, J. M., Stevens, C. M., Kalyanpur, M. G., and Umbarger, H. E. The absolute configuration of α-hydroxy-β-carboxyisocaproic acid (3-isopropylmalic acid), an intermediate in leucine biosynthesis. Biochemistry 3 (1964) 2024–2027. [PMID: 14269331]
3.	Cole, F.E., Kalyanpur, M. G. and Stevens, C. M. Absolute configuration of α-isopropylmalate and the mechanism of its conversion to β-isopropylmalate in the biosynthesis of leucine. Biochemistry 12 (1973) 3346–3350. [PMID: 4270046]
4.	Jang, S. and Imlay, J.A. Micromolar intracellular hydrogen peroxide disrupts metabolism by damaging iron-sulfur enzymes. J. Biol. Chem. 282 (2007) 929–937. [DOI] [PMID: 17102132]

[EC 4.2.1.33 created 1972, modified 1976, modified 2012]

4.2.1.52

Transferred entry:

dihydrodipicolinate synthase. Now EC 4.3.3.7, 4-hydroxy-2,3,4,5-tetrahydrodipicolinate synthase.

[EC 4.2.1.52 created 1972, deleted 2012]

*EC

4.2.1.54

Accepted name:

lactoyl-CoA dehydratase

Reaction:

(R)-lactoyl-CoA = acryloyl-CoA + H₂O

Other name(s):

lactoyl coenzyme A dehydratase; lactyl-coenzyme A dehydrase; lactyl CoA dehydratase; acrylyl coenzyme A hydratase; lactoyl-CoA hydro-lyase

Systematic name:

(R)-lactoyl-CoA hydro-lyase (acryloyl-CoA-forming)

Comments:

A bacterial enzyme that is involved in propanoate fermentation (also known as the acrylate pathway).

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, KEGG, CAS registry number: 9031-12-3

References:

1.	Baldwin, R.L., Wood, W.A. and Emery, R.S. Lactate metabolism by Peptostreptococcus elsdenii: evidence for lactyl coenzyme a dehydrase. Biochim. Biophys. Acta 97 (1965) 202–213. [DOI] [PMID: 14292829]
2.	Schweiger, G. and Buckel, W. On the dehydration of (R)-lactate in the fermentation of alanine to propionate by Clostridium propionicum. FEBS Lett. 171 (1984) 79–84. [DOI] [PMID: 6586495]
3.	Kuchta, R.D. and Abeles, R.H. Lactate reduction in Clostridium propionicum. Purification and properties of lactyl-CoA dehydratase. J. Biol. Chem. 260 (1985) 13181–13189. [PMID: 4055736]
4.	Kuchta, R.D., Hanson, G.R., Holmquist, B. and Abeles, R.H. Fe-S centers in lactyl-CoA dehydratase. Biochemistry 25 (1986) 7301–7307. [PMID: 3026450]
5.	Hofmeister, A.E. and Buckel, W. (R)-Lactyl-CoA dehydratase from Clostridium propionicum. Stereochemistry of the dehydration of (R)-2-hydroxybutyryl-CoA to crotonyl-CoA. Eur. J. Biochem. 206 (1992) 547–552. [DOI] [PMID: 1597194]

[EC 4.2.1.54 created 1972, modified 2012]

4.2.1.58

Deleted entry:

crotonoyl-[acyl-carrier-protein] hydratase. The reaction described is covered by EC 4.2.1.59.

[EC 4.2.1.58 created 1972, deleted 2012]

*EC

4.2.1.59

Accepted name:

3-hydroxyacyl-[acyl-carrier-protein] dehydratase

Reaction:

a (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H₂O

Other name(s):

fabZ (gene name); fabA (gene name); D-3-hydroxyoctanoyl-[acyl carrier protein] dehydratase; D-3-hydroxyoctanoyl-acyl carrier protein dehydratase; β-hydroxyoctanoyl-acyl carrier protein dehydrase; β-hydroxyoctanoyl thioester dehydratase; β-hydroxyoctanoyl-ACP-dehydrase; (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase; (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase (oct-2-enoyl-[acyl-carrier protein]-forming); 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase

Systematic name:

(3R)-3-hydroxyacyl-[acyl-carrier protein] hydro-lyase (trans-2-enoyl-[acyl-carrier protein]-forming)

Comments:

This enzyme is responsible for the dehydration step of the dissociated (type II) fatty-acid biosynthesis system that occurs in plants and bacteria. The enzyme uses fatty acyl thioesters of ACP in vivo. Different forms of the enzyme may have preferences for substrates with different chain length. For example, the activity of FabZ, the ubiquitous enzyme in bacteria, decreases with increasing chain length. Gram-negative bacteria that produce unsaturated fatty acids, such as Escherichia coli, have another form (FabA) that prefers intermediate chain length, and also catalyses EC 5.3.3.14, trans-2-decenoyl-[acyl-carrier protein] isomerase. Despite the differences both forms can catalyse all steps leading to the synthesis of palmitate (C16:0). FabZ, but not FabA, can also accept unsaturated substrates [4].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9030-85-7

References:

1.	Mizugaki, M., Swindell, A.C. and Wkil, S.J. Intermediate- and long-chain β-hydroxyacyl-ACP dehydrases from E. coli fatty acid synthetase. Biochem. Biophys. Res. Commun. 33 (1968) 520–527. [DOI] [PMID: 4881058]
2.	Sharma, A., Henderson, B.S., Schwab, J.M. and Smith, J.L. Crystallization and preliminary X-ray analysis of β-hydroxydecanoyl thiol ester dehydrase from Escherichia coli. J. Biol. Chem. 265 (1990) 5110–5112. [PMID: 2180957]
3.	Mohan, S., Kelly, T.M., Eveland, S.S., Raetz, C.R. and Anderson, M.S. An Escherichia coli gene (FabZ) encoding (3R)-hydroxymyristoyl acyl carrier protein dehydrase. Relation to fabA and suppression of mutations in lipid A biosynthesis. J. Biol. Chem. 269 (1994) 32896–32903. [PMID: 7806516]
4.	Heath, R.J. and Rock, C.O. Roles of the FabA and FabZ β-hydroxyacyl-acyl carrier protein dehydratases in Escherichia coli fatty acid biosynthesis. J. Biol. Chem. 271 (1996) 27795–27801. [DOI] [PMID: 8910376]

[EC 4.2.1.59 created 1972, modified 2012]

4.2.1.60

Deleted entry:

3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase. The reaction described is covered by EC 4.2.1.59.

[EC 4.2.1.60 created 1972, modified 2006, deleted 2012]

4.2.1.61

Deleted entry:

3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase. The reaction described is covered by EC 4.2.1.59.

[EC 4.2.1.61 created 1972, deleted 2012]

*EC

4.2.1.93

Accepted name:

ATP-dependent NAD(P)H-hydrate dehydratase

Reaction:

(1) ATP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = ADP + phosphate + NADH
(2) ATP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = ADP + phosphate + NADPH

For diagram of reaction, click here

Glossary:

(6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = (S)-NADH-hydrate = (S)-NADHX
(6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = (S)-NADPH-hydrate = (S)-NADPHX

Other name(s):

reduced nicotinamide adenine dinucleotide hydrate dehydratase; ATP-dependent H₄NAD(P)⁺OH dehydratase; (6S)-β-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase(ATP-hydrolysing); (6S)-6-β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ATP-hydrolysing; NADH-forming)

Systematic name:

(6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ATP-hydrolysing; NADH-forming)

Comments:

Acts equally well on hydrated NADH and hydrated NADPH. NAD(P)H spontaneously hydrates to both the (6S)- and (6R)- isomers, and these are interconverted by EC 5.1.99.6, NAD(P)H-hydrate epimerase, to a 60:40 ratio [4]. Hence EC 4.2.1.93 together with EC 5.1.99.6 can restore the mixture of hydrates into NAD(P)H [3,4]. The enzyme from eukaryotes has no activity with ADP, contrary to the enzyme from bacteria (cf. EC 4.2.1.136, ADP-dependent NAD(P)H-hydrate dehydratase) [4].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 116669-08-0

References:

1.	Meinhart, J.O., Chaykin, S. and Krebs, E.G. Enzymatic conversion of a reduced diphosphopyridine nucleotide derivative to reduced diphosphopyridine nucleotide. J. Biol. Chem. 220 (1956) 821–829. [PMID: 13331940]
2.	Regueiro Varela, B., Amelunxen, R. and Grisolia, S. Synthesis and degradation of monohydroxytetrahydronicotinamide adenine dinucleotide phosphate. Physiol. Chem. Phys. 2 (1970) 445–454.
3.	Acheson, S.A., Kirkman, H.N. and Wolfenden, R. Equilibrium of 5,6-hydration of NADH and mechanism of ATP-dependent dehydration. Biochemistry 27 (1988) 7371–7375. [PMID: 3061454]
4.	Marbaix, A.Y., Noel, G., Detroux, A.M., Vertommen, D., Van Schaftingen, E. and Linster, C.L. Extremely conserved ATP- or ADP-dependent enzymatic system for nicotinamide nucleotide repair. J. Biol. Chem. 286 (2011) 41246–41252. [DOI] [PMID: 21994945]

[EC 4.2.1.93 created 1992, modified 2012]

4.2.1.134

Accepted name:

very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase

Reaction:

a very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain trans-2,3-dehydroacyl-CoA + H₂O

Glossary:

a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.

Other name(s):

PHS1 (gene name); PAS2 (gene name)

Systematic name:

very-long-chain (3R)-3-hydroxyacyl-CoA hydro-lyase

Comments:

This is the third component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long chain acyl CoAs. cf. EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase.

Links to other databases:

References:

Bach, L., Michaelson, L.V., Haslam, R., Bellec, Y., Gissot, L., Marion, J., Da Costa, M., Boutin, J.P., Miquel, M., Tellier, F., Domergue, F., Markham, J.E., Beaudoin, F., Napier, J.A. and Faure, J.D. The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTICCINO₂ is essential and limiting for plant development. Proc. Natl. Acad. Sci. USA 105 (2008) 14727–14731. [DOI] [PMID: 18799749]

Kihara, A., Sakuraba, H., Ikeda, M., Denpoh, A. and Igarashi, Y. Membrane topology and essential amino acid residues of Phs1, a 3-hydroxyacyl-CoA dehydratase involved in very long-chain fatty acid elongation. J. Biol. Chem. 283 (2008) 11199–11209. [DOI] [PMID: 18272525]

[EC 4.2.1.134 created 2012, modified 2014]

4.2.1.135

Accepted name:

UDP-N-acetylglucosamine 4,6-dehydratase (configuration-retaining)

Reaction:

UDP-N-acetyl-α-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-α-D-xylo-hex-4-ulose + H₂O

For diagram of legionaminic acid biosynthesis, click here, and for mechanism, click here

Glossary:

N,N′-diacetylbacillosamine = 2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose

Other name(s):

PglF

Systematic name:

UDP-N-acetyl-α-D-glucosamine hydro-lyase (configuration-retaining; UDP-2-acetamido-2,6-dideoxy-α-D-xylo-hex-4-ulose-forming)

Comments:

Contains NAD⁺ as a cofactor [2]. This is the first enzyme in the biosynthetic pathway of N,N′-diacetylbacillosamine [1], the first carbohydrate in the glycoprotein N-linked heptasaccharide in Campylobacter jejuni. This enzyme belongs to the short-chain dehydrogenase/reductase family of enzymes.

Links to other databases:

References:

1.	Schoenhofen, I.C., McNally, D.J., Vinogradov, E., Whitfield, D., Young, N.M., Dick, S., Wakarchuk, W.W., Brisson, J.R. and Logan, S.M. Functional characterization of dehydratase/aminotransferase pairs from Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic acid and bacillosamine biosynthetic pathways. J. Biol. Chem. 281 (2006) 723–732. [DOI] [PMID: 16286454]
2.	Olivier, N.B., Chen, M.M., Behr, J.R. and Imperiali, B. In vitro biosynthesis of UDP-N,N′-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system. Biochemistry 45 (2006) 13659–13669. [DOI] [PMID: 17087520]

[EC 4.2.1.135 created 2012]

4.2.1.136

Accepted name:

ADP-dependent NAD(P)H-hydrate dehydratase

Reaction:

(1) ADP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = AMP + phosphate + NADH
(2) ADP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = AMP + phosphate + NADPH

Glossary:

Other name(s):

(6S)-β-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase(ADP-hydrolysing); (6S)-6-β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ADP-hydrolysing; NADH-forming)

Systematic name:

(6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ADP-hydrolysing; NADH-forming)

Comments:

Acts equally well on hydrated NADH and hydrated NADPH. NAD(P)H spontaneously hydrates to both the (6S)- and (6R)- isomers. The enzyme from bacteria consists of two domains, one of which acts as an NAD(P)H-hydrate epimerase that interconverts the two isomers to a 60:40 ratio (cf. EC 5.1.99.6), while the other catalyses the dehydration. Hence the enzyme can restore the complete mixture of isomers into NAD(P)H. The enzyme has no activity with ATP, contrary to the enzyme from eukaryotes (cf. EC 4.2.1.93, ATP-dependent NAD(P)H-hydrate dehydratase).

Links to other databases:

References:

1.	Marbaix, A.Y., Noel, G., Detroux, A.M., Vertommen, D., Van Schaftingen, E. and Linster, C.L. Extremely conserved ATP- or ADP-dependent enzymatic system for nicotinamide nucleotide repair. J. Biol. Chem. 286 (2011) 41246–41252. [DOI] [PMID: 21994945]

[EC 4.2.1.136 created 2012]

4.2.1.137

Accepted name:

sporulenol synthase

Reaction:

sporulenol = tetraprenyl-β-curcumene + H₂O

For diagram of sesquarterpenoid biosynthesis, click here

Glossary:

sporulenol = (1R,2R,4aS,4bR,6aS,10aS,10bR,12aS)-2,4b,7,7,10a,12a-hexamethyl-1-[(3R)-3-(4-methylcyclohexa-1,4-dien-1-yl)butyl]octadecahydrochrysen-2-ol

Other name(s):

sqhC (gene name)

Systematic name:

tetraprenyl-β-curcumene—sporulenol cyclase

Comments:

The reaction occurs in the reverse direction. Isolated from Bacillus subtilis. Similar sesquarterpenoids are present in a number of Bacillus species.

Links to other databases:

References:

Sato, T., Yoshida, S., Hoshino, H., Tanno, M., Nakajima, M. and Hoshino, T. Sesquarterpenes (C₃₅ terpenes) biosynthesized via the cyclization of a linear C₃₅ isoprenoid by a tetraprenyl-β-curcumene synthase and a tetraprenyl-β-curcumene cyclase: identification of a new terpene cyclase. J. Am. Chem. Soc. 133 (2011) 9734–9737. [DOI] [PMID: 21627333]

[EC 4.2.1.137 created 2012]

*EC

4.2.3.32

Accepted name:

levopimaradiene synthase

Reaction:

(+)-copalyl diphosphate = abieta-8(14),12-diene + diphosphate

For diagram of abietadiene, abietate, isopimaradiene, labdadienol and sclareol biosynthesis, click here and for diagram of abietadiene, levopimaradiene and isopimara-7,15-diene biosynthesis, click here

Glossary:

levopimaradiene = abieta-8(14),12-diene

Other name(s):

PtTPS-LAS; LPS; copalyl-diphosphate diphosphate-lyase [abieta-8(14),12-diene-forming]

Systematic name:

(+)-copalyl-diphosphate diphosphate-lyase [abieta-8(14),12-diene-forming]

Comments:

In Ginkgo, the enzyme catalyses the initial cyclization step in the biosynthesis of ginkgolides, a structurally unique family of diterpenoids that are highly specific platelet-activating-factor receptor antagonists [1]. Levopimaradiene is widely distributed in higher plants. In some species the enzyme also forms abietadiene, palustradiene, and neoabietadiene [2].

Links to other databases:

References:

1.	Schepmann, H.G., Pang, J. and Matsuda, S.P. Cloning and characterization of Ginkgo biloba levopimaradiene synthase which catalyzes the first committed step in ginkgolide biosynthesis. Arch. Biochem. Biophys. 392 (2001) 263–269. [DOI] [PMID: 11488601]
2.	Ro, D.K. and Bohlmann, J. Diterpene resin acid biosynthesis in loblolly pine (Pinus taeda): functional characterization of abietadiene/levopimaradiene synthase (PtTPS-LAS) cDNA and subcellular targeting of PtTPS-LAS and abietadienol/abietadienal oxidase (PtAO, CYP720B1). Phytochemistry 67 (2006) 1572–1578. [DOI] [PMID: 16497345]

[EC 4.2.3.32 created 2008, modified 2012]

4.2.3.131

Accepted name:

miltiradiene synthase

Reaction:

(+)-copalyl diphosphate = miltiradiene + diphosphate

For diagram of abietane diterpenoids biosynthesis, click here

Other name(s):

SmMDS; SmiKSL; RoKSL

Systematic name:

(+)-copalyl-diphosphate diphosphate-lyase (cyclizing, miltiradiene-forming)

Comments:

Isolated from the plants Rosmarinus officinalis (rosemary) and Salvia miltiorrhiza. The enzyme from the plant Selaginella moellendorffii is mutifunctional and also catalyses EC 5.5.1.12, copalyl diphosphate synthase [2].

Links to other databases:

References:

1.	Gao, W., Hillwig, M.L., Huang, L., Cui, G., Wang, X., Kong, J., Yang, B. and Peters, R.J. A functional genomics approach to tanshinone biosynthesis provides stereochemical insights. Org. Lett. 11 (2009) 5170–5173. [DOI] [PMID: 19905026]
2.	Sugai, Y., Ueno, Y., Hayashi, K., Oogami, S., Toyomasu, T., Matsumoto, S., Natsume, M., Nozaki, H. and Kawaide, H. Enzymatic ¹³C labeling and multidimensional NMR analysis of miltiradiene synthesized by bifunctional diterpene cyclase in Selaginella moellendorffii. J. Biol. Chem. 286 (2011) 42840–42847. [DOI] [PMID: 22027823]
3.	Bruckner, K., Bozic, D., Manzano, D., Papaefthimiou, D., Pateraki, I., Scheler, U., Ferrer, A., de Vos, R.C., Kanellis, A.K. and Tissier, A. Characterization of two genes for the biosynthesis of abietane-type diterpenes in rosemary (Rosmarinus officinalis) glandular trichomes. Phytochemistry 101 (2014) 52–64. [DOI] [PMID: 24569175]

[EC 4.2.3.131 created 2012]

4.2.3.132

Accepted name:

neoabietadiene synthase

Reaction:

(+)-copalyl diphosphate = neoabietadiene + diphosphate

For diagram of abietane diterpenoids biosynthesis, click here

Glossary:

neoabietadiene = abieta-8(14),13(15)-diene

Other name(s):

TPS-LAS

Systematic name:

(+)-copaly-diphosphate diphosphate-lyase (cyclizing, neoabietadiene-forming)

Comments:

Isolated from Abies grandis (grand fir) [1]. This class I enzyme forms about equal proportions of abietadiene, levopimaradiene and neoabietadiene. See also EC 4.2.3.18, abieta-7,13-diene synthase and EC 4.2.3.32, levopimaradiene synthase. An X-ray study of this multifunctional enzyme showed that the class I activity is in the α domain, while (+)-copalyl diphosphate synthase activity (EC 5.5.1.12, a class II activity) is in the β and γ domains [2]. In Pinus taeda (loblolly pine) the major product is levopimaradiene, with less abietadiene and neoabietadiene [3].

Links to other databases:

References:

1.	Peters, R.J., Flory, J.E., Jetter, R., Ravn, M.M., Lee, H.J., Coates, R.M. and Croteau, R.B. Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. Biochemistry 39 (2000) 15592–15602. [DOI] [PMID: 11112547]
2.	Zhou, K., Gao, Y., Hoy, J.A., Mann, F.M., Honzatko, R.B. and Peters, R.J. Insights into diterpene cyclization from structure of bifunctional abietadiene synthase from Abies grandis. J. Biol. Chem. 287 (2012) 6840–6850. [DOI] [PMID: 22219188]
3.	Ro, D.K. and Bohlmann, J. Diterpene resin acid biosynthesis in loblolly pine (Pinus taeda): functional characterization of abietadiene/levopimaradiene synthase (PtTPS-LAS) cDNA and subcellular targeting of PtTPS-LAS and abietadienol/abietadienal oxidase (PtAO, CYP720B1). Phytochemistry 67 (2006) 1572–1578. [DOI] [PMID: 16497345]

[EC 4.2.3.132 created 2012]

4.2.3.133

Accepted name:

α-copaene synthase

Reaction:

(2E,6E)-farnesyl diphosphate = (-)-α-copaene + diphosphate

For diagram of cadinane sesquiterpenoid biosynthesis, click here

Glossary:

(-)-α-copaene = (1R,2S,6S,7S,8S)-1,3-dimethyl-8-(propan-2-yl)tricyclo[4.4.0.0^2,7]dec-3-ene
For diagram of the structures of α-copaene and β-copaene, click here

Systematic name:

(2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, α-copaene-forming)

Comments:

Isolated from Helianthus annuus (sunflower). The enzyme also produces β-caryophyllene, δ-cadinene and traces of other sesquiterpenoids. See EC 4.2.3.13 (+)-δ-cadinene synthase, EC 4.2.3.57 (-)-β-caryophyllene synthase.

Links to other databases:

References:

1.	Gopfert, J.C., Macnevin, G., Ro, D.K. and Spring, O. Identification, functional characterization and developmental regulation of sesquiterpene synthases from sunflower capitate glandular trichomes. BMC Plant Biol. 9:86 (2009). [DOI] [PMID: 19580670]
2.	Xie, X., Kirby, J. and Keasling, J.D. Functional characterization of four sesquiterpene synthases from Ricinus communis (castor bean). Phytochemistry 78 (2012) 20–28. [DOI] [PMID: 22459969]

[EC 4.2.3.133 created 2012]

4.2.3.134

Accepted name:

5-phosphooxy-L-lysine phospho-lyase

Reaction:

(5R)-5-phosphooxy-L-lysine + H₂O = (S)-2-amino-6-oxohexanoate + NH₃ + phosphate

Other name(s):

5-phosphohydroxy-L-lysine ammoniophospholyase; AGXT2L2 (gene name); (5R)-5-phosphonooxy-L-lysine phosphate-lyase (deaminating; (S)-2-amino-6-oxohexanoate-forming); 5-phosphonooxy-L-lysine phospho-lyase

Systematic name:

(5R)-5-phosphooxy-L-lysine phosphate-lyase (deaminating; (S)-2-amino-6-oxohexanoate-forming)

Comments:

A pyridoxal-phosphate protein. Has no activity with phosphoethanolamine (cf. EC 4.2.3.2, ethanolamine-phosphate phospho-lyase).

Links to other databases:

References:

1.	Tsai, C.H. and Henderson, L.M. Degradation of O-phosphohydroxylysine by rat liver. Purification of the phospho-lyase. J. Biol. Chem. 249 (1974) 5784–5789. [PMID: 4412716]
2.	Veiga-da-Cunha, M., Hadi, F., Balligand, T., Stroobant, V. and Van Schaftingen, E. Molecular identification of hydroxylysine kinase and of ammoniophospholyases acting on 5-phosphohydroxy-L-lysine and phosphoethanolamine. J. Biol. Chem. 287 (2012) 7246–7255. [DOI] [PMID: 22241472]

[EC 4.2.3.134 created 2012]

4.2.3.135

Accepted name:

Δ⁶-protoilludene synthase

Reaction:

(2E,6E)-farnesyl diphosphate = Δ⁶-protoilludene + diphosphate

For diagram of bicyclic and tricyclic sesquiterpenoids derived from humuladienyl cation, click here

Glossary:

Δ⁶-protoilludene = (4aS,7aS,7bR)-3,6,6,7b-tetramethyl-2,4,4a,5,6,7,7a,7b-octahydro-1H-cyclobuta[1,2-e]indene

Other name(s):

6-protoilludene synthase

Systematic name:

(2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, Δ⁶-protoilludene-forming)

Comments:

Isolated from the fungus Armillaria gallica. Δ⁶-Protoilludene is the first step in the biosynthesis of the melleolides.

Links to other databases:

References:

Engels, B., Heinig, U., Grothe, T., Stadler, M. and Jennewein, S. Cloning and characterization of an Armillaria gallica cDNA encoding protoilludene synthase, which catalyzes the first committed step in the synthesis of antimicrobial melleolides. J. Biol. Chem. 286 (2011) 6871–6878. [DOI] [PMID: 21148562]

[EC 4.2.3.135 created 2012]

4.2.3.136

Accepted name:

α-isocomene synthase

Reaction:

(2E,6E)-farnesyl diphosphate = (-)-α-isocomene + diphosphate

For diagram of bicyclic and tricyclic sesquiterpenoids derived from humuladienyl cation, click here and for mechanism, click here

Glossary:

(-)-α-isocomene = (1R,3aS,5aS,8aR)-1,3a,4,5a-tetramethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene

Other name(s):

MrTPS2

Systematic name:

(2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, (-)-α-isocomene-forming)

Comments:

Isolated from the roots of the plant Matricaria chamomilla var. recutita (chamomile). The enzyme also produced traces of five other sesquiterpenoids.

Links to other databases:

References:

1.	Irmisch, S., Krause, S.T., Kunert, G., Gershenzon, J., Degenhardt, J. and Kollner, T.G. The organ-specific expression of terpene synthase genes contributes to the terpene hydrocarbon composition of chamomile essential oils. BMC Plant Biol. 12:84 (2012). [DOI] [PMID: 22682202]

[EC 4.2.3.136 created 2012]

4.2.3.137

Accepted name:

(E)-2-epi-β-caryophyllene synthase

Reaction:

(2E,6E)-farnesyl diphosphate = (E)-2-epi-β-caryophyllene + diphosphate

Other name(s):

2-epi-(E)-β-caryophyllene synthase; SmMTPSL26

Systematic name:

(2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, (E)-2-epi-β-caryophyllene-forming)

Comments:

Isolated from the plant Selaginella moellendorfii. The enzyme also gives two other sesquiterpenoids.

Links to other databases:

References:

1.	Li, G., Kollner, T.G., Yin, Y., Jiang, Y., Chen, H., Xu, Y., Gershenzon, J., Pichersky, E. and Chen, F. Nonseed plant Selaginella moellendorfii has both seed plant and microbial types of terpene synthases. Proc. Natl. Acad. Sci. USA 109 (2012) 14711–14715. [DOI] [PMID: 22908266]

[EC 4.2.3.137 created 2012]

4.2.3.138

Accepted name:

(+)-epi-α-bisabolol synthase

Reaction:

(2E,6E)-farnesyl diphosphate + H₂O = (+)-epi-α-bisabolol + diphosphate

For diagram of bisabolene biosynthesis, click here

Glossary:

(+)-epi-α-bisabolol = (2S)-6-methyl-2-[(1R)-4-methylcyclohex-3-en-1-yl]hept-5-en-2-ol

Systematic name:

(2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, (+)-epi-α-bisabolol-forming)

Comments:

Isolated from the plant Phyla dulcis (Aztec sweet herb). (+)-epi-α-Bisabolol is the precursor of the sweetener hernandulcin.

Links to other databases:

References:

1.	Attia, M., Kim, S.U. and Ro, D.K. Molecular cloning and characterization of (+)-epi-α-bisabolol synthase, catalyzing the first step in the biosynthesis of the natural sweetener, hernandulcin, in Lippia dulcis. Arch. Biochem. Biophys. 527 (2012) 37–44. [DOI] [PMID: 22867794]

[EC 4.2.3.138 created 2012]

4.2.3.139

Accepted name:

valerena-4,7(11)-diene synthase

Reaction:

(2E,6E)-farnesyl diphosphate = valerena-4,7(11)-diene + diphosphate

For mechanism, click here

Glossary:

valerena-4,7(11)-diene = (4S,7R,7aR)-3,7-dimethyl-4-(2-methylprop-1-en-1-yl)-2,4,5,6,7,7a-hexahydro-1H-indene

Other name(s):

VoTPS2; VoTPS7

Systematic name:

(2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, valerena-4,7(11)-diene-forming)

Comments:

Isolated from the plant Valeriana officinalis (valerian). Note that due to a different numbering system the product is also known as valerena-1,10-diene.

Links to other databases:

References:

Pyle, B.W., Tran, H.T., Pickel, B., Haslam, T.M., Gao, Z., Macnevin, G., Vederas, J.C., Kim, S.U. and Ro, D.K. Enzymatic synthesis of valerena-4,7(11)-diene by a unique sesquiterpene synthase from the valerian plant (Valeriana officinalis). FEBS J. 279 (2012) 3136–3146. [DOI] [PMID: 22776156]

Yeo, Y.S., Nybo, S.E., Chittiboyina, A.G., Weerasooriya, A.D., Wang, Y.H., Gongora-Castillo, E., Vaillancourt, B., Buell, C.R., DellaPenna, D., Celiz, M.D., Jones, A.D., Wurtele, E.S., Ransom, N., Dudareva, N., Shaaban, K.A., Tibrewal, N., Chandra, S., Smillie, T., Khan, I.A., Coates, R.M., Watt, D.S. and Chappell, J. Functional identification of valerena-1,10-diene synthase, a terpene synthase catalyzing a unique chemical cascade in the biosynthesis of biologically active sesquiterpenes in Valeriana officinalis. J. Biol. Chem. 288 (2013) 3163–3173. [DOI] [PMID: 23243312]

[EC 4.2.3.139 created 2012]

4.2.3.140

Accepted name:

cis-abienol synthase

Reaction:

(13E)-8α-hydroxylabd-13-en-15-yl diphosphate = cis-abienol + diphosphate

For diagram of hydroxylabdenyl diphosphate derived diterpenoids, click here

Glossary:

cis-abienol = (12Z)-labda-12,14-dien-8α-ol
(13E)-8α-hydroxylabd-13-en-15-yl diphosphate = 8-hydroxycopalyl diphosphate

Other name(s):

Z-abienol synthase; CAS; ABS

Systematic name:

(13E)-8α-hydroxylabd-13-en-15-yl-diphosphate-lyase (cis-abienol-forming)

Comments:

Isolated from the plants Abies balsamea (balsam fir) [1] and Nicotiana tabacum (tobacco) [2].

Links to other databases:

References:

1.	Zerbe, P., Chiang, A., Yuen, M., Hamberger, B., Hamberger, B., Draper, J.A., Britton, R. and Bohlmann, J. Bifunctional cis-abienol synthase from Abies balsamea discovered by transcriptome sequencing and its implications for diterpenoid fragrance production. J. Biol. Chem. 287 (2012) 12121–12131. [DOI] [PMID: 22337889]
2.	Sallaud, C., Giacalone, C., Topfer, R., Goepfert, S., Bakaher, N., Rosti, S. and Tissier, A. Characterization of two genes for the biosynthesis of the labdane diterpene Z-abienol in tobacco (Nicotiana tabacum) glandular trichomes. Plant J. 72 (2012) 1–17. [DOI] [PMID: 22672125]

[EC 4.2.3.140 created 2012]

4.3.1.28

Accepted name:

L-lysine cyclodeaminase

Reaction:

L-lysine = L-pipecolate + NH₃

Other name(s):

rapL (gene name); fkbL (gene name); tubZ (gene name); visC (gene name)

Systematic name:

L-lysine ammonia-lyase (cyclizing; ammonia-forming)

Comments:

Requires bound NAD⁺. The enzyme produces the non-proteinogenic amino acid L-pipecolate, which is incorporated into multiple secondary metabolite products, including rapamycin, tobulysin, virginiamycin and pristinamycin.

Links to other databases:

References:

1.	Khaw, L.E., Bohm, G.A., Metcalfe, S., Staunton, J. and Leadlay, P.F. Mutational biosynthesis of novel rapamycins by a strain of Streptomyces hygroscopicus NRRL 5491 disrupted in rapL, encoding a putative lysine cyclodeaminase. J. Bacteriol. 180 (1998) 809–814. [PMID: 9473033]
2.	Gatto, G.J., Jr., Boyne, M.T., 2nd, Kelleher, N.L. and Walsh, C.T. Biosynthesis of pipecolic acid by RapL, a lysine cyclodeaminase encoded in the rapamycin gene cluster. J. Am. Chem. Soc. 128 (2006) 3838–3847. [DOI] [PMID: 16536560]
3.	Tsotsou, G.E. and Barbirato, F. Biochemical characterisation of recombinant Streptomyces pristinaespiralis L-lysine cyclodeaminase. Biochimie 89 (2007) 591–604. [DOI] [PMID: 17291665]

[EC 4.3.1.28 created 2012]

4.3.2.6

Accepted name:

γ-L-glutamyl-butirosin B γ-glutamyl cyclotransferase

Reaction:

γ-L-glutamyl-butirosin B = butirosin B + 5-oxo-L-proline

Glossary:

γ-L-glutamyl-butirosin B = (1R,2R,3S,4R,6S)-6-amino-4-{[(2R)-4-(γ-L-glutamylamino)-2-hydroxybutanoyl]amino}-3-hydroxy-2-(α-D-ribofuranosyloxy)cyclohexyl

Other name(s):

btrG (gene name); γ-L-glutamyl-butirosin B γ-glutamyl cyclotransferase (5-oxoproline producing)

Systematic name:

γ-L-glutamyl-butirosin B γ-glutamyl cyclotransferase (5-oxo-L-proline producing)

Comments:

The enzyme catalyses the last step in the biosynthesis of the aminoglycoside antibiotic butirosin B. The enzyme acts as a cyclotransferase, cleaving the amide bond via transamidation using the α-amine of the terminal γ-L-glutamate of the side chain, releasing it as the cyclic 5-oxo-L-proline.

Links to other databases:

References:

1.	Llewellyn, N.M., Li, Y. and Spencer, J.B. Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain. Chem. Biol. 14 (2007) 379–386. [DOI] [PMID: 17462573]

[EC 4.3.2.6 created 2012]

4.3.3.7

Accepted name:

4-hydroxy-tetrahydrodipicolinate synthase

Reaction:

pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H₂O

For diagram of lysine biosynthesis (early stages), click here

Glossary:

(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate

Other name(s):

dihydrodipicolinate synthase (incorrect); dihydropicolinate synthetase (incorrect); dihydrodipicolinic acid synthase (incorrect); L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and cyclizing); dapA (gene name).

Systematic name:

L-aspartate-4-semialdehyde hydro-lyase [adding pyruvate and cyclizing; (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate-forming]

Comments:

The reaction can be divided into three consecutive steps: Schiff base formation with pyruvate, the addition of L-aspartate-semialdehyde, and finally transimination leading to cyclization with simultaneous dissociation of the product. The product of the enzyme was initially thought to be (S)-2,3-dihydrodipicolinate [1,2], and the enzyme was classified accordingly as EC 4.2.1.52, dihydrodipicolinate synthase. Later studies of the enzyme from the bacterium Escherichia coli have suggested that the actual product of the enzyme is (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate [3], and thus the enzyme has been reclassified as 4-hydroxy-tetrahydrodipicolinate synthase. However, the identity of the product is still controversial, as more recently it has been suggested that it may be (S)-2,3-dihydrodipicolinate after all [5].

Links to other databases:

References:

1.	Yugari, Y. and Gilvarg, C. The condensation step in diaminopimelate synthesis. J. Biol. Chem. 240 (1965) 4710–4716. [PMID: 5321309]
2.	Blickling, S., Renner, C., Laber, B., Pohlenz, H.D., Holak, T.A. and Huber, R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry 36 (1997) 24–33. [DOI] [PMID: 8993314]
3.	Devenish, S.R., Blunt, J.W. and Gerrard, J.A. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J. Med. Chem. 53 (2010) 4808–4812. [DOI] [PMID: 20503968]
4.	Soares da Costa, T.P., Muscroft-Taylor, A.C., Dobson, R.C., Devenish, S.R., Jameson, G.B. and Gerrard, J.A. How essential is the ’essential’ active-site lysine in dihydrodipicolinate synthase. Biochimie 92 (2010) 837–845. [DOI] [PMID: 20353808]
5.	Karsten, W.E., Nimmo, S.A., Liu, J. and Chooback, L. Identification of 2,3-dihydrodipicolinate as the product of the dihydrodipicolinate synthase reaction from Escherichia coli. Arch. Biochem. Biophys. 653 (2018) 50–62. [PMID: 29944868]

[EC 4.3.3.7 created 1972 as EC 4.2.1.52, transferred 2012 to EC 4.3.3.7, modified 2020]

4.4.1.26

Accepted name:

olivetolic acid cyclase

Reaction:

3,5,7-trioxododecanoyl-CoA = CoA + 2,4-dihydroxy-6-pentylbenzoate

For diagram of cannabinoid biosynthesis, click here

Glossary:

2,4-dihydroxy-6-pentylbenzoate = olivetolate

Other name(s):

OAC

Systematic name:

3,5,7-trioxododecanoyl-CoA CoA-lyase (2,4-dihydroxy-6-pentylbenzoate-forming)

Comments:

Part of the cannabinoids biosynthetic pathway in the plant Cannabis sativa.

Links to other databases:

References:

1.	Gagne, S.J., Stout, J.M., Liu, E., Boubakir, Z., Clark, S.M. and Page, J.E. Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides. Proc. Natl. Acad. Sci. USA 109 (2012) 12811–12816. [DOI] [PMID: 22802619]

[EC 4.4.1.26 created 2012]

*EC

5.1.3.14

Accepted name:

UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)

Reaction:

UDP-N-acetyl-α-D-glucosamine = UDP-N-acetyl-α-D-mannosamine

For diagram of UDP-N-acetylgalactosamine and UDP-N-acetylmannosamine biosynthesis, click here

Other name(s):

UDP-N-acetylglucosamine 2′-epimerase (ambiguous); uridine diphosphoacetylglucosamine 2′-epimerase (ambiguous); uridine diphospho-N-acetylglucosamine 2′-epimerase (ambiguous); uridine diphosphate-N-acetylglucosamine-2′-epimerase (ambiguous); rffE (gene name); mnaA (gene name); UDP-N-acetyl-D-glucosamine 2-epimerase

Systematic name:

UDP-N-acetyl-α-D-glucosamine 2-epimerase

Comments:

This bacterial enzyme catalyses the reversible interconversion of UDP-GlcNAc and UDP-ManNAc. The latter is used in a variety of bacterial polysaccharide biosyntheses. cf. EC 3.2.1.183, UDP-N-acetylglucosamine 2-epimerase (hydrolysing).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9037-71-2

References:

1.	Kawamura, T., Kimura, M., Yamamori, S. and Ito, E. Enzymatic formation of uridine diphosphate N-acetyl-D-mannosamine. J. Biol. Chem. 253 (1978) 3595–3601. [PMID: 418068]
2.	Meier-Dieter, U., Starman, R., Barr, K., Mayer, H. and Rick, P.D. Biosynthesis of enterobacterial common antigen in Escherichia coli. Biochemical characterization of Tn10 insertion mutants defective in enterobacterial common antigen synthesis. J. Biol. Chem. 265 (1990) 13490–13497. [PMID: 2166030]
3.	Morgan, P. M., Sala, R. F., and Tanner, M. E. Eliminations in the reactions catalyzed by UDP-N-acetylglucosamine 2-epimerase. J. Am. Chem. Soc. 119 (1997) 10269–10277.
4.	Campbell, R.E., Mosimann, S.C., Tanner, M.E. and Strynadka, N.C. The structure of UDP-N-acetylglucosamine 2-epimerase reveals homology to phosphoglycosyl transferases. Biochemistry 39 (2000) 14993–15001. [DOI] [PMID: 11106477]
5.	Samuel, J. and Tanner, M.E. Active site mutants of the "non-hydrolyzing" UDP-N-acetylglucosamine 2-epimerase from Escherichia coli. Biochim. Biophys. Acta 1700 (2004) 85–91. [DOI] [PMID: 15210128]
6.	Soldo, B., Lazarevic, V., Pooley, H.M. and Karamata, D. Characterization of a Bacillus subtilis thermosensitive teichoic acid-deficient mutant: gene mnaA (yvyH) encodes the UDP-N-acetylglucosamine 2-epimerase. J. Bacteriol. 184 (2002) 4316–4320. [DOI] [PMID: 12107153]

[EC 5.1.3.14 created 1976, modified 2012]

5.1.3.25

Accepted name:

dTDP-L-rhamnose 4-epimerase

Reaction:

dTDP-6-deoxy-β-L-talose = dTDP-β-L-rhamnose

Glossary:

dTDP-β-L-rhamnose = dTDP-6-deoxy-β-L-mannose
dTDP-6-deoxy-β-L-talose = dTDP-β-L-pneumose

Other name(s):

dTDP-4-L-rhamnose 4-epimerase; wbiB (gene name)

Systematic name:

dTDP-6-deoxy-β-L-talose 4-epimerase

Comments:

The equilibrium is strongly towards dTDP-β-L-rhamnose.

Links to other databases:

References:

1.	Yoo, H.G., Kwon, S.Y., Karki, S. and Kwon, H.J. A new route to dTDP-6-deoxy-L-talose and dTDP-L-rhamnose: dTDP-L-rhamnose 4-epimerase in Burkholderia thailandensis. Bioorg. Med. Chem. Lett. 21 (2011) 3914–3917. [DOI] [PMID: 21640586]

[EC 5.1.3.25 created 2012]

5.1.99.6

Accepted name:

NAD(P)H-hydrate epimerase

Reaction:

(1) (6R)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide
(2) (6R)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate

Glossary:

6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = NADHX = NADH-hydrate
6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = NADPHX = NADPH-hydrate

Other name(s):

NAD(P)HX epimerase

Systematic name:

(6R)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide 6-epimerase

Comments:

The enzyme can use either (R)-NADH-hydrate or (R)-NADPH-hydrate as a substrate. Its physiological role is to convert the (R) forms to the (S) forms, which could then be restored to active dinucleotides by EC 4.2.1.93, ATP-dependent NAD(P)H-hydrate dehydratase.

Links to other databases:

References:

1.	Marbaix, A.Y., Noel, G., Detroux, A.M., Vertommen, D., Van Schaftingen, E. and Linster, C.L. Extremely conserved ATP- or ADP-dependent enzymatic system for nicotinamide nucleotide repair. J. Biol. Chem. 286 (2011) 41246–41252. [DOI] [PMID: 21994945]

[EC 5.1.99.6 created 2012]

5.2.1.14

Accepted name:

β-carotene isomerase

Reaction:

all-trans-β-carotene = 9-cis-β-carotene

For diagram of strigol biosynthesis, click here

Other name(s):

DWARF27 (gene name)

Systematic name:

β-carotene 9-cis-all-trans isomerase

Comments:

The enzyme participates in a pathway leading to biosynthesis of strigolactones, plant hormones involved in promotion of symbiotic associations known as arbuscular mycorrhiza.

Links to other databases:

References:

1.	Lin, H., Wang, R., Qian, Q., Yan, M., Meng, X., Fu, Z., Yan, C., Jiang, B., Su, Z., Li, J. and Wang, Y. DWARF27, an iron-containing protein required for the biosynthesis of strigolactones, regulates rice tiller bud outgrowth. Plant Cell 21 (2009) 1512–1525. [DOI] [PMID: 19470589]
2.	Alder, A., Jamil, M., Marzorati, M., Bruno, M., Vermathen, M., Bigler, P., Ghisla, S., Bouwmeester, H., Beyer, P. and Al-Babili, S. The path from β-carotene to carlactone, a strigolactone-like plant hormone. Science 335 (2012) 1348–1351. [DOI] [PMID: 22422982]

[EC 5.2.1.14 created 2012]

5.3.2.6

Accepted name:

2-hydroxymuconate tautomerase

Reaction:

(2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (3E)-2-oxohex-3-enedioate

For diagram of catechol catabolism (meta ring cleavage), click here

Glossary:

(2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (2Z,4E)-2-hydroxymuconate

Other name(s):

4-oxalocrotonate tautomerase (misleading); 4-oxalocrotonate isomerase (misleading); cnbG (gene name); praC (gene name); xylH (gene name)

Systematic name:

(2Z,4E)-2-hydroxyhexa-2,4-dienedioate keto—enol isomerase

Comments:

Involved in the meta-cleavage pathway for the degradation of phenols, modified phenols and catechols. The enol form (2Z,4E)-2-hydroxyhexa-2,4-dienedioate is produced as part of this pathway and is converted to the keto form (3E)-2-oxohex-3-enedioate by the enzyme [6]. Another keto form, (4E)-2-oxohex-4-enedioate (4-oxalocrotonate), was originally thought to be produced by the enzyme [1,2] but later shown to be produced non-enzymically [5].

Links to other databases:

References:

1.	Whitman, C.P., Aird, B.A., Gillespie, W.R. and Stolowich, N.J. Chemical and enzymatic ketonization of 2-hydroxymuconate, a conjugated enol. J. Am. Chem. Soc. 113 (1991) 3154–3162.
2.	Whitman, C.P., Hajipour, G., Watson, R.J., Johnson, W.H., Jr., Bembenek, M.E. and Stolowich, N.J. Stereospecific ketonization of 2-hydroxymuconate by 4-oxalocrotonate tautomerase and 5-(carboxymethyl)-2-hydroxymuconate isomerase. J. Am. Chem. Soc. 114 (1992) 10104–10110.
3.	Subramanya, H.S., Roper, D.I., Dauter, Z., Dodson, E.J., Davies, G.J., Wilson, K.S. and Wigley, D.B. Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases. Biochemistry 35 (1996) 792–802. [DOI] [PMID: 8547259]
4.	Stivers, J.T., Abeygunawardana, C., Mildvan, A.S., Hajipour, G., Whitman, C.P. and Chen, L.H. Catalytic role of the amino-terminal proline in 4-oxalocrotonate tautomerase: affinity labeling and heteronuclear NMR studies. Biochemistry 35 (1996) 803–813. [DOI] [PMID: 8547260]
5.	Wang, S.C., Johnson, W.H., Jr., Czerwinski, R.M., Stamps, S.L. and Whitman, C.P. Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions. Biochemistry 46 (2007) 11919–11929. [DOI] [PMID: 17902707]
6.	Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758–6768. [DOI] [PMID: 19717587]

[EC 5.3.2.6 created 2012]

5.4.3.9

Accepted name:

glutamate 2,3-aminomutase

Reaction:

L-glutamate = 3-aminopentanedioate

Glossary:

3-aminopentanedioate = isoglutamate

Systematic name:

L-glutamate 2,3-aminomutase

Comments:

This enzyme is a member of the ’AdoMet radical’ (radical SAM) family. It contains pyridoxal phosphate and a [4Fe-4S] cluster, which is coordinated by 3 cysteines and binds an exchangeable S-adenosyl-L-methionine molecule. During the reaction cycle, the AdoMet forms a 5′-deoxyadenosyl radical, which is regenerated at the end of the reaction.

Links to other databases:

References:

1.	Ruzicka, F.J. and Frey, P.A. Glutamate 2,3-aminomutase: a new member of the radical SAM superfamily of enzymes. Biochim. Biophys. Acta 1774 (2007) 286–296. [DOI] [PMID: 17222594]

[EC 5.4.3.9 created 2012]

5.4.99.58

Accepted name:

methylornithine synthase

Reaction:

L-lysine = (3R)-3-methyl-D-ornithine

Glossary:

(3R)-3-methyl-D-ornithine = (2R,3R)-2,5-diamino-3-methylpentanoate

Other name(s):

PylB

Systematic name:

L-lysine carboxy-aminomethylmutase

Comments:

The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes. Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The reaction is part of the biosynthesis pathway of pyrrolysine, a naturally occurring amino acid found in some archaeal methyltransferases.

Links to other databases:

References:

1.	Gaston, M.A., Zhang, L., Green-Church, K.B. and Krzycki, J.A. The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature 471 (2011) 647–650. [DOI] [PMID: 21455182]
2.	Quitterer, F., List, A., Eisenreich, W., Bacher, A. and Groll, M. Crystal structure of methylornithine synthase (PylB): insights into the pyrrolysine biosynthesis. Angew. Chem. Int. Ed. Engl. 51 (2012) 1339–1342. [DOI] [PMID: 22095926]

[EC 5.4.99.58 created 2012]

*EC

5.5.1.12

Accepted name:

copalyl diphosphate synthase

Reaction:

geranylgeranyl diphosphate = (+)-copalyl diphosphate

For diagram of abietadiene, abietate, isopimaradiene, labdadienol and sclareol biosynthesis, click here, for diagram of labdane diterpenoids biosynthesis, click here and for diagram of pimarane diterpenoids biosynthesis, click here

Other name(s):

(+)-copalyl-diphosphate lyase (decyclizing)

Systematic name:

(+)-copalyl-diphosphate lyase (ring-opening)

Comments:

In some plants, such as Salvia miltiorrhiza, this enzyme is monofunctional. In other plants this activity is often a part of a bifunctional enzyme. For example, in Selaginella moellendorffii this activity is catalysed by a bifunctional enzyme that also catalyses EC 4.2.3.131, miltiradiene synthase, while in the tree Abies grandis (grand fir) it is catalysed by a bifunctional enzyme that also catalyses EC 4.2.3.18, abietadiene synthase.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 157972-08-2

References:

1.	Peters, R.J., Ravn, M.M., Coates, R.M. and Croteau, R.B. Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites. J. Am. Chem. Soc. 123 (2001) 8974–8978. [DOI] [PMID: 11552804]
2.	Sugai, Y., Ueno, Y., Hayashi, K., Oogami, S., Toyomasu, T., Matsumoto, S., Natsume, M., Nozaki, H. and Kawaide, H. Enzymatic ¹³C labeling and multidimensional NMR analysis of miltiradiene synthesized by bifunctional diterpene cyclase in Selaginella moellendorffii. J. Biol. Chem. 286 (2011) 42840–42847. [DOI] [PMID: 22027823]
3.	Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement. Proc. Natl. Acad. Sci. USA 99 (2002) 580–584. [DOI] [PMID: 11805316]
4.	Ravn, M.M., Peters, R.J., Coates, R.M. and Croteau, R. Mechanism of abietadiene synthase catalysis: stereochemistry and stabilization of the cryptic pimarenyl carbocation intermediates. J. Am. Chem. Soc. 124 (2002) 6998–7006. [DOI] [PMID: 12059223]
5.	Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate. Biochemistry 41 (2002) 1836–1842. [DOI] [PMID: 11827528]

[EC 5.5.1.12 created 2002, modified 2012]

6.1.1.25

Deleted entry:

lysine—tRNA^Pyl ligase. The tRNA^Pyl is now known only to be charged with pyrrolysine (cf. EC 6.1.1.26).

[EC 6.1.1.25 created 2002, deleted 2012]

6.2.1.39

Accepted name:

[butirosin acyl-carrier protein]—L-glutamate ligase

Reaction:

(1) ATP + L-glutamate + BtrI acyl-carrier protein = ADP + phosphate + L-glutamyl-[BtrI acyl-carrier protein]
(2) ATP + L-glutamate + 4-amino butanoyl-[BtrI acyl-carrier protein] = ADP + phosphate + 4-(γ-L-glutamylamino)butanoyl-[BtrI acyl-carrier protein]

Other name(s):

[BtrI acyl-carrier protein]—L-glutamate ligase; BtrJ

Systematic name:

[BtrI acyl-carrier protein]:L-glutamate ligase (ADP-forming)

Comments:

Catalyses two steps in the biosynthesis of the side chain of the aminoglycoside antibiotics of the butirosin family. The enzyme adds one molecule of L-glutamate to a dedicated acyl-carrier protein, and following decarboxylation of the product by EC 4.1.1.95, L-glutamyl-[BtrI acyl-carrier protein] decarboxylase, adds a second L-glutamate molecule. Requires Mg²⁺ or Mn²⁺, and activity is enhanced in the presence of Mn²⁺.

Links to other databases:

References:

1.	Li, Y., Llewellyn, N.M., Giri, R., Huang, F. and Spencer, J.B. Biosynthesis of the unique amino acid side chain of butirosin: possible protective-group chemistry in an acyl carrier protein-mediated pathway. Chem. Biol. 12 (2005) 665–675. [DOI] [PMID: 15975512]

[EC 6.2.1.39 created 2012]

6.3.2.27

Deleted entry:

The activity is covered by two independent enzymes, EC 6.3.2.38 N²-citryl-N⁶-acetyl-N⁶-hydroxylysine synthase, and EC 6.3.2.39, aerobactin synthase

[EC 6.3.2.27 created 2002, modified 2006, deleted 2012]

6.3.2.38

Accepted name:

N²-citryl-N⁶-acetyl-N⁶-hydroxylysine synthase

Reaction:

2 ATP + citrate + N⁶-acetyl-N⁶-hydroxy-L-lysine + H₂O = 2 ADP + 2 phosphate + N⁶-acetyl-N²-citryl-N⁶-hydroxy-L-lysine

For diagram of aerobactin biosynthesis, click here

Glossary:

citryl = 3-hydroxy-3,4-dicarboxybutanoyl

Other name(s):

N^α-citryl-N^ε-acetyl-N^ε-hydroxylysine synthase; iucA (gene name)

Systematic name:

citrate:N⁶-acetyl-N⁶-hydroxy-L-lysine ligase (AMP-forming)

Comments:

Requires Mg²⁺. The enzyme is involved in the biosynthesis of aerobactin, a dihydroxamate siderophore. It belongs to a class of siderophore synthases known as type A nonribosomal peptide synthase-independent synthases (NIS). Type A enzymes are responsible for the formation of amide or ester bonds between polyamines or amino alcohols and a prochiral carboxyl group of citrate. The enzyme is believed to form an adenylate intermediate prior to ligation.

Links to other databases:

References:

1.	Gibson, F. and Magrath, D.I. The isolation and characterization of a hydroxamic acid (aerobactin) formed by Aerobacter aerogenes 62-I. Biochim. Biophys. Acta 192 (1969) 175–184. [DOI] [PMID: 4313071]
2.	Maurer, P.J. and Miller, M. Microbial iron chelators: total synthesis of aerobactin and its constituent amino acid, N⁶-acetyl-N⁶-hydroxylysine. J. Am. Chem. Soc. 104 (1982) 3096–3101.
3.	de Lorenzo, V., Bindereif, A., Paw, B.H. and Neilands, J.B. Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12. J. Bacteriol. 165 (1986) 570–578. [DOI] [PMID: 2935523]
4.	Appanna, D.L., Grundy, B.J., Szczepan, E.W. and Viswanatha, T. Aerobactin synthesis in a cell-free system of Aerobacter aerogenes 62-1. Biochim. Biophys. Acta 801 (1984) 437–443.
5.	Challis, G.L. A widely distributed bacterial pathway for siderophore biosynthesis independent of nonribosomal peptide synthetases. ChemBioChem 6 (2005) 601–611. [DOI] [PMID: 15719346]
6.	Oves-Costales, D., Kadi, N. and Challis, G.L. The long-overlooked enzymology of a nonribosomal peptide synthetase-independent pathway for virulence-conferring siderophore biosynthesis. Chem. Commun. (Camb.) (2009) 6530–6541. [PMID: 19865642]

[EC 6.3.2.38 created 2012, modified 2019]

6.3.2.39

Accepted name:

aerobactin synthase

Reaction:

ATP + N²-citryl-N⁶-acetyl-N⁶-hydroxy-L-lysine + N⁶-acetyl-N⁶-hydroxy-L-lysine = AMP + diphosphate + aerobactin

For diagram of aerobactin biosynthesis, click here

Other name(s):

iucC (gene name)

Systematic name:

N²-citryl-N⁶-acetyl-N⁶-hydroxy-L-lysine:N⁶-acetyl-N⁶-hydroxy-L-lysine ligase (AMP-forming)

Comments:

Requires Mg²⁺. The enzyme is involved in the biosynthesis of aerobactin, a dihydroxamate siderophore. It belongs to a class of siderophore synthases known as type C nonribosomal peptide synthase-independent synthases (NIS). Type C enzymes are responsible for the formation of amide or ester bonds between a variety of substrates and a prochiral carboxyl group of a citrate molecule that is already linked to a different moiety at its other prochiral carboxyl group. The enzyme is believed to form an adenylate intermediate prior to ligation.

Links to other databases: