Proposed Changes to the Enzyme List

References:

1.	Brinkmann-Chen, S., Cahn, J.K. and Arnold, F.H. Uncovering rare NADH-preferring ketol-acid reductoisomerases. Metab. Eng. 26C (2014) 17–22. [DOI] [PMID: 25172159]

[EC 1.1.1.382 created 2015]

1.1.1.383

Accepted name:

ketol-acid reductoisomerase [NAD(P)⁺]

Reaction:

(2R)-2,3-dihydroxy-3-methylbutanoate + NAD(P)⁺ = (2S)-2-hydroxy-2-methyl-3-oxobutanoate + NAD(P)H + H⁺

Glossary:

(2S)-2-hydroxy-2-methyl-3-oxobutanoate = (2S)-2-acetolactate

Systematic name:

(2R)-2,3-dihydroxy-3-methylbutanoate:NAD(P)⁺ oxidoreductase (isomerizing)

Comments:

The enzyme, characterized from the bacteria Hydrogenobaculum sp. and Syntrophomonas wolfei subsp. wolfei and from the archaea Metallosphaera sedula and Ignisphaera aggregans, can use both NADH and NADPH with similar efficiency [cf. EC 1.1.1.86, ketol-acid reductoisomerase (NADP⁺) and EC 1.1.1.382, ketol-acid reductoisomerase (NAD⁺)].

Links to other databases:

BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9075-02-9

References:

1.	Brinkmann-Chen, S., Cahn, J.K. and Arnold, F.H. Uncovering rare NADH-preferring ketol-acid reductoisomerases. Metab. Eng. 26C (2014) 17–22. [DOI] [PMID: 25172159]

[EC 1.1.1.383 created 2015]

1.1.1.384

Accepted name:

dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose 3-reductase

Reaction:

dTDP-4-dehydro-2,6-dideoxy-α-D-glucose + NADP⁺ = dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose + NADPH + H⁺

For diagram of dTDP-forosamine biosynthesis, click here

Glossary:

dTDP-4-dehydro-2,6-dideoxy-α-D-glucose = dTDP-2,6-dideoxy-α-D-threo-hexopyranos-4-ulose
dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose = thymidine 5′-[(2R,6R)-6-methyl-4,5-dioxotetrahydro-2H-pyran-2-yl] diphosphate

Other name(s):

KijD10; dTDP-4-keto-2,6-dideoxy-D-glucose 3-oxidoreductase; dTDP-4-dehydro-2,6-dideoxy-α-D-glucose 3-oxidoreductase

Systematic name:

dTDP-4-dehydro-2,6-dideoxy-α-D-glucose:NADP⁺ 3-oxidoreductase

Comments:

The enzyme is involved in the biosynthesis of several deoxysugars, including L-digitoxose, L- and D-olivose, L-oliose, D-mycarose and forosamine.

Links to other databases:

References:

1.	Aguirrezabalaga, I., Olano, C., Allende, N., Rodriguez, L., Brana, A.F., Mendez, C. and Salas, J.A. Identification and expression of genes involved in biosynthesis of L-oleandrose and its intermediate L-olivose in the oleandomycin producer Streptomyces antibioticus. Antimicrob. Agents Chemother. 44 (2000) 1266–1275. [DOI] [PMID: 10770761]
2.	Wang, L., White, R.L. and Vining, L.C. Biosynthesis of the dideoxysugar component of jadomycin B: genes in the jad cluster of Streptomyces venezuelae ISP5230 for L-digitoxose assembly and transfer to the angucycline aglycone. Microbiology 148 (2002) 1091–1103. [DOI] [PMID: 11932454]
3.	Hong, L., Zhao, Z., Melancon, C.E., 3rd, Zhang, H. and Liu, H.W. In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J. Am. Chem. Soc. 130 (2008) 4954–4967. [DOI] [PMID: 18345667]
4.	Kubiak, R.L. and Holden, H.M. Combined structural and functional investigation of a C-3′′-ketoreductase involved in the biosynthesis of dTDP-L-digitoxose. Biochemistry 50 (2011) 5905–5917. [DOI] [PMID: 21598943]

[EC 1.1.1.384 created 2015]

1.1.1.385

Accepted name:

dihydroanticapsin dehydrogenase

Reaction:

L-dihydroanticapsin + NAD⁺ = L-anticapsin + NADH + H⁺

For diagram of bacilysin biosynthesis, click here

Glossary:

L-dihydroanticapsin = 3-[(1R,2S,5R,6S)-5-hydroxy-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine

Other name(s):

BacC; ywfD (gene name)

Systematic name:

L-dihydroanticapsin:NAD⁺ oxidoreductase

Comments:

The enzyme, characterized from the bacterium Bacillus subtilis, is involved in the biosynthesis of the nonribosomally synthesized dipeptide antibiotic bacilysin, composed of L-alanine and L-anticapsin.

Links to other databases:

References:

1.	Parker, J.B. and Walsh, C.T. Action and timing of BacC and BacD in the late stages of biosynthesis of the dipeptide antibiotic bacilysin. Biochemistry 52 (2013) 889–901. [DOI] [PMID: 23317005]

[EC 1.1.1.385 created 2015]

1.1.1.386

Accepted name:

ipsdienol dehydrogenase

Reaction:

(R)-ipsdienol + NAD(P)⁺ = ipsdienone + NAD(P)H + H⁺

For diagram of acyclic monoterpenoid biosynthesis, click here

Glossary:

ipsdienone = 2-methyl-6-methyleneocta-2,7-dien-4-one
(R)-ipsdienol = (4R)-2-methyl-6-methyleneocta-2,7-dien-4-ol

Other name(s):

IDOLDH

Systematic name:

(R)-ipsdienol:NAD(P)⁺ oxidoreductase

Comments:

The enzyme is involved in pheromone production by the pine engraver beetle, Ips pini.

Links to other databases:

References:

1.	Figueroa-Teran, R., Welch, W.H., Blomquist, G.J. and Tittiger, C. Ipsdienol dehydrogenase (IDOLDH): a novel oxidoreductase important for Ips pini pheromone production. Insect Biochem. Mol. Biol. 42 (2012) 81–90. [DOI] [PMID: 22101251]

[EC 1.1.1.386 created 2015]

1.2.5.2

Accepted name:

aldehyde dehydrogenase (quinone)

Reaction:

an aldehyde + a quinone + H₂O = a carboxylate + a quinol

Other name(s):

aldehyde dehydrogenase (acceptor)

Systematic name:

aldehyde:quinone oxidoreductase

Comments:

Wide specificity; acts on straight-chain aldehydes up to C₁₀, aromatic aldehydes, glyoxylate and glyceraldehyde. The enzymes contains a PQQ cofactor and multiple hemes that deliver the electrons to the membrane quinone pool.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, CAS registry number: 75536-77-5

References:

1.	Ameyama, M. and Adachi, O. Aldehyde dehydrogenase from acetic acid bacteria, membrane-bound. Methods Enzymol. 89 (1982) 491–497.
2.	Ameyama, M., Osada, K., Shinagawa, E., Matsushita, K. and Adachi, O. Purification and characterization of aldehyde dehydrogenase of Acetobacter aceti. Agric. Biol. Chem. 45 (1981) 1189–1890.
3.	Patel, R.N., Hou, C.T., Derelanko, P. and Felix, A. Purification and properties of a heme-containing aldehyde dehydrogenase from Methylosinus trichosporium. Arch. Biochem. Biophys. 203 (1980) 654–662. [DOI] [PMID: 6779711]
4.	Gomez-Manzo, S., Chavez-Pacheco, J.L., Contreras-Zentella, M., Sosa-Torres, M.E., Arreguin-Espinosa, R., Perez de la Mora, M., Membrillo-Hernandez, J. and Escamilla, J.E. Molecular and catalytic properties of the aldehyde dehydrogenase of Gluconacetobacter diazotrophicus, a quinoheme protein containing pyrroloquinoline quinone, cytochrome b, and cytochrome c. J. Bacteriol. 192 (2010) 5718–5724. [DOI] [PMID: 20802042]

[EC 1.2.5.2 created 1983 as EC 1.2.99.3, modified 1989, transferred 2015 to EC 1.2.5.2 ]

1.2 Acting on the aldehyde or oxo group of donors

1.2.98 With other, known, physiological acceptors

1.2.98.1

Accepted name:

formaldehyde dismutase

Reaction:

2 formaldehyde + H₂O = formate + methanol

Other name(s):

aldehyde dismutase; cannizzanase; nicotinoprotein aldehyde dismutase

Systematic name:

formaldehyde:formaldehyde oxidoreductase

Comments:

The enzyme contains a tightly but noncovalently bound NADP(H) cofactor, as well as Zn²⁺ and Mg²⁺. Enzyme-bound NADPH formed by oxidation of formaldehyde to formate is oxidized back to NADP⁺ by reaction with a second formaldehyde, yielding methanol. The enzyme from the bacterium Mycobacterium sp. DSM 3803 also catalyses the reactions of EC 1.1.99.36, alcohol dehydrogenase (nicotinoprotein) and EC 1.1.99.37, methanol dehydrogenase (nicotinoprotein) [3]. Formaldehyde and acetaldehyde can act as donors; formaldehyde, acetaldehyde and propanal can act as acceptors [1,2].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 85204-94-0

References:

1.	Kato, N., Shirakawa, K., Kobayashi, H. and Sakazawa, C. The dismutation of aldehydes by a bacterial enzyme. Agric. Biol. Chem. 47 (1983) 39–46.
2.	Kato, N., Yamagami, T., Shimao, M. and Sakazawa, C. Formaldehyde dismutase, a novel NAD-binding oxidoreductase from Pseudomonas putida F61. Eur. J. Biochem. 156 (1986) 59–64. [DOI] [PMID: 3514215]
3.	Park, H., Lee, H., Ro, Y.T. and Kim, Y.M. Identification and functional characterization of a gene for the methanol : N,N′-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). Microbiology 156 (2010) 463–471. [DOI] [PMID: 19875438]

[EC 1.2.98.1 created 1986 as EC 1.2.99.4, modified 2012, transferred 2015 to EC 1.2.98.1]

1.2.99.3

Transferred entry:

aldehyde dehydrogenase (pyrroloquinoline-quinone). Now EC 1.2.5.2, aldehyde dehydrogenase (quinone)

[EC 1.2.99.3 created 1983, modified 1989, deleted 2015]

1.2.99.4

Transferred entry:

formaldehyde dismutase. Now EC 1.2.98.1, formaldehyde dismutase.

[EC 1.2.99.4 created 1986, modified 2012, deleted 2015]

1.3.8.12

Accepted name:

(2S)-methylsuccinyl-CoA dehydrogenase

Reaction:

(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein = 2-methylfumaryl-CoA + reduced electron-transfer flavoprotein

Glossary:

2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA

Other name(s):

Mcd

Systematic name:

(2S)-methylsuccinyl-CoA:electron-transfer flavoprotein oxidoreductase

Comments:

The enzyme, characterized from the bacterium Rhodobacter sphaeroides, is involved in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. The enzyme contains FAD.

Links to other databases:

References:

1.	Erb, T.J., Fuchs, G. and Alber, B.E. (2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. Mol. Microbiol. 73 (2009) 992–1008. [DOI] [PMID: 19703103]

[EC 1.3.8.12 created 2015]

*EC

1.5.1.1

Accepted name:

1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H]

Reaction:

(1) L-pipecolate + NAD(P)⁺ = 1-piperideine-2-carboxylate + NAD(P)H + H⁺
(2) L-proline + NAD(P)⁺ = 1-pyrroline-2-carboxylate + NAD(P)H + H⁺

Other name(s):

Δ¹-pyrroline-2-carboxylate reductase; DELTA1-pyrroline-2-carboxylate reductase; DELTA1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (ambiguous); AbLhpI; pyrroline-2-carboxylate reductase; L-proline:NAD(P)⁺ 2-oxidoreductase

Systematic name:

L-pipecolate/L-proline:NAD(P)⁺ 2-oxidoreductase

Comments:

The enzymes, characterized from the bacterium Azospirillum brasilense, is involved in trans-3-hydroxy-L-proline metabolism. In contrast to EC 1.5.1.21, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH), which is specific for NADPH, this enzyme shows similar activity with NADPH and NADH.

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, CAS registry number: 9029-16-7

References:

1.	Meister, A., Radhakrishnan, A.N. and Buckley, S.D. Enzymatic synthesis of L-pipecolic acid and L-proline. J. Biol. Chem. 229 (1957) 789–800. [PMID: 13502341]
2.	Watanabe, S., Tanimoto, Y., Yamauchi, S., Tozawa, Y., Sawayama, S. and Watanabe, Y. Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Δ¹-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria. FEBS Open Bio 4 (2014) 240–250. [DOI] [PMID: 24649405]

[EC 1.5.1.1 created 1961, modified 2015]

*EC

1.5.1.21

Accepted name:

1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH)

Reaction:

(1) L-pipecolate + NADP⁺ = 1-piperideine-2-carboxylate + NADPH + H⁺
(2) L-proline + NADP⁺ = 1-pyrroline-2-carboxylate + NADPH + H⁺

Glossary:

1-piperideine-2-carboxylate = 3,4,5,6-tetrahydropyridine-2-carboxylate

Other name(s):

Pyr2C reductase; 1,2-didehydropipecolate reductase; P₂C reductase; 1,2-didehydropipecolic reductase; DELTA1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (ambiguous); L-pipecolate:NADP⁺ 2-oxidoreductase; DELTA1-piperideine-2-carboxylate reductase; Δ¹-piperideine-2-carboxylate reductase

Systematic name:

L-pipecolate/L-proline:NADP⁺ 2-oxidoreductase

Comments:

The enzyme is involved in the catabolism of D-lysine and D-proline in bacteria that belong to the Pseudomonas genus. In contrast to EC 1.5.1.1, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H], which shows similar activity with NADPH and NADH, this enzyme is specific for NADPH.

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 52037-88-4

References:

1.	Payton, C.W. and Chang, Y.-F. Δ¹-Piperideine-2-carboxylate reductase of Pseudomonas putida. J. Bacteriol. 149 (1982) 864–871. [PMID: 6801013]
2.	Muramatsu, H., Mihara, H., Kakutani, R., Yasuda, M., Ueda, M., Kurihara, T. and Esaki, N. The putative malate/lactate dehydrogenase from Pseudomonas putida is an NADPH-dependent Δ¹-piperideine-2-carboxylate/Δ¹-pyrroline-2-carboxylate reductase involved in the catabolism of D-lysine and D-proline. J. Biol. Chem. 280 (2005) 5329–5335. [DOI] [PMID: 15561717]
3.	Watanabe, S., Tanimoto, Y., Yamauchi, S., Tozawa, Y., Sawayama, S. and Watanabe, Y. Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Δ¹-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria. FEBS Open Bio 4 (2014) 240–250. [DOI] [PMID: 24649405]

[EC 1.5.1.21 created 1984 (EC 1.5.1.14 created 1976, incorporated 1989), modified 2015]

1.5.1.49

Accepted name:

1-pyrroline-2-carboxylate reductase [NAD(P)H]

Reaction:

L-proline + NAD(P)⁺ = 1-pyrroline-2-carboxylate + NAD(P)H + H⁺

Systematic name:

L-proline:NAD(P)⁺ 2-oxidoreductase

Comments:

The enzyme from the bacterium Colwellia psychrerythraea is involved in trans-3-hydroxy-L-proline metabolism. In contrast to EC 1.5.1.1, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H], which shows similar activity with 1-piperideine-2-carboxylate and 1-pyrroline-2-carboxylate, this enzyme is specific for the latter. While the enzyme is active with both NADH and NADPH, activity is higher with NADPH.

Links to other databases:

References:

Watanabe, S., Tanimoto, Y., Yamauchi, S., Tozawa, Y., Sawayama, S. and Watanabe, Y. Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Δ¹-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria. FEBS Open Bio 4 (2014) 240–250. [DOI] [PMID: 24649405]

[EC 1.5.1.49 created 2015]

1.6.5.11

Deleted entry:

NADH dehydrogenase (quinone). Identical to EC 1.6.5.9, NADH:quinone reductase (non-electrogenic)

[EC 1.6.5.11 created 1972 as EC 1.6.99.5, transferred 2015 to EC 1.6.5.11, deleted 2019]

1.6.99.5

Transferred entry:

NADH dehydrogenase (quinone). Transferred to EC 1.6.5.11, NADH dehydrogenase (quinone)

[EC 1.6.99.5 created 1972, deleted 2014]

*EC

1.7.3.6

Accepted name:

hydroxylamine oxidase (cytochrome)

Reaction:

hydroxylamine + O₂ = nitrite + H₂O + H⁺ (overall reaction)
(1a) hydroxylamine + 2 ferricytochrome c = nitroxyl + 2 ferrocytochrome c + 2 H⁺
(1b) nitroxyl + 2 ferrocytochrome c + O₂ + H⁺ = nitrite + 2 ferricytochrome c + H₂O (spontaneous)

Other name(s):

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

Systematic name:

hydroxylamine:oxygen oxidoreductase

Comments:

The enzyme from the heterotrophic nitrifying bacterium Paracoccus denitrificans contains three to five non-heme, non-iron-sulfur iron atoms and interacts with cytochrome c₅₅₆ and pseudoazurin [2,3]. Under anaerobic conditions in vitro only nitrous oxide is formed [3]. Presumably nitroxyl is released and combines with a second nitroxyl to give nitrous oxide and water. When oxygen is present, nitrite is formed.

Links to other databases:

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

References:

1.	Kurokawa, M, Fukumori, Y and Yamanaka, T A hydroxylamine - cytochrome c reductase occurs in the heterotrophic nitrifier Arthrobacter globiformis. Plant Cell Physiol. 26 (1985) 1439–1442.
2.	Wehrfritz, J.M., Reilly, A., Spiro, S. and Richardson, D.J. Purification of hydroxylamine oxidase from Thiosphaera pantotropha. Identification of electron acceptors that couple heterotrophic nitrification to aerobic denitrification. FEBS Lett. 335 (1993) 246–250. [DOI] [PMID: 8253206]
3.	Moir, J.W., Wehrfritz, J.M., Spiro, S. and Richardson, D.J. The biochemical characterization of a novel non-haem-iron hydroxylamine oxidase from Paracoccus denitrificans GB17. Biochem. J. 319 (1996) 823–827. [PMID: 8920986]
4.	Wehrfritz, J., Carter, J.P., Spiro, S. and Richardson, D.J. Hydroxylamine oxidation in heterotrophic nitrate-reducing soil bacteria and purification of a hydroxylamine-cytochrome c oxidoreductase from a Pseudomonas species. Arch. Microbiol. 166 (1996) 421–424. [PMID: 9082922]

[EC 1.7.3.6 created 1972 as EC 1.7.3.4, part transferred 2013 to EC 1.7.3.6, modified 2015]

1.10 Acting on diphenols and related substances as donors

1.10.5 With a quinone or related compound as acceptor

1.10.5.1

Accepted name:

ribosyldihydronicotinamide dehydrogenase (quinone)

Reaction:

1-(β-D-ribofuranosyl)-1,4-dihydronicotinamide + a quinone = 1-(β-D-ribofuranosyl)nicotinamide + a quinol

For diagram of reaction, click here

Other name(s):

NRH:quinone oxidoreductase 2; NQO2; NAD(P)H:quinone oxidoreductase-2 (misleading); QR2; quinone reductase 2; N-ribosyldihydronicotinamide dehydrogenase (quinone); NAD(P)H:quinone oxidoreductase2 (misleading)

Systematic name:

1-(β-D-ribofuranosyl)-1,4-dihydronicotinamide:quinone oxidoreductase

Comments:

A flavoprotein. Unlike EC 1.6.5.2, NAD(P)H dehydrogenase (quinone), this quinone reductase cannot use NADH or NADPH; instead it uses N-ribosyl- and N-alkyldihydronicotinamides. Polycyclic aromatic hydrocarbons, such as benz[a]anthracene, and the estrogens 17β-estradiol and diethylstilbestrol are potent inhibitors, but dicoumarol is only a very weak inhibitor [2]. This enzyme can catalyse both 2-electron and 4-electron reductions, but one-electron acceptors, such as potassium ferricyanide, cannot be reduced [3].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 667919-86-0

References:

1.	Liao, S., Dulaney, J.T. and Williams-Ashman, H.G. Purification and properties of a flavoprotein catalyzing the oxidation of reduced ribosyl nicotinamide. J. Biol. Chem. 237 (1962) 2981–2987. [PMID: 14465018]
2.	Zhao, Q., Yang, X.L., Holtzclaw, W.D. and Talalay, P. Unexpected genetic and structural relationships of a long-forgotten flavoenzyme to NAD(P)H:quinone reductase (DT-diaphorase). Proc. Natl. Acad. Sci. USA 94 (1997) 1669–1674. [DOI] [PMID: 9050836]
3.	Wu, K., Knox, R., Sun, X.Z., Joseph, P., Jaiswal, A.K., Zhang, D., Deng, P.S. and Chen, S. Catalytic properties of NAD(P)H:quinone oxidoreductase-2 (NQO₂), a dihydronicotinamide riboside dependent oxidoreductase. Arch. Biochem. Biophys. 347 (1997) 221–228. [DOI] [PMID: 9367528]
4.	Jaiswal, A.K. Human NAD(P)H:quinone oxidoreductase2. Gene structure, activity, and tissue-specific expression. J. Biol. Chem. 269 (1994) 14502–14508. [PMID: 8182056]

[EC 1.10.5.1 created 2005 as EC 1.10.99.2, transferred 2015 to EC 1.10.5.1]

1.10.99.2

Transferred entry:

ribosyldihydronicotinamide dehydrogenase (quinone). Now classified as EC 1.10.5.1, ribosyldihydronicotinamide dehydrogenase (quinone).

[EC 1.10.99.2 created 2005, deleted 2014]

1.10.99.3

Transferred entry:

violaxanthin de-epoxidase. Now classified as EC 1.23.5.1, violaxanthin de-epoxidase.

[EC 1.10.99.3 created 2005, deleted 2014]

*EC

1.11.1.19

Accepted name:

dye decolorizing peroxidase

Reaction:

Reactive Blue 5 + 2 H₂O₂ = phthalate + 2,2′-disulfonyl azobenzene + 3-[(4-amino-6-chloro-1,3,5-triazin-2-yl)amino]benzenesulfonate + 2 H₂O

Glossary:

Reactive Blue 5 = 1-amino-4-{[3-({4-chloro-6-[(3-sulfophenyl)amino]-1,3,5-triazin-2-yl}amino)-4-sulfophenyl]amino}-9,10-dihydro-9,10-dioxoanthracene-2-sulfonic acid

Other name(s):

DyP; DyP-type peroxidase

Systematic name:

Reactive-Blue-5:hydrogen-peroxide oxidoreductase

Comments:

Heme proteins with proximal histidine secreted by basidiomycetous fungi and eubacteria. They are similar to EC 1.11.1.16 versatile peroxidase (oxidation of Reactive Black 5, phenols, veratryl alcohol), but differ from the latter in their ability to efficiently oxidize a number of recalcitrant anthraquinone dyes, and inability to oxidize Mn(II). The model substrate Reactive Blue 5 is converted with high efficiency via a so far unique mechanism that combines oxidative and hydrolytic steps and leads to the formation of phthalic acid. Bacterial TfuDyP catalyses sulfoxidation.

Links to other databases:

References:

1.	Kim, S.J. and Shoda, M. Purification and characterization of a novel peroxidase from Geotrichum candidum dec 1 involved in decolorization of dyes. Appl. Environ. Microbiol. 65 (1999) 1029–1035. [PMID: 10049859]
2.	Sugano, Y., Ishii, Y. and Shoda, M. Role of H164 in a unique dye-decolorizing heme peroxidase DyP. Biochem. Biophys. Res. Commun. 322 (2004) 126–132. [DOI] [PMID: 15313183]
3.	Zubieta, C., Joseph, R., Krishna, S.S., McMullan, D., Kapoor, M., Axelrod, H.L., Miller, M.D., Abdubek, P., Acosta, C., Astakhova, T., Carlton, D., Chiu, H.J., Clayton, T., Deller, M.C., Duan, L., Elias, Y., Elsliger, M.A., Feuerhelm, J., Grzechnik, S.K., Hale, J., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Kozbial, P., Kumar, A., Marciano, D., Morse, A.T., Murphy, K.D., Nigoghossian, E., Okach, L., Oommachen, S., Reyes, R., Rife, C.L., Schimmel, P., Trout, C.V., van den Bedem, H., Weekes, D., White, A., Xu, Q., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A. and Wilson, I.A. Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA. Proteins 69 (2007) 234–243. [DOI] [PMID: 17654547]
4.	Sugano, Y., Matsushima, Y., Tsuchiya, K., Aoki, H., Hirai, M. and Shoda, M. Degradation pathway of an anthraquinone dye catalyzed by a unique peroxidase DyP from Thanatephorus cucumeris Dec 1. Biodegradation 20 (2009) 433–440. [DOI] [PMID: 19009358]
5.	Sugano, Y. DyP-type peroxidases comprise a novel heme peroxidase family. Cell. Mol. Life Sci. 66 (2009) 1387–1403. [DOI] [PMID: 19099183]
6.	Ogola, H.J., Kamiike, T., Hashimoto, N., Ashida, H., Ishikawa, T., Shibata, H. and Sawa, Y. Molecular characterization of a novel peroxidase from the cyanobacterium Anabaena sp. strain PCC 7120. Appl. Environ. Microbiol. 75 (2009) 7509–7518. [DOI] [PMID: 19801472]
7.	van Bloois, E., Torres Pazmino, D.E., Winter, R.T. and Fraaije, M.W. A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily. Appl. Microbiol. Biotechnol. 86 (2010) 1419–1430. [DOI] [PMID: 19967355]
8.	Liers, C., Bobeth, C., Pecyna, M., Ullrich, R. and Hofrichter, M. DyP-like peroxidases of the jelly fungus Auricularia auricula-judae oxidize nonphenolic lignin model compounds and high-redox potential dyes. Appl. Microbiol. Biotechnol. 85 (2010) 1869–1879. [DOI] [PMID: 19756587]
9.	Hofrichter, M., Ullrich, R., Pecyna, M.J., Liers, C. and Lundell, T. New and classic families of secreted fungal heme peroxidases. Appl. Microbiol. Biotechnol. 87 (2010) 871–897. [DOI] [PMID: 20495915]

[EC 1.11.1.19 created 2011, modified 2015]

1.13.11.80

Accepted name:

(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase

Reaction:

(3,5-dihydroxyphenyl)acetyl-CoA + O₂ = 2-(3,5-dihydroxyphenyl)-2-oxoacetate + CoA

Glossary:

(3,5-dihydroxyphenyl)acetyl-CoA = 2-(3,5-dihydroxyphenyl)acetyl-CoA

Other name(s):

DpgC

Systematic name:

(3,5-dihydroxyphenyl)acetyl-CoA:oxygen oxidoreductase

Comments:

The enzyme, characterized from bacteria Streptomyces toyocaensis and Amycolatopsis orientalis, is involved in the biosynthesis of (3,5-dihydroxyphenyl)glycine, a component of the glycopeptide antibiotic vancomycin.

Links to other databases:

References:

1.	Chen, H., Tseng, C.C., Hubbard, B.K. and Walsh, C.T. Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine. Proc. Natl. Acad. Sci. USA 98 (2001) 14901–14906. [DOI] [PMID: 11752437]
2.	Widboom, P.F., Fielding, E.N., Liu, Y. and Bruner, S.D. Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis. Nature 447 (2007) 342–345. [DOI] [PMID: 17507985]
3.	Fielding, E.N., Widboom, P.F. and Bruner, S.D. Substrate recognition and catalysis by the cofactor-independent dioxygenase DpgC. Biochemistry 46 (2007) 13994–14000. [DOI] [PMID: 18004875]

[EC 1.13.11.80 created 2015]

1.13.12.22

Accepted name:

deoxynogalonate monooxygenase

Reaction:

deoxynogalonate + O₂ = nogalonate + H₂O

For diagram of nogalamycin biosynthesis, click here

Glossary:

deoxynogalonate = [4,5-dihydroxy-10-oxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate
nogalonate = [4,5-dihydroxy-9,10-dioxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate

Other name(s):

SnoaB (gene name); 12-deoxynogalonic acid oxidoreductase; [4,5-dihydroxy-10-oxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate oxidase; [4,5-dihydroxy-10-oxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate monooxygenase; deoxynogalonate oxidoreductase

Systematic name:

deoxynogalonate:oxygen oxidoreductase

Comments:

The enzyme, characterized from the bacterium Streptomyces nogalater, is involved in the biosynthesis of the aromatic polyketide nogalamycin.

Links to other databases:

References:

1.	Koskiniemi, H., Grocholski, T., Schneider, G. and Niemi, J. Expression, purification and crystallization of the cofactor-independent monooxygenase SnoaB from the nogalamycin biosynthetic pathway. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 256–259. [DOI] [PMID: 19255477]
2.	Grocholski, T., Koskiniemi, H., Lindqvist, Y., Mantsala, P., Niemi, J. and Schneider, G. Crystal structure of the cofactor-independent monooxygenase SnoaB from Streptomyces nogalater: implications for the reaction mechanism. Biochemistry 49 (2010) 934–944. [DOI] [PMID: 20052967]

[EC 1.13.12.22 created 2015]

1.14.11.48

Accepted name:

xanthine dioxygenase

Reaction:

xanthine + 2-oxoglutarate + O₂ = urate + succinate + CO₂

For diagram of AMP catabolism, click here

Other name(s):

XanA; α-ketoglutarate-dependent xanthine hydroxylase

Systematic name:

xanthine,2-oxoglutarate:oxygen oxidoreductase

Comments:

Requires Fe²⁺ and L-ascorbate. The enzyme, which was characterized from fungi, is specific for xanthine.

Links to other databases:

References:

1.	Cultrone, A., Scazzocchio, C., Rochet, M., Montero-Moran, G., Drevet, C. and Fernandez-Martin, R. Convergent evolution of hydroxylation mechanisms in the fungal kingdom: molybdenum cofactor-independent hydroxylation of xanthine via α-ketoglutarate-dependent dioxygenases. Mol. Microbiol. 57 (2005) 276–290. [DOI] [PMID: 15948966]
2.	Montero-Moran, G.M., Li, M., Rendon-Huerta, E., Jourdan, F., Lowe, D.J., Stumpff-Kane, A.W., Feig, M., Scazzocchio, C. and Hausinger, R.P. Purification and characterization of the Fe^II- and α-ketoglutarate-dependent xanthine hydroxylase from Aspergillus nidulans. Biochemistry 46 (2007) 5293–5304. [DOI] [PMID: 17429948]
3.	Li, M., Muller, T.A., Fraser, B.A. and Hausinger, R.P. Characterization of active site variants of xanthine hydroxylase from Aspergillus nidulans. Arch. Biochem. Biophys. 470 (2008) 44–53. [DOI] [PMID: 18036331]

[EC 1.14.11.48 created 2015]

1.14.13.201

Transferred entry:

β-amyrin 28-monooxygenase. Now EC 1.14.14.126, β-amyrin 28-monooxygenase

[EC 1.14.13.201 created 2015, deleted 2018]

1.14.13.202

Transferred entry:

methyl farnesoate epoxidase. Now EC 1.14.14.127, methyl farnesoate epoxidase

[EC 1.14.13.202 created 2015, deleted 2018]

1.14.13.203

Transferred entry:

farnesoate epoxidase. Now EC 1.14.14.128, farnesoate epoxidase

[EC 1.14.13.203 created 2015, deleted 2018]

1.14.19.10

Accepted name:

icosanoyl-CoA 5-desaturase

Reaction:

icosanoyl-CoA + 2 ferrocytochrome b₅ + O₂ + 2 H⁺ = (Z)-icos-5-enoyl-CoA + 2 ferricytochrome b₅ + 2 H₂O

Other name(s):

acyl-CoA Δ⁵-desaturase (ambiguous)

Systematic name:

icosanoyl-CoA,ferrocytochrome b₅:oxygen oxidoreductase (5,6 cis-dehydrogenating)

Comments:

The enzyme, characterized from the plant Limnanthes douglasii (meadowfoam), is involved in the biosynthesis of (5Z)-icos-5-enoate, an unusual monounsaturated fatty acid that makes up to 60% of the total fatty acids in Limnanthes sp. seed oil. The enzyme only acts on saturated fatty acids.

Links to other databases:

References:

1.	Cahoon, E.B., Marillia, E.F., Stecca, K.L., Hall, S.E., Taylor, D.C. and Kinney, A.J. Production of fatty acid components of meadowfoam oil in somatic soybean embryos. Plant Physiol. 124 (2000) 243–251. [PMID: 10982439]

[EC 1.14.19.10 created 2015]

*EC

1.17.99.1

Transferred entry:

4-methylphenol dehydrogenase (hydroxylating). Now EC 1.17.9.1, 4-methylphenol dehydrogenase (hydroxylating)

[EC 1.17.99.1 created 1983, modified 2001, modified 2011, modified 2015, deleted 2018]

*EC

1.20.4.1

Accepted name:

arsenate reductase (glutathione/glutaredoxin)

Reaction:

arsenate + glutathione + glutaredoxin = arsenite + a glutaredoxin-glutathione disulfide + H₂O

For diagram of arsenate catabolism, click here

Other name(s):

ArsC (ambiguous); arsenate:glutaredoxin oxidoreductase; arsenate reductase (glutaredoxin)

Systematic name:

arsenate:glutathione/glutaredoxin oxidoreductase

Comments:

The enzyme is part of a system for detoxifying arsenate. The substrate binds to a catalytic cysteine residue, forming a covalent thiolate—As(V) intermediate. A tertiary intermediate is then formed between the arsenic, the enzyme’s cysteine, and a glutathione cysteine. This intermediate is reduced by glutaredoxin, which forms a dithiol with the glutathione, leading to the dissociation of arsenite. Thus reduction of As(V) is mediated by three cysteine residues: one in ArsC, one in glutathione, and one in glutaredoxin. Although the arsenite formed is more toxic than arsenate, it can be extruded from some bacteria by EC 7.3.2.7, arsenite-transporting ATPase; in other organisms, arsenite can be methylated by EC 2.1.1.137, arsenite methyltransferase, in a pathway that produces non-toxic organoarsenical compounds. cf. EC 1.20.4.4, arsenate reductase (thioredoxin).

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 146907-46-2

References:

1.	Gladysheva, T., Liu, J.Y. and Rosen, B.P. His-8 lowers the pKa of the essential Cys-12 residue of the ArsC arsenate reductase of plasmid R773. J. Biol. Chem. 271 (1996) 33256–33260. [DOI] [PMID: 8969183]
2.	Gladysheva, T.B., Oden, K.L. and Rosen, B.P. Properties of the arsenate reductase of plasmid R773. Biochemistry 33 (1994) 7288–7293. [PMID: 8003492]
3.	Holmgren, A. and Aslund, F. Glutaredoxin. Methods Enzymol. 252 (1995) 283–292. [DOI] [PMID: 7476363]
4.	Krafft, T. and Macy, J.M. Purification and characterization of the respiratory arsenate reductase of Chrysiogenes arsenatis. Eur. J. Biochem. 255 (1998) 647–653. [DOI] [PMID: 9738904]
5.	Martin, J.L. Thioredoxin - a fold for all reasons. Structure 3 (1995) 245–250. [DOI] [PMID: 7788290]
6.	Radabaugh, T.R. and Aposhian, H.V. Enzymatic reduction of arsenic compounds in mammalian systems: reduction of arsenate to arsenite by human liver arsenate reductase. Chem. Res. Toxicol. 13 (2000) 26–30. [DOI] [PMID: 10649963]
7.	Sato, T. and Kobayashi, Y. The ars operon in the skin element of Bacillus subtilis confers resistance to arsenate and arsenite. J. Bacteriol. 180 (1998) 1655–1661. [PMID: 9537360]
8.	Shi, J., Vlamis-Gardikas, V., Aslund, F., Holmgren, A. and Rosen, B.P. Reactivity of glutaredoxins 1, 2, and 3 from Escherichia coli shows that glutaredoxin 2 is the primary hydrogen donor to ArsC-catalyzed arsenate reduction. J. Biol. Chem. 274 (1999) 36039–36042. [DOI] [PMID: 10593884]
9.	Mukhopadhyay, R. and Rosen, B.P. Arsenate reductases in prokaryotes and eukaryotes. Environ Health Perspect 110 Suppl 5 (2002) 745–748. [PMID: 12426124]
10.	Messens, J. and Silver, S. Arsenate reduction: thiol cascade chemistry with convergent evolution. J. Mol. Biol. 362 (2006) 1–17. [PMID: 16905151]

[EC 1.20.4.1 created 2000 as EC 1.97.1.5, transferred 2001 to EC 1.20.4.1, modified 2015, modified 2019, modified 2020]

1.20.4.4

Accepted name:

arsenate reductase (thioredoxin)

Reaction:

arsenate + thioredoxin = arsenite + thioredoxin disulfide + H₂O

For diagram of arsenate catabolism, click here

Other name(s):

ArsC (ambiguous)

Systematic name:

arsenate:thioredoxin oxidoreductase

Comments:

The enzyme, characterized in bacteria of the Firmicutes phylum, is specific for thioredoxin [1]. It has no activity with glutaredoxin [cf. EC 1.20.4.1, arsenate reductase (glutaredoxin)]. Although the arsenite formed is more toxic than arsenate, it can be extruded from some bacteria by EC 7.3.2.7, arsenite-transporting ATPase; in other organisms, arsenite can be methylated by EC 2.1.1.137, arsenite methyltransferase, in a pathway that produces non-toxic organoarsenical compounds. The enzyme also has the activity of EC 3.1.3.48, protein-tyrosine-phosphatase [3].

Links to other databases:

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

References:

1.	Ji, G., Garber, E.A., Armes, L.G., Chen, C.M., Fuchs, J.A. and Silver, S. Arsenate reductase of Staphylococcus aureus plasmid pI258. Biochemistry 33 (1994) 7294–7299. [PMID: 8003493]
2.	Messens, J., Hayburn, G., Desmyter, A., Laus, G. and Wyns, L. The essential catalytic redox couple in arsenate reductase from Staphylococcus aureus. Biochemistry 38 (1999) 16857–16865. [DOI] [PMID: 10606519]
3.	Zegers, I., Martins, J.C., Willem, R., Wyns, L. and Messens, J. Arsenate reductase from S. aureus plasmid pI258 is a phosphatase drafted for redox duty. Nat. Struct. Biol. 8 (2001) 843–847. [DOI] [PMID: 11573087]
4.	Messens, J., Martins, J.C., Van Belle, K., Brosens, E., Desmyter, A., De Gieter, M., Wieruszeski, J.M., Willem, R., Wyns, L. and Zegers, I. All intermediates of the arsenate reductase mechanism, including an intramolecular dynamic disulfide cascade. Proc. Natl. Acad. Sci. USA 99 (2002) 8506–8511. [DOI] [PMID: 12072565]

[EC 1.20.4.4 created 2015, modified 2019]

1.23 Reducing C-O-C group as acceptor

1.23.5 With a quinone or similar compound as acceptor

1.23.5.1

Accepted name:

violaxanthin de-epoxidase

Reaction:

violaxanthin + 2 L-ascorbate = zeaxanthin + 2 L-dehydroascorbate + 2 H₂O (overall reaction)
(1a) violaxanthin + L-ascorbate = antheraxanthin + L-dehydroascorbate + H₂O
(1b) antheraxanthin + L-ascorbate = zeaxanthin + L-dehydroascorbate + H₂O

For diagram of the xanthophyll cycle, click here

Glossary:

violaxanthin = (3S,3′S,5R,5′R,6S,6′S)-5,6:5′,6′-diepoxy-5,5′,6,6′-tetrahydro-β,β-carotene-3,3′-diol
antheraxanthin = (3R,3′S,5′R,6′S)-5′,6′-epoxy-5′,6′-dihydro-β,β-carotene-3,3′-diol
zeaxanthin = (3R,3′R)-β,β-carotene-3,3′-diol

Other name(s):

VDE

Systematic name:

violaxanthin:ascorbate oxidoreductase

Comments:

Along with EC 1.14.15.21, zeaxanthin epoxidase, this enzyme forms part of the xanthophyll (or violaxanthin) cycle for controlling the concentration of zeaxanthin in chloroplasts. It is activated by a low pH of the thylakoid lumen (produced by high light intensity). Zeaxanthin induces the dissipation of excitation energy in the chlorophyll of the light-harvesting protein complex of photosystem II. In higher plants the enzyme reacts with all-trans-diepoxides, such as violaxanthin, and all-trans-monoepoxides, but in the alga Mantoniella squamata, only the diepoxides are good substrates.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 57534-73-3

References:

1.	Yamamoto, H.Y. and Higashi, R.M. Violaxanthin de-epoxidase. Lipid composition and substrate specificity. Arch. Biochem. Biophys. 190 (1978) 514–522. [DOI] [PMID: 102251]
2.	Rockholm, D.C. and Yamamoto, H.Y. Violaxanthin de-epoxidase. Plant Physiol. 110 (1996) 697–703. [PMID: 8742341]
3.	Bugos, R.C., Hieber, A.D. and Yamamoto, H.Y. Xanthophyll cycle enzymes are members of the lipocalin family, the first identified from plants. J. Biol. Chem. 273 (1998) 15321–15324. [DOI] [PMID: 9624110]
4.	Kuwabara, T., Hasegawa, M., Kawano, M. and Takaichi, S. Characterization of violaxanthin de-epoxidase purified in the presence of Tween 20: effects of dithiothreitol and pepstatin A. Plant Cell Physiol. 40 (1999) 1119–1126. [PMID: 10635115]
5.	Latowski, D., Kruk, J., Burda, K., Skrzynecka-Jaskierm, M., Kostecka-Gugala, A. and Strzalka, K. Kinetics of violaxanthin de-epoxidation by violaxanthin de-epoxidase, a xanthophyll cycle enzyme, is regulated by membrane fluidity in model lipid bilayers. Eur. J. Biochem. 269 (2002) 4656–4665. [DOI] [PMID: 12230579]
6.	Goss, R. Substrate specificity of the violaxanthin de-epoxidase of the primitive green alga Mantoniella squamata (Prasinophyceae). Planta 217 (2003) 801–812. [DOI] [PMID: 12748855]
7.	Latowski, D., Akerlund, H.E. and Strzalka, K. Violaxanthin de-epoxidase, the xanthophyll cycle enzyme, requires lipid inverted hexagonal structures for its activity. Biochemistry 43 (2004) 4417–4420. [DOI] [PMID: 15078086]

[EC 1.23.5.1 created 2005 as EC 1.10.99.3, transferred 2015 to EC 1.23.5.1]

*EC

2.1.1.98

Accepted name:

diphthine synthase

Reaction:

3 S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = 3 S-adenosyl-L-homocysteine + diphthine-[translation elongation factor 2] (overall reaction)
(1a) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-[(3S)-3-carboxy-3-(methylamino)propyl]-L-histidine-[translation elongation factor 2]
(1b) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-(methylamino)propyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-[(3S)-3-carboxy-3-(dimethylamino)propyl]-L-histidine-[translation elongation factor 2]
(1c) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-(dimethylamino)propyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + diphthine-[translation elongation factor 2]

For diagram of diphthamide biosynthesis, click here

Glossary:

diphthine = 2-[(3S)-3-carboxy-3-(trimethylamino)propyl]-L-histidine

Other name(s):

S-adenosyl-L-methionine:elongation factor 2 methyltransferase (ambiguous); diphthine methyltransferase (ambiguous); S-adenosyl-L-methionine:2-(3-carboxy-3-aminopropyl)-L-histidine-[translation elongation factor 2] methyltransferase; Dph5 (ambiguous)

Systematic name:

S-adenosyl-L-methionine:2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] methyltransferase (diphthine-[translation elongation factor 2]-forming)

Comments:

This archaeal enzyme produces the trimethylated product diphthine, which is converted into diphthamide by EC 6.3.1.14, diphthine—ammonia ligase. Different from the eukaryotic enzyme, which produces diphthine methyl ester (cf. EC 2.1.1.314). In the archaeon Pyrococcus horikoshii the enzyme acts on His⁶⁰⁰ of elongation factor 2.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 114514-25-9

References:

1.	Zhu, X., Kim, J., Su, X. and Lin, H. Reconstitution of diphthine synthase activity in vitro. Biochemistry 49 (2010) 9649–9657. [DOI] [PMID: 20873788]

[EC 2.1.1.98 created 1990, modified 2013, modified 2015]

2.1.1.314

Accepted name:

diphthine methyl ester synthase

Reaction:

4 S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = 4 S-adenosyl-L-homocysteine + diphthine methyl ester-[translation elongation factor 2]

For diagram of diphthamide biosynthesis, click here

Glossary:

diphthine methyl ester = 2-[(3S)-4-methoxy-4-oxo-3-(trimethylammonio)butyl]-L-histidine

Other name(s):

S-adenosyl-L-methionine:elongation factor 2 methyltransferase (ambiguous); diphthine methyltransferase (ambiguous); Dph5 (ambiguous)

Systematic name:

S-adenosyl-L-methionine:2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] methyltransferase (diphthine methyl ester-[translation elongation factor 2]-forming)

Comments:

This eukaryotic enzyme is part of the biosynthetic pathway of diphthamide. Different from the archaeal enzyme, which performs only 3 methylations, producing diphthine (cf. EC 2.1.1.98). The relevant histidine of elongation factor 2 is His⁷¹⁵ in mammals and His⁶⁹⁹ in yeast. The order of the 4 methylations is not known.

Links to other databases:

References:

1.	Chen, J.-Y.C. and Bodley, J.W. Biosynthesis of diphthamide in Saccharomyces cerevisiae. Partial purification and characterization of a specific S-adenosylmethionine:elongation factor 2 methyltransferase. J. Biol. Chem. 263 (1988) 11692–11696. [PMID: 3042777]
2.	Moehring, J.M. and Moehring, T.J. The post-translational trimethylation of diphthamide studied in vitro. J. Biol. Chem. 263 (1988) 3840–3844. [PMID: 3346227]
3.	Lin, Z., Su, X., Chen, W., Ci, B., Zhang, S. and Lin, H. Dph7 catalyzes a previously unknown demethylation step in diphthamide biosynthesis. J. Am. Chem. Soc. 136 (2014) 6179–6182. [DOI] [PMID: 24739148]

[EC 2.1.1.314 created 2015]

2.1.1.315

Accepted name:

27-O-demethylrifamycin SV methyltransferase

Reaction:

S-adenosyl-L-methionine + 27-O-demethylrifamycin SV = S-adenosyl-L-homocysteine + rifamycin SV

Glossary:

rifamycin SV = (7S,9E,11S,12R,13S,14R,15R,16R,17S,18S,19E,21Z)-2,15,17,27,29-pentahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-6,23-dioxo-8,30-dioxa-24-azatetracyclo[23.3.1.14,7.05,28]triaconta-1(28),2,4,9, 19,21,25(29),26-octaen-13-yl acetate

Other name(s):

AdoMet:27-O-demethylrifamycin SV methyltransferase

Systematic name:

S-adenosyl-L-methionine:27-O-demethylrifamycin-SV 27-O-methyltransferase

Comments:

The enzyme, characterized from the bacterium Amycolatopsis mediterranei, is involved in biosynthesis of the antitubercular drug rifamycin B.

Links to other databases:

References:

Xu, J., Mahmud, T. and Floss, H.G. Isolation and characterization of 27-O-demethylrifamycin SV methyltransferase provides new insights into the post-PKS modification steps during the biosynthesis of the antitubercular drug rifamycin B by Amycolatopsis mediterranei S699. Arch. Biochem. Biophys. 411 (2003) 277–288. [DOI] [PMID: 12623077]

[EC 2.1.1.315 created 2015]

*EC

2.3.1.161

Accepted name:

lovastatin nonaketide synthase

Reaction:

9 malonyl-CoA + 11 NADPH + 10 H⁺ + S-adenosyl-L-methionine + holo-[lovastatin nonaketide synthase] = dihydromonacolin L-[lovastatin nonaketide synthase] + 9 CoA + 9 CO₂ + 11 NADP⁺ + S-adenosyl-L-homocysteine + 6 H₂O

For diagram of polyketides biosynthesis, click here

Glossary:

dihydromonacolin L acid = (3R,5R)-7-[(1S,2S,4aR,6R,8aS)-2,6-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]-3,5-dihydroxyheptanoate

Other name(s):

LNKS; LovB; LovC; acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing, thioester-hydrolysing)

Systematic name:

acyl-CoA:malonyl-CoA C-acyltransferase (dihydromonacolin L acid-forming)

Comments:

This fungal enzyme system comprises a multi-functional polyketide synthase (PKS) and an enoyl reductase. The PKS catalyses many of the chain building reactions of EC 2.3.1.85, fatty-acid synthase system, as well as a reductive methylation and a Diels-Alder reaction, while the reductase is responsible for three enoyl reductions that are necessary for dihydromonacolin L acid production.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 235426-97-8

References:

1.	Ma, S.M., Li, J.W., Choi, J.W., Zhou, H., Lee, K.K., Moorthie, V.A., Xie, X., Kealey, J.T., Da Silva, N.A., Vederas, J.C. and Tang, Y. Complete reconstitution of a highly reducing iterative polyketide synthase. Science 326 (2009) 589–592. [DOI] [PMID: 19900898]
2.	Kennedy, J., Auclair, K., Kendrew, S.G., Park, C., Vederas, J.C. and Hutchinson, C.R. Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science 284 (1999) 1368–1372. [DOI] [PMID: 10334994]
3.	Auclair, K., Sutherland, A., Kennedy, J., Witter, D.J., van der Heever, J.P., Hutchinson, C.R. and Vederas, J.C. Lovastatin nonaketide synthase catalyses an intramolecular Diels-Alder reaction of a substrate analogue. J. Am. Chem. Soc. 122 (2000) 11519–11520.

[EC 2.3.1.161 created 2002, modified 2015, modified 2016, modified 2019]

2.3.1.244

Accepted name:

2-methylbutanoate polyketide synthase

Reaction:

2 malonyl-CoA + [2-methylbutanoate polyketide synthase] + 2 NADPH + 3 H⁺ + S-adenosyl-L-methionine = (S)-2-methylbutanoyl-[2-methylbutanoate polyketide synthase] + 2 CoA + 2 CO₂ + 2 NADP⁺ + S-adenosyl-L-homocysteine + H₂O

For diagram of lovastatin biosynthesis, click here

Other name(s):

LovF

Systematic name:

acyl-CoA:malonyl-CoA C-acyltransferase (2-methylbutanoate-forming)

Comments:

This polyketide synthase enzyme forms the (S)-2-methylbutanoate side chain during lovastatin biosynthesis by the filamentous fungus Aspergillus terreus. The overall reaction comprises a single condensation reaction followed by α-methylation, β-ketoreduction, dehydration, and α,β-enoyl reduction.

Links to other databases:

References:

1.	Kennedy, J., Auclair, K., Kendrew, S.G., Park, C., Vederas, J.C. and Hutchinson, C.R. Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science 284 (1999) 1368–1372. [DOI] [PMID: 10334994]
2.	Meehan, M.J., Xie, X., Zhao, X., Xu, W., Tang, Y. and Dorrestein, P.C. FT-ICR-MS characterization of intermediates in the biosynthesis of the α-methylbutyrate side chain of lovastatin by the 277 kDa polyketide synthase LovF. Biochemistry 50 (2011) 287–299. [DOI] [PMID: 21069965]

[EC 2.3.1.244 created 2015, modified 2016]

2.3.1.245

Accepted name:

3-hydroxy-5-phosphooxypentane-2,4-dione thiolase

Reaction:

glycerone phosphate + acetyl-CoA = 3-hydroxy-2,4-dioxopentyl phosphate + CoA

Glossary:

(4S)-4,5-dihydroxypentane-2,3-dione = autoinducer 2 = AI-2

Other name(s):

lsrF (gene name); 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase

Systematic name:

acetyl-CoA:glycerone phosphate C-acetyltransferase

Comments:

The enzyme participates in a degradation pathway of the bacterial quorum-sensing autoinducer molecule AI-2.

Links to other databases:

References:

1.	Diaz, Z., Xavier, K.B. and Miller, S.T. The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF. PLoS One 4:e6820 (2009). [DOI] [PMID: 19714241]
2.	Marques, J.C., Oh, I.K., Ly, D.C., Lamosa, P., Ventura, M.R., Miller, S.T. and Xavier, K.B. LsrF, a coenzyme A-dependent thiolase, catalyzes the terminal step in processing the quorum sensing signal autoinducer-2. Proc. Natl. Acad. Sci. USA 111 (2014) 14235–14240. [DOI] [PMID: 25225400]

[EC 2.3.1.245 created 2015, modified 2021]

2.3.1.246

Accepted name:

3,5-dihydroxyphenylacetyl-CoA synthase

Reaction:

4 malonyl-CoA = (3,5-dihydroxyphenylacetyl)-CoA + 3 CoA + 4 CO₂ + H₂O

Other name(s):

DpgA

Systematic name:

malonyl-CoA:malonyl-CoA malonyltransferase (3,5-dihydroxyphenylacetyl-CoA-forming)

Comments:

The enzyme, characterized from the bacterium Amycolatopsis mediterranei, is involved in biosynthesis of the nonproteinogenic amino acid (S)-3,5-dihydroxyphenylglycine, a component of the vancomycin-type antibiotic balhimycin.

Links to other databases:

References:

1.	Pfeifer, V., Nicholson, G.J., Ries, J., Recktenwald, J., Schefer, A.B., Shawky, R.M., Schroder, J., Wohlleben, W. and Pelzer, S. A polyketide synthase in glycopeptide biosynthesis: the biosynthesis of the non-proteinogenic amino acid (S)-3,5-dihydroxyphenylglycine. J. Biol. Chem. 276 (2001) 38370–38377. [DOI] [PMID: 11495926]
2.	Chen, H., Tseng, C.C., Hubbard, B.K. and Walsh, C.T. Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine. Proc. Natl. Acad. Sci. USA 98 (2001) 14901–14906. [DOI] [PMID: 11752437]
3.	Tseng, C.C., McLoughlin, S.M., Kelleher, N.L. and Walsh, C.T. Role of the active site cysteine of DpgA, a bacterial type III polyketide synthase. Biochemistry 43 (2004) 970–980. [DOI] [PMID: 14744141]
4.	Wu, H.C., Li, Y.S., Liu, Y.C., Lyu, S.Y., Wu, C.J. and Li, T.L. Chain elongation and cyclization in type III PKS DpgA. ChemBioChem 13 (2012) 862–871. [DOI] [PMID: 22492619]

[EC 2.3.1.246 created 2015]

*EC

2.3.3.5

Accepted name:

2-methylcitrate synthase

Reaction:

propanoyl-CoA + H₂O + oxaloacetate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate + CoA

For diagram of reaction, click here

Glossary:

2-methylcitrate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate

Other name(s):

2-methylcitrate oxaloacetate-lyase; MCS; methylcitrate synthase; methylcitrate synthetase

Systematic name:

propanoyl-CoA:oxaloacetate C-propanoyltransferase (thioester-hydrolysing, 1-carboxyethyl-forming)

Comments:

The enzyme acts on acetyl-CoA, propanoyl-CoA, butanoyl-CoA and pentanoyl-CoA. The relative rate of condensation of acetyl-CoA and oxaloacetate is 140% of that of propanoyl-CoA and oxaloacetate, but the enzyme is distinct from EC 2.3.3.1, citrate (Si)-synthase. Oxaloacetate cannot be replaced by glyoxylate, pyruvate or 2-oxoglutarate.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 57827-78-8

References:

1.	Uchiyama, H. and Tabuchi, T. Properties of methylcitrate synthase from Candida lipolytica. Agric. Biol. Chem. 40 (1976) 1411–1418.
2.	Textor, S., Wendisch, V.F., De Graaf, A.A., Muller, U., Linder, M.I., Linder, D. and Buckel, W. Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria. Arch. Microbiol. 168 (1997) 428–436. [PMID: 9325432]
3.	Horswill, A.R. and Escalante-Semerena, J.C. Salmonella typhimurium LT2 catabolizes propionate via the 2-methylcitric acid cycle. J. Bacteriol. 181 (1999) 5615–5623. [PMID: 10482501]
4.	Brock, M., Maerker, C., Schütz, A., Völker, U. and Buckel, W. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur. J. Biochem. 269 (2002) 6184–6194. [DOI] [PMID: 12473114]
5.	Domin, N., Wilson, D. and Brock, M. Methylcitrate cycle activation during adaptation of Fusarium solani and Fusarium verticillioides to propionyl-CoA-generating carbon sources. Microbiology 155 (2009) 3903–3912. [DOI] [PMID: 19661181]

[EC 2.3.3.5 created 1978 as EC 4.1.3.31, transferred 2002 to EC 2.3.3.5, modified 2015]

2.7.1.187

Accepted name:

acarbose 7^IV-phosphotransferase

Reaction:

ATP + acarbose = ADP + acarbose 7^IV-phosphate

Glossary:

acarbose = 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)-2-cyclohexen-1-yl]amino}-α-D-glucopyranosyl-(1→4)-α-D-glucopyranosyl-(1→4)-β-D-glucopyranose

Other name(s):

acarbose 7-kinase; AcbK

Systematic name:

ATP:acarbose 7^IV-phosphotransferase

Comments:

The enzyme, characterized from the bacterium Actinoplanes sp. SE50/110, is specific for acarbose.

Links to other databases:

References:

1.	Drepper, A. and Pape, H. Acarbose 7-phosphotransferase from Actinoplanes sp.: purification, properties, and possible physiological function. J. Antibiot. (Tokyo) 49 (1996) 664–668. [PMID: 8784428]
2.	Goeke, K., Drepper, A. and Pape, H. Formation of acarbose phosphate by a cell-free extract from the acarbose producer Actinoplanes sp. J. Antibiot. (Tokyo) 49 (1996) 661–663. [PMID: 8784426]
3.	Zhang, C.S., Stratmann, A., Block, O., Bruckner, R., Podeschwa, M., Altenbach, H.J., Wehmeier, U.F. and Piepersberg, W. Biosynthesis of the C₇-cyclitol moiety of acarbose in Actinoplanes species SE50/110. 7-O-phosphorylation of the initial cyclitol precursor leads to proposal of a new biosynthetic pathway. J. Biol. Chem. 277 (2002) 22853–22862. [DOI] [PMID: 11937512]

[EC 2.7.1.187 created 2015]

2.7.1.188

Accepted name:

2-epi-5-epi-valiolone 7-kinase

Reaction:

ATP + 2-epi-5-epi-valiolone = ADP + 2-epi-5-epi-valiolone 7-phosphate

For diagram of valiolone biosynthesis, click here

Glossary:

2-epi-5-epi-valiolone = (2S,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexan-1-one

Other name(s):

AcbM

Systematic name:

ATP:2-epi-5-epi-valiolone 7-phosphotransferase

Comments:

The enzyme, characterized from the bacterium Actinoplanes sp. SE50/110, is involved in the biosynthesis of the oligosaccharide acarbose.

Links to other databases:

References:

Zhang, C.S., Stratmann, A., Block, O., Bruckner, R., Podeschwa, M., Altenbach, H.J., Wehmeier, U.F. and Piepersberg, W. Biosynthesis of the C₇-cyclitol moiety of acarbose in Actinoplanes species SE50/110. 7-O-phosphorylation of the initial cyclitol precursor leads to proposal of a new biosynthetic pathway. J. Biol. Chem. 277 (2002) 22853–22862. [DOI] [PMID: 11937512]

[EC 2.7.1.188 created 2015]

2.7.4.29

Accepted name:

Kdo₂-lipid A phosphotransferase

Reaction:

ditrans-octacis-undecaprenyl diphosphate + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A = ditrans-octacis-undecaprenyl phosphate + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A 1-diphosphate

Glossary:

lipid A = 2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid A 1-diphosphate =
2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl diphosphate

Other name(s):

lipid A undecaprenyl phosphotransferase; LpxT; YeiU

Systematic name:

ditrans-octacis-undecaprenyl-diphosphate:α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid-A phosphotransferase

Comments:

An inner-membrane protein. The activity of the enzyme is regulated by PmrA. In vitro the enzyme can use diacylglycerol 3-diphosphate as the phosphate donor.

Links to other databases:

References:

1.	Touze, T., Tran, A.X., Hankins, J.V., Mengin-Lecreulx, D. and Trent, M.S. Periplasmic phosphorylation of lipid A is linked to the synthesis of undecaprenyl phosphate. Mol. Microbiol. 67 (2008) 264–277. [DOI] [PMID: 18047581]
2.	Herrera, C.M., Hankins, J.V. and Trent, M.S. Activation of PmrA inhibits LpxT-dependent phosphorylation of lipid A promoting resistance to antimicrobial peptides. Mol. Microbiol. 76 (2010) 1444–1460. [DOI] [PMID: 20384697]

[EC 2.7.4.29 created 2015]

3.1.2.31

Accepted name:

dihydromonacolin L-[lovastatin nonaketide synthase] thioesterase

Reaction:

dihydromonacolin L-[lovastatin nonaketide synthase] + H₂O = holo-[lovastatin nonaketide synthase] + dihydromonacolin L acid

For diagram of lovastatin biosynthesis, click here

Glossary:

dihydromonacolin L acid = (3R,5R)-7-[(1S,2S,4aR,6R,8aS)-2,6-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]-3,5-dihydroxyheptanoate

Other name(s):

LovG

Systematic name:

dihydromonacolin L-[lovastatin nonaketide synthase] hydrolase

Comments:

Dihydromonacolin L acid is synthesized while bound to an acyl-carrier protein domain of the lovastatin nonaketide synthase (EC 2.3.1.161). Since that enzyme lacks a thioesterase domain, release of the dihydromonacolin L acid moiety from the polyketide synthase requires this dedicated enzyme.

Links to other databases:

References:

1.	Xu, W., Chooi, Y.H., Choi, J.W., Li, S., Vederas, J.C., Da Silva, N.A. and Tang, Y. LovG: the thioesterase required for dihydromonacolin L release and lovastatin nonaketide synthase turnover in lovastatin biosynthesis. Angew. Chem. Int. Ed. Engl. 52 (2013) 6472–6475. [DOI] [PMID: 23653178]

[EC 3.1.2.31 created 2015]

3.1.3.97

Accepted name:

3′,5′-nucleoside bisphosphate phosphatase

Reaction:

nucleoside 3′,5′-bisphosphate + H₂O = nucleoside 5′-phosphate + phosphate

Systematic name:

nucleoside-3′,5′-bisphosphate 3′-phosphohydrolase

Comments:

The enzyme, characterized from the bacterium Chromobacterium violaceum, has similar catalytic efficiencies with all the bases. The enzyme has similar activity with ribonucleoside and 2′-deoxyribonucleoside 3′,5′-bisphosphates, but shows no activity with nucleoside 2′,5′-bisphosphates (cf. EC 3.1.3.7, 3′(2′),5′-bisphosphate nucleotidase).

Links to other databases:

References:

1.	Cummings, J.A., Vetting, M., Ghodge, S.V., Xu, C., Hillerich, B., Seidel, R.D., Almo, S.C. and Raushel, F.M. Prospecting for unannotated enzymes: discovery of a 3′,5′-nucleotide bisphosphate phosphatase within the amidohydrolase superfamily. Biochemistry 53 (2014) 591–600. [DOI] [PMID: 24401123]

[EC 3.1.3.97 created 2015]

3.3.2.14

Accepted name:

2,4-dinitroanisole O-demethylase

Reaction:

2,4-dinitroanisole + H₂O = methanol + 2,4-dinitrophenol

Glossary:

2,4-dinitroanisole = 1-methoxy-2,4-dinitrobenzene

Other name(s):

2,4-dinitroanisole ether hydrolase; dnhA (gene name); dnhB (gene name); DNAN demethylase

Systematic name:

2,4-dinitroanisole methanol hydrolase

Comments:

The enzyme, characterized from the bacterium Nocardioides sp. JS1661, is involved in the degradation of 2,4-dinitroanisole. Unlike other known O-demethylases, such as EC 1.14.99.15, 4-methoxybenzoate monooxygenase (O-demethylating), or EC 1.14.11.32, codeine 3-O-demethylase, it does not require oxygen or electron donors, and produces methanol rather than formaldehyde.

Links to other databases:

References:

1.	Fida, T.T., Palamuru, S., Pandey, G. and Spain, J.C. Aerobic biodegradation of 2,4-dinitroanisole by Nocardioides sp. strain JS1661. Appl. Environ. Microbiol. 80 (2014) 7725–7731. [DOI] [PMID: 25281383]

[EC 3.3.2.14 created 2015]

3.4.14.13

Accepted name:

γ-D-glutamyl-L-lysine dipeptidyl-peptidase

Reaction:

The enzyme releases L-Ala-γ-D-Glu dipeptides from cell wall peptides via cleavage of an L-Ala-γ-D-Glu┼L-Lys bond.

Other name(s):

YkfC

Comments:

The enzyme, characterized from the bacterium Bacillus subtilis, is involved in the recycling of the murein peptide.

Links to other databases:

References:

Schmidt, D.M., Hubbard, B.K. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases. Biochemistry 40 (2001) 15707–15715. [DOI] [PMID: 11747447]

Xu, Q., Abdubek, P., Astakhova, T., Axelrod, H.L., Bakolitsa, C., Cai, X., Carlton, D., Chen, C., Chiu, H.J., Chiu, M., Clayton, T., Das, D., Deller, M.C., Duan, L., Ellrott, K., Farr, C.L., Feuerhelm, J., Grant, J.C., Grzechnik, A., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Kozbial, P., Krishna, S.S., Kumar, A., Lam, W.W., Marciano, D., Miller, M.D., Morse, A.T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Tien, H.J., Trame, C.B., van den Bedem, H., Weekes, D., Wooten, T., Yeh, A., Hodgson, K.O., Wooley, J., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A. and Wilson, I.A. Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (2010) 1354–1364. [DOI] [PMID: 20944232]

[EC 3.4.14.13 created 2015]

3.5.1.118

Accepted name:

γ-glutamyl hercynylcysteine S-oxide hydrolase

Reaction:

γ-L-glutamyl-S-(hercyn-2-yl)-L-cysteine S-oxide + H₂O = S-(hercyn-2-yl)-L-cysteine S-oxide + L-glutamate

For diagram of ergothioneine and ovothiol biosynthesis, click here

Glossary:

hercynine = N^α,N^α,N^α-trimethyl-L-histidine = 3-(1H-imidazol-5-yl)-2-(trimethylamino)propanoate
S-(hercyn-2-yl)-L-cysteine S-oxide = S-(N,N,N-trimethyl-L-histidin-2-yl)-L-cysteine S-oxide

Other name(s):

EgtC

Systematic name:

γ-glutamyl-S-(hercyn-2-yl)cysteine S-oxide amidohydrolase

Comments:

The enzyme is part of the biosynthesis pathway of ergothioneine in mycobacteria.

Links to other databases:

References:

1.	Seebeck, F.P. In vitro reconstitution of mycobacterial ergothioneine biosynthesis. J. Am. Chem. Soc. 132 (2010) 6632–6633. [DOI] [PMID: 20420449]

[EC 3.5.1.118 created 2015]

4.1.1.100

Accepted name:

prephenate decarboxylase

Reaction:

prephenate = 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate + CO₂

For diagram of bacilysin biosynthesis, click here

Glossary:

L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine

Other name(s):

BacA; AerD; SalX; non-aromatizing prephenate decarboxylase

Systematic name:

prephenate carboxy-lyase (3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate-forming)

Comments:

Links to other databases:

References:

1.	Mahlstedt, S.A. and Walsh, C.T. Investigation of anticapsin biosynthesis reveals a four-enzyme pathway to tetrahydrotyrosine in Bacillus subtilis. Biochemistry 49 (2010) 912–923. [DOI] [PMID: 20052993]
2.	Mahlstedt, S., Fielding, E.N., Moore, B.S. and Walsh, C.T. Prephenate decarboxylases: a new prephenate-utilizing enzyme family that performs nonaromatizing decarboxylation en route to diverse secondary metabolites. Biochemistry 49 (2010) 9021–9023. [DOI] [PMID: 20863139]
3.	Parker, J.B. and Walsh, C.T. Olefin isomerization regiochemistries during tandem action of BacA and BacB on prephenate in bacilysin biosynthesis. Biochemistry 51 (2012) 3241–3251. [DOI] [PMID: 22483065]

[EC 4.1.1.100 created 2015]

4.1.99.21

Transferred entry:

(5-formylfuran-3-yl)methyl phosphate synthase. Now EC 4.2.3.153 (5-formylfuran-3-yl)methyl phosphate synthase.

[EC 4.1.99.21 created 2015, deleted 2015]

4.2.1.155

Accepted name:

(methylthio)acryloyl-CoA hydratase

Reaction:

3-(methylsulfanyl)acryloyl-CoA + 2 H₂O = acetaldehyde + methanethiol + CoA + CO₂ (overall reaction)
(1a) 3-(methylsulfanyl)acryloyl-CoA + H₂O = 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA
(1b) 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA = 3-oxopropanoyl-CoA + methanethiol
(1c) 3-oxopropanoyl-CoA + H₂O = 3-oxopropanoate + CoA
(1d) 3-oxopropanoate = acetaldehyde + CO₂

Glossary:

3-(methylsulfanyl)acryloyl-CoA = 3-(methylsulfanyl)prop-2-enoyl-CoA

Other name(s):

DmdD

Systematic name:

3-(methylsulfanyl)prop-2-enoyl-CoA hydro-lyase (acetaldehyde-forming)

Comments:

The enzyme is involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton. Isolated from the bacterium Ruegeria pomeroyi.

Links to other databases:

References:

1.	Tan, D., Crabb, W.M., Whitman, W.B. and Tong, L. Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA. PLoS One 8:e63870 (2013). [DOI] [PMID: 23704947]

[EC 4.2.1.155 created 2015]

4.2.3.152

Accepted name:

2-epi-5-epi-valiolone synthase

Reaction:

α-D-sedoheptulopyranose 7-phosphate = 2-epi-5-epi-valiolone + phosphate

For diagram of valiolone biosynthesis, click here

Glossary:

2-epi-5-epi-valiolone = (2S,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexan-1-one

Other name(s):

AcbC; ValA; CetA; SalQ; C₇-cyclitol synthase

Systematic name:

α-D-sedoheptulopyranose-7-phosphate phosphate-lyase (cyclizing; 2-epi-5-epi-valiolone-forming)

Comments:

The enzyme is highly specific for α-D-sedoheptulopyranose 7-phosphate. It requires a divalent metal ion (Zn²⁺ or Co²⁺) and an NAD⁺ cofactor, which is transiently reduced during the reaction. The enzyme is involved in the biosynthesis of C₇N-aminocyclitol natural products, such as the valienamine moiety of the antidiabetic drug acarbose and the crop protectant validamycin A. cf. EC 4.2.3.155, 2-epi-valiolone synthase and EC 4.2.3.154, demethyl-4-deoxygadusol synthase.

Links to other databases:

References:

1.	Stratmann, A., Mahmud, T., Lee, S., Distler, J., Floss, H.G. and Piepersberg, W. The AcbC protein from Actinoplanes species is a C₇-cyclitol synthase related to 3-dehydroquinate synthases and is involved in the biosynthesis of the α-glucosidase inhibitor acarbose. J. Biol. Chem. 274 (1999) 10889–10896. [DOI] [PMID: 10196166]
2.	Yu, Y., Bai, L., Minagawa, K., Jian, X., Li, L., Li, J., Chen, S., Cao, E., Mahmud, T., Floss, H.G., Zhou, X. and Deng, Z. Gene cluster responsible for validamycin biosynthesis in Streptomyces hygroscopicus subsp. jinggangensis 5008. Appl. Environ. Microbiol. 71 (2005) 5066–5076. [DOI] [PMID: 16151088]
3.	Wu, X., Flatt, P.M., Schlorke, O., Zeeck, A., Dairi, T. and Mahmud, T. A comparative analysis of the sugar phosphate cyclase superfamily involved in primary and secondary metabolism. ChemBioChem 8 (2007) 239–248. [DOI] [PMID: 17195255]
4.	Choi, W.S., Wu, X., Choeng, Y.H., Mahmud, T., Jeong, B.C., Lee, S.H., Chang, Y.K., Kim, C.J. and Hong, S.K. Genetic organization of the putative salbostatin biosynthetic gene cluster including the 2-epi-5-epi-valiolone synthase gene in Streptomyces albus ATCC 21838. Appl. Microbiol. Biotechnol. 80 (2008) 637–645. [DOI] [PMID: 18648803]
5.	Kean, K.M., Codding, S.J., Asamizu, S., Mahmud, T. and Karplus, P.A. Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus. Biochemistry 53 (2014) 4250–4260. [DOI] [PMID: 24832673]

[EC 4.2.3.152 created 2015, modified 2016]

4.4.1.29

Accepted name:

phycobiliprotein cysteine-84 phycobilin lyase

Reaction:

(1) [C-phycocyanin β-subunit]-Cys⁸⁴-phycocyanobilin = apo-[C-phycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(2) [phycoerythrocyanin β-subunit]-Cys⁸⁴-phycocyanobilin = apo-[phycoerythrocyanin β-subunit] + (2R,3E)-phycocyanobilin
(3) [allophycocyanin α-subunit]-Cys⁸⁴-phycocyanobilin = apo-[allophycocyanin α-subunit] + (2R,3E)-phycocyanobilin
(4) [allophycocyanin β-subunit]-Cys⁸⁴-phycocyanobilin = apo-[allophycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(5) [C-phycoerythrin α-subunit]-Cys⁸⁴-phycoerythrobilin = apo-[C-phycoerythrin α-subunit] + (2R,3E)-phycoerythrobilin
(6) [C-phycoerythrin β-subunit]-Cys⁸⁴-phycoerythrobilin = apo-[C-phycoerythrin β-subunit] + (2R,3E)-phycoerythrobilin

Glossary:

phycocyanobilin = 3,3¹-didehydro-2,3-dihydromesobiliverdin
phycoerythrobilin = 3,3¹,18¹,18²-tetradehydro-2,3,15,16-tetrahydromesobiliverdin

Other name(s):

cpcS (gene name); cpeS (gene name); cpcS1 (gene name); cpcU (gene name); phycocyanobilin:Cys-β84-phycobiliprotein lyase

Systematic name:

[phycobiliprotein]-Cys⁸⁴-phycobilin:phycobilin lyase

Comments:

The enzyme, found in cyanobacteria and red algae, catalyses the attachment of phycobilin chromophores to cysteine 84 of several phycobiliproteins (the numbering used here corresponds to the enzyme from Anabaena, in other organisms the number may vary slightly). It can attach phycocyanobilin to the β subunits of C-phycocyanin and phycoerythrocyanin and to both subunits of allophycocyanin. In addition, it can attach phycoerythrobilin to both subunits of C-phycoerythrin.

Links to other databases:

References:

1.	Zhao, K.H., Su, P., Li, J., Tu, J.M., Zhou, M., Bubenzer, C. and Scheer, H. Chromophore attachment to phycobiliprotein β-subunits: phycocyanobilin:cysteine-β84 phycobiliprotein lyase activity of CpeS-like protein from Anabaena Sp. PCC7120. J. Biol. Chem. 281 (2006) 8573–8581. [DOI] [PMID: 16452471]
2.	Zhao, K.H., Su, P., Tu, J.M., Wang, X., Liu, H., Ploscher, M., Eichacker, L., Yang, B., Zhou, M. and Scheer, H. Phycobilin:cystein-84 biliprotein lyase, a near-universal lyase for cysteine-84-binding sites in cyanobacterial phycobiliproteins. Proc. Natl. Acad. Sci. USA 104 (2007) 14300–14305. [DOI] [PMID: 17726096]
3.	Saunee, N.A., Williams, S.R., Bryant, D.A. and Schluchter, W.M. Biogenesis of phycobiliproteins: II. CpcS-I and CpcU comprise the heterodimeric bilin lyase that attaches phycocyanobilin to Cys-82 of β-phycocyanin and Cys-81 of allophycocyanin subunits in Synechococcus sp. PCC 7002. J. Biol. Chem. 283 (2008) 7513–7522. [DOI] [PMID: 18199753]
4.	Kupka, M., Zhang, J., Fu, W.L., Tu, J.M., Bohm, S., Su, P., Chen, Y., Zhou, M., Scheer, H. and Zhao, K.H. Catalytic mechanism of S-type phycobiliprotein lyase: chaperone-like action and functional amino acid residues. J. Biol. Chem. 284 (2009) 36405–36414. [DOI] [PMID: 19864423]

[EC 4.4.1.29 created 2015]

4.4.1.30

Accepted name:

phycobiliprotein β-cysteine-155 phycobilin lyase

Reaction:

(1) [C-phycocyanin β-subunit]-Cys¹⁵⁵-phycocyanobilin = apo-[C-phycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(2) [phycoerythrocyanin β-subunit]-Cys¹⁵⁵-phycocyanobilin = apo-[phycoerythrocyanin β-subunit] + (2R,3E)-phycocyanobilin

Glossary:

phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin

Other name(s):

cpcT (gene name); cpeT1 (gene name); cpcT1 (gene name)

Systematic name:

[phycobiliprotein β-subunit]-Cys¹⁵⁵-phycocyanobilin:phycocyanobilin lyase

Comments:

The enzyme, found in cyanobacteria and red algae, catalyses the attachment of the phycobilin chromophore phycocyanobilin to cysteine 155 of the β subunits of the phycobiliproteins C-phycocyanin and phycoerythrocyanin. The numbering used here corresponds to the enzyme from Anabaena, and could vary slightly in other organisms.

Links to other databases:

References:

1.	Zhao, K.H., Zhang, J., Tu, J.M., Bohm, S., Ploscher, M., Eichacker, L., Bubenzer, C., Scheer, H., Wang, X. and Zhou, M. Lyase activities of CpcS- and CpcT-like proteins from Nostoc PCC7120 and sequential reconstitution of binding sites of phycoerythrocyanin and phycocyanin β-subunits. J. Biol. Chem. 282 (2007) 34093–34103. [DOI] [PMID: 17895251]
2.	Zhang, R., Feng, X.T., Wu, F., Ding, Y., Zang, X.N., Zhang, X.C., Yuan, D.Y. and Zhao, B.R. Molecular cloning and expression analysis of a new bilin lyase: the cpcT gene encoding a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the β-subunit of phycocyanin in Arthrospira platensis FACHB314. Gene 544 (2014) 191–197. [DOI] [PMID: 24768724]
3.	Zhou, W., Ding, W.L., Zeng, X.L., Dong, L.L., Zhao, B., Zhou, M., Scheer, H., Zhao, K.H. and Yang, X. Structure and mechanism of the phycobiliprotein lyase CpcT. J. Biol. Chem. 289 (2014) 26677–26689. [DOI] [PMID: 25074932]

[EC 4.4.1.30 created 2015]

4.4.1.31

Accepted name:

phycoerythrocyanin α-cysteine-84 phycoviolobilin lyase/isomerase

Reaction:

[phycoerythrocyanin α-subunit]-Cys⁸⁴-phycoviolobilin = apo-[phycoerythrocyanin α-subunit] + (2R,3E)-phycocyanobilin

Glossary:

phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
phycoviolobilin = 1⁵,1⁶-dihydrobiliverdin IIIa

Other name(s):

pecE (gene name); pecF (gene name); phycoviolobilin phycoerythrocyanin-α84-cystein-lyase; PecE/PecF; PEC-Cys-R84 PCB lyase/isomerase

Systematic name:

[phycoerythrocyanin α-subunit]-Cys⁸⁴-phycoviolobilin:(2R,3E)-phycocyanobilin lyase/isomerase

Comments:

The enzyme, characterized from the cyanobacteria Nostoc sp. PCC 7120 and Mastigocladus laminosus, catalyses the covalent attachment of the phycobilin chromophore phycocyanobilin to cysteine 84 of the β subunit of the phycobiliprotein phycoerythrocyanin and its isomerization to phycoviolobilin.

Links to other databases:

References:

1.	Jung, L.J., Chan, C.F. and Glazer, A.N. Candidate genes for the phycoerythrocyanin α subunit lyase. Biochemical analysis of pecE and pecF interposon mutants. J. Biol. Chem. 270 (1995) 12877–12884. [DOI] [PMID: 7759546]
2.	Zhao, K.H., Deng, M.G., Zheng, M., Zhou, M., Parbel, A., Storf, M., Meyer, M., Strohmann, B. and Scheer, H. Novel activity of a phycobiliprotein lyase: both the attachment of phycocyanobilin and the isomerization to phycoviolobilin are catalyzed by the proteins PecE and PecF encoded by the phycoerythrocyanin operon. FEBS Lett. 469 (2000) 9–13. [DOI] [PMID: 10708746]
3.	Storf, M., Parbel, A., Meyer, M., Strohmann, B., Scheer, H., Deng, M.G., Zheng, M., Zhou, M. and Zhao, K.H. Chromophore attachment to biliproteins: specificity of PecE/PecF, a lyase-isomerase for the photoactive 3¹-cys-α 84-phycoviolobilin chromophore of phycoerythrocyanin. Biochemistry 40 (2001) 12444–12456. [DOI] [PMID: 11591166]
4.	Zhao, K.H., Wu, D., Wang, L., Zhou, M., Storf, M., Bubenzer, C., Strohmann, B. and Scheer, H. Characterization of phycoviolobilin phycoerythrocyanin-α 84-cystein-lyase-(isomerizing) from Mastigocladus laminosus. Eur. J. Biochem. 269 (2002) 4542–4550. [DOI] [PMID: 12230566]

[EC 4.4.1.31 created 2015]

4.4.1.32

Accepted name:

C-phycocyanin α-cysteine-84 phycocyanobilin lyase

Reaction:

[C-phycocyanin α-subunit]-Cys⁸⁴-phycocyanobilin = apo-[C-phycocyanin α-subunit] + (2R,3E)-phycocyanobilin

Glossary:

phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin

Other name(s):

cpcE (gene name); cpcF (gene name)

Systematic name:

[C-phycocyanin α-subunit]-Cys⁸⁴-phycocyanobilin:(2R,3E)-phycocyanobilin lyase

Comments:

The enzyme, characterized from the cyanobacterium Synechococcus elongatus PCC 7942, catalyses the covalent attachment of the phycobilin chromophore phycocyanobilin to cysteine 84 of the α subunit of the phycobiliprotein C-phycocyanin.

Links to other databases:

References:

1.	Fairchild, C.D., Zhao, J., Zhou, J., Colson, S.E., Bryant, D.A. and Glazer, A.N. Phycocyanin α-subunit phycocyanobilin lyase. Proc. Natl. Acad. Sci. USA 89 (1992) 7017–7021. [DOI] [PMID: 1495995]
2.	Fairchild, C.D. and Glazer, A.N. Oligomeric structure, enzyme kinetics, and substrate specificity of the phycocyanin α subunit phycocyanobilin lyase. J. Biol. Chem. 269 (1994) 8686–8694. [PMID: 8132596]
3.	Bhalerao, R.P., Lind, L.K. and Gustafsson, P. Cloning of the cpcE and cpcF genes from Synechococcus sp. PCC 6301 and their inactivation in Synechococcus sp. PCC 7942. Plant Mol. Biol. 26 (1994) 313–326. [PMID: 7524727]

[EC 4.4.1.32 created 2015]

4.4.1.33

Accepted name:

R-phycocyanin α-cysteine-84 phycourobilin lyase/isomerase

Reaction:

[R-phycocyanin α-subunit]-Cys⁸⁴-phycourobilin = apo-[R-phycocyanin α-subunit] + (2R,3E)-phycoerythrobilin

Other name(s):

rpcG (gene name)

Systematic name:

[R-phycocyanin α-subunit]-Cys⁸⁴-phycourobilin:(2R,3E)-phycoerythrobilin lyase/isomerase

Comments:

The enzyme, characterized from the cyanobacterium Synechococcus sp. WH8102, catalyses the covalent attachment of the phycobilin chromophore phycoerythrobilin to cysteine 84 of the α subunit of the phycobiliprotein R-phycocyanin and its isomerization to phycourobilin.

Links to other databases:

References:

Blot, N., Wu, X.J., Thomas, J.C., Zhang, J., Garczarek, L., Bohm, S., Tu, J.M., Zhou, M., Ploscher, M., Eichacker, L., Partensky, F., Scheer, H. and Zhao, K.H. Phycourobilin in trichromatic phycocyanin from oceanic cyanobacteria is formed post-translationally by a phycoerythrobilin lyase-isomerase. J. Biol. Chem. 284 (2009) 9290–9298. [DOI] [PMID: 19182270]

[EC 4.4.1.33 created 2015]

5.1.1.20

Accepted name:

L-Ala-D/L-Glu epimerase

Reaction:

L-alanyl-D-glutamate = L-alanyl-L-glutamate

Other name(s):

YkfB; YcjG; AEE; AE epimerase

Systematic name:

L-alanyl-D-glutamate epimerase

Comments:

The enzyme, characterized from the bacteria Escherichia coli and Bacillus subtilis, is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. In vitro the enzyme from Escherichia coli epimerizes several L-Ala-L-X dipeptides with broader specificity than the enzyme from Bacillus subtilis.

Links to other databases:

References:

1.	Schmidt, D.M., Hubbard, B.K. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases. Biochemistry 40 (2001) 15707–15715. [DOI] [PMID: 11747447]
2.	Gulick, A.M., Schmidt, D.M., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis. Biochemistry 40 (2001) 15716–15724. [DOI] [PMID: 11747448]

[EC 5.1.1.20 created 2015]

5.3.1.32

Accepted name:

(4S)-4-hydroxy-5-phosphooxypentane-2,3-dione isomerase

Reaction:

(2S)-2-hydroxy-3,4-dioxopentyl phosphate = 3-hydroxy-2,4-dioxopentyl phosphate

Glossary:

(2S)-2-hydroxy-3,4-dioxopentyl phosphate = (4S)-4-hydroxy-5-phosphooxypentane-2,3-dione
(4S)-4,5-dihydroxypentane-2,3-dione = autoinducer 2 = AI-2

Other name(s):

lsrG (gene name); phospho-AI-2 isomerase; (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione aldose-ketose-isomerase; (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase; (4S)-4-hydroxy-5-phosphooxypentane-2,3-dione aldose-ketose-isomerase

Systematic name:

(2S)-2-hydroxy-3,4-dioxopentyl phosphate aldose-ketose-isomerase

Comments:

The enzyme participates in a degradation pathway of the bacterial quorum-sensing autoinducer molecule AI-2.

Links to other databases:

References:

1.	Xavier, K.B., Miller, S.T., Lu, W., Kim, J.H., Rabinowitz, J., Pelczer, I., Semmelhack, M.F. and Bassler, B.L. Phosphorylation and processing of the quorum-sensing molecule autoinducer-2 in enteric bacteria. ACS Chem. Biol. 2 (2007) 128–136. [DOI] [PMID: 17274596]
2.	Marques, J.C., Lamosa, P., Russell, C., Ventura, R., Maycock, C., Semmelhack, M.F., Miller, S.T. and Xavier, K.B. Processing the interspecies quorum-sensing signal autoinducer-2 (AI-2): characterization of phospho-(S)-4,5-dihydroxy-2,3-pentanedione isomerization by LsrG protein. J. Biol. Chem. 286 (2011) 18331–18343. [DOI] [PMID: 21454635]

[EC 5.3.1.32 created 2015]

5.5.1.26

Accepted name:

nogalonic acid methyl ester cyclase

Reaction:

nogalaviketone = methyl nogalonate

Glossary:

methyl nogalonate = methyl [4,5-dihydroxy-9,10-dioxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate
nogalaviketone = methyl 5,7-dihydroxy-2-methyl-4,6,11-trioxo-3,4,6,11-tetrahydrotetracene-1-carboxylate

Other name(s):

methyl nogalonate cyclase; SnoaL (gene name); methyl nogalonate lyase (cyclizing)

Systematic name:

nogalaviketone lyase (ring-opening)

Comments:

The enzyme, characterized from the bacterium Streptomyces nogalater, is involved in the biosynthesis of the aromatic polyketide nogalamycin.

Links to other databases:

References:

1.	Sultana, A., Kallio, P., Jansson, A., Wang, J.S., Niemi, J., Mantsala, P. and Schneider, G. Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation. EMBO J. 23 (2004) 1911–1921. [DOI] [PMID: 15071504]
2.	Sultana, A., Kallio, P., Jansson, A., Niemi, J., Mantsala, P. and Schneider, G. Crystallization and preliminary crystallographic data of SnoaL, a polyketide cyclase in nogalamycin biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1118–1120. [DOI] [PMID: 15159574]

[EC 5.5.1.26 created 2015]

*EC

6.3.2.37

Accepted name:

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—D-lysine ligase

Reaction:

ATP + UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate + D-lysine = ADP + phosphate + UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-N^ε-D-lysine

Glossary:

muramic acid = 2-amino-3-O-[(R)-1-carboxyethyl]-2-deoxy-D-glucose

Other name(s):

UDP-MurNAc-L-Ala-D-Glu:D-Lys ligase; D-lysine-adding enzyme

Systematic name:

UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate:D-lysine γ-ligase (ADP-forming)

Comments:

Involved in the synthesis of cell-wall peptidoglycan. The D-lysine is attached to the peptide chain at the N⁶ position. The enzyme from Thermotoga maritima also performs the reaction of EC 6.3.2.7, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase.

Links to other databases:

References:

1.	Boniface, A., Bouhss, A., Mengin-Lecreulx, D. and Blanot, D. The MurE synthetase from Thermotoga maritima is endowed with an unusual D-lysine adding activity. J. Biol. Chem. 281 (2006) 15680–15686. [DOI] [PMID: 16595662]

[EC 6.3.2.37 created 2011, modified 2015]

6.3.2.46

Accepted name:

fumarate—(S)-2,3-diaminopropanoate ligase

Reaction:

ATP + fumarate + L-2,3-diaminopropanoate = AMP + diphosphate + N³-fumaroyl-L-2,3-diaminopropanoate

Glossary:

N³-fumaroyl-L-2,3-diaminopropanoate = (2E)-4-{[(2S)-2-amino-2-carboxyethyl]amino}-4-oxobut-2-enoate
L-2,3-diaminopropanoate = (S)-2,3-diaminopropanoate

Other name(s):

DdaG; fumarate:(S)-2,3-diaminopropanoate ligase (AMP-forming)

Systematic name:

fumarate:L-2,3-diaminopropanoate ligase (AMP-forming)

Comments:

The enzyme, characterized from the bacterium Enterobacter agglomerans, is involved in biosynthesis of dapdiamide tripeptide antibiotics, a family of fumaramoyl- and epoxysuccinamoyl-peptides named for the presence of an L-2,3-diaminopropanoate (DAP) moiety and two amide linkages in their scaffold.

Links to other databases:

References:

1.	Hollenhorst, M.A., Clardy, J. and Walsh, C.T. The ATP-dependent amide ligases DdaG and DdaF assemble the fumaramoyl-dipeptide scaffold of the dapdiamide antibiotics. Biochemistry 48 (2009) 10467–10472. [DOI] [PMID: 19807062]

[EC 6.3.2.46 created 2015]

6.3.2.47

Accepted name:

dapdiamide synthase

Reaction:

(1) ATP + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine + L-valine = ADP + phosphate + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-valine
(2) ATP + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine + L-isoleucine = ADP + phosphate + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-isoleucine
(3) ATP + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine + L-leucine = ADP + phosphate + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-leucine
(4) ATP + 3-({[(2R,3R)-3-carbamoyloxiran-2-yl]carbonyl}amino)-L-alanine + L-valine = ADP + phosphate + 3-({[(2R,3R)-3-carbamoyloxiran-2-yl]carbonyl}amino)-L-alanyl-L-valine

Glossary:

dapdiamide A = 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-valine
dapdiamide B = 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-isoleucine
dapdiamide C = 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-leucine

Other name(s):

DdaF; dapdiamide A synthase

Systematic name:

3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine:L-valine ligase (ADP-forming)

Comments:

The enzyme, characterized from the bacterium Pantoea agglomerans, is involved in biosynthesis of dapdiamide tripeptide antibiotics, a family of fumaramoyl- and epoxysuccinamoyl-peptides named for the presence of an (S)-2,3-diaminopropanoate (DAP) moiety and two amide linkages in their scaffold.

Links to other databases: