Proposed Changes to the Enzyme List

References:

Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl. Acad. Sci. USA 113 (2016) E4161–E4169. [DOI] [PMID: 27402745]

[EC 1.1.1.408 created 2017]

1.1.1.409

Accepted name:

4-phospho-D-erythronate 3-dehydrogenase

Reaction:

4-phospho-D-erythronate + NAD⁺ = glycerone phosphate + CO₂ + NADH + H⁺ (overall reaction)
(1a) 4-phospho-D-erythronate + NAD⁺ = 3-dehydro-4-phospho-L-threonate + NADH + H⁺
(1b) 3-dehydro-4-phospho-L-threonate = glycerone phosphate + CO₂ (spontaneous)

For diagram of erythronate and threonate catabolism, click here

Glossary:

D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate

Other name(s):

pdxA2 (gene name) (ambiguous)

Systematic name:

4-phospho-D-erythronate:NAD⁺ 3-oxidoreductase

Comments:

The enzyme, characterized from bacteria, is involved in a pathway for D-erythronate catabolism.

Links to other databases:

References:

[EC 1.1.1.409 created 2017]

1.1.1.410

Accepted name:

D-erythronate 2-dehydrogenase

Reaction:

D-erythronate + NAD⁺ = 2-dehydro-D-erythronate + NADH + H⁺

For diagram of erythronate and threonate catabolism, click here

Glossary:

D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
2-dehydro-D-erythronate = (3R)-3,4-dihydroxy-2-oxobutanoate

Other name(s):

denD (gene name)

Systematic name:

D-erythronate:NAD⁺ 2-oxidoreductase

Comments:

The enzyme, characterized from bacteria, is involved in D-erythronate catabolism.

Links to other databases:

References:

[EC 1.1.1.410 created 2017]

1.1.1.411

Accepted name:

L-threonate 2-dehydrogenase

Reaction:

L-threonate + NAD⁺ = 2-dehydro-L-erythronate + NADH + H⁺

For diagram of erythronate and threonate catabolism, click here

Glossary:

L-threonate = (2R,3S)-2,3,4-trihydroxybutanoate
2-dehydro-L-erythronate = (3R)-3,4-dihydroxy-2-oxobutanoate

Other name(s):

ltnD (gene name)

Systematic name:

L-threonate:NAD⁺ 2-oxidoreductase

Comments:

The enzyme, characterized from bacteria, is involved in L-threonate catabolism.

Links to other databases:

References:

[EC 1.1.1.411 created 2017]

1.2.1.99

Accepted name:

4-(γ-glutamylamino)butanal dehydrogenase

Reaction:

4-(γ-L-glutamylamino)butanal + NAD(P)⁺ + H₂O = 4-(γ-L-glutamylamino)butanoate + NAD(P)H + H⁺

Other name(s):

puuC (gene name)

Systematic name:

4-(γ-L-glutamylamino)butanal:NAD(P)⁺ oxidoreductase

Comments:

The enzyme, characterized from the bacterium Escherichia coli, is involved in a putrescine catabolic pathway. It has a broad substrate range, and can also catalyse the activities of EC 1.2.1.19, aminobutyraldehyde dehydrogenase, and EC 1.2.1.24, succinate-semialdehyde dehydrogenase (NAD⁺).

Links to other databases:

References:

1.	Kurihara, S., Oda, S., Kato, K., Kim, H.G., Koyanagi, T., Kumagai, H. and Suzuki, H. A novel putrescine utilization pathway involves γ-glutamylated intermediates of Escherichia coli K-12. J. Biol. Chem. 280 (2005) 4602–4608. [DOI] [PMID: 15590624]
2.	Jo, J.E., Mohan Raj, S., Rathnasingh, C., Selvakumar, E., Jung, W.C. and Park, S. Cloning, expression, and characterization of an aldehyde dehydrogenase from Escherichia coli K-12 that utilizes 3-hydroxypropionaldehyde as a substrate. Appl. Microbiol. Biotechnol. 81 (2008) 51–60. [DOI] [PMID: 18668238]
3.	Schneider, B.L. and Reitzer, L. Pathway and enzyme redundancy in putrescine catabolism in Escherichia coli. J. Bacteriol. 194 (2012) 4080–4088. [DOI] [PMID: 22636776]

[EC 1.2.1.99 created 2017]

1.2.7.12

Accepted name:

formylmethanofuran dehydrogenase

Reaction:

a formylmethanofuran + H₂O + 2 oxidized ferredoxin [iron-sulfur] cluster = CO₂ + a methanofuran + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H⁺

For diagram of methane biosynthesis, click here

Glossary:

methanofuran a = 4-[4-(2-{[(4R*,5S*)-4,5,7-tricarboxyheptanoyl]-γ-L-glutamyl-γ-L-glutamylamino}ethyl)phenoxymethyl]furan-2-ylmethanamine

Other name(s):

formylmethanofuran:acceptor oxidoreductase

Systematic name:

formylmethanofuran:ferredoxin oxidoreductase

Comments:

Contains a molybdopterin cofactor and numerous [4Fe-4S] clusters. In some organisms an additional subunit enables the incorporation of tungsten when molybdenum availability is low. The enzyme catalyses a reversible reaction in methanogenic archaea, and is involved in methanogenesis from CO₂ as well as the oxidation of coenzyme M to CO₂. The reaction is endergonic, and is driven by coupling with the soluble CoB-CoM heterodisulfide reductase via electron bifurcation.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 119940-12-4

References:

1.	Karrasch, M., Börner, G., Enssle, M. and Thauer, R.K. The molybdoenzyme formylmethanofuran dehydrogenase from Methanosarcina barkeri contains a pterin cofactor. Eur. J. Biochem. 194 (1990) 367–372. [DOI] [PMID: 2125267]
2.	Bertram, P.A., Schmitz, R.A., Linder, D. and Thauer, R.K. Tungstate can substitute for molybdate in sustaining growth of Methanobacterium thermoautotrophicum. Identification and characterization of a tungsten isoenzyme of formylmethanofuran dehydrogenase. Arch. Microbiol. 161 (1994) 220–228. [PMID: 8161283]
3.	Bertram, P.A., Karrasch, M., Schmitz, R.A., Bocher, R., Albracht, S.P. and Thauer, R.K. Formylmethanofuran dehydrogenases from methanogenic Archaea. Substrate specificity, EPR properties and reversible inactivation by cyanide of the molybdenum or tungsten iron-sulfur proteins. Eur. J. Biochem. 220 (1994) 477–484. [DOI] [PMID: 8125106]
4.	Vorholt, J.A. and Thauer, R.K. The active species of ’CO₂’ utilized by formylmethanofuran dehydrogenase from methanogenic Archaea. Eur. J. Biochem. 248 (1997) 919–924. [DOI] [PMID: 9342247]
5.	Meuer, J., Kuettner, H.C., Zhang, J.K., Hedderich, R. and Metcalf, W.W. Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc. Natl. Acad. Sci. USA 99 (2002) 5632–5637. [DOI] [PMID: 11929975]
6.	Kaster, A.K., Moll, J., Parey, K. and Thauer, R.K. Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc. Natl. Acad. Sci. USA 108 (2011) 2981–2986. [DOI] [PMID: 21262829]
7.	Wagner, T., Ermler, U. and Shima, S. The methanogenic CO₂ reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters. Science 354 (2016) 114–117. [PMID: 27846502]

[EC 1.2.7.12 created 1992 as EC 1.2.99.5, transferred 2017 to EC 1.2.7.12]

*EC

1.5.8.4

Accepted name:

dimethylglycine dehydrogenase

Reaction:

N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein = sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein

Glossary:

sarcosine = N-methylglycine

Other name(s):

N,N-dimethylglycine oxidase; N,N-dimethylglycine:(acceptor) oxidoreductase (demethylating); Me2GlyDH; N,N-dimethylglycine:electron-transfer flavoprotein oxidoreductase (demethylating)

Systematic name:

N,N-dimethylglycine,5,6,7,8-tetrahydrofolate:electron-transferflavoprotein oxidoreductase (demethylating,5,10-methylenetetrahydrofolate-forming)

Comments:

A flavoprotein, containing a histidyl(N^π)-(8α)FAD linkage at position 91 in the human protein. An imine intermediate is channeled from the FAD binding site to the 5,6,7,8-tetrahydrofolate binding site through a 40 Å tunnel [5,8,9]. In the absence of 5,6,7,8-tetrahydrofolate the enzyme forms formaldehyde [5,9].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37256-30-7

References:

1.	Frisell, W.R. and MacKenzie, C.G. Separation and purification of sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 237 (1962) 94–98. [DOI] [PMID: 13895406]
2.	Hoskins, D.D. and MacKenzie, C.G. Solubilization and electron transfer flavoprotein requirement of mitochondrial sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 236 (1961) 177–183. [DOI] [PMID: 13716069]
3.	Wittwer, A.J. and Wagner, C. Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Purification and folate-binding characteristics. J. Biol. Chem. 256 (1981) 4102–4108. [PMID: 6163777]
4.	Wittwer, A.J. and Wagner, C. Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Flavoprotein nature and enzymatic properties of the purified proteins. J. Biol. Chem. 256 (1981) 4109–4115. [DOI] [PMID: 6163778]
5.	Porter, D.H., Cook, R.J. and Wagner, C. Enzymatic properties of dimethylglycine dehydrogenase and sarcosine dehydrogenase from rat liver. Arch. Biochem. Biophys. 243 (1985) 396–407. [DOI] [PMID: 2417560]
6.	Brizio, C., Brandsch, R., Bufano, D., Pochini, L., Indiveri, C. and Barile, M. Over-expression in Escherichia coli, functional characterization and refolding of rat dimethylglycine dehydrogenase. Protein Expr. Purif. 37 (2004) 434–442. [DOI] [PMID: 15358367]
7.	Brizio, C., Brandsch, R., Douka, M., Wait, R. and Barile, M. The purified recombinant precursor of rat mitochondrial dimethylglycine dehydrogenase binds FAD via an autocatalytic reaction. Int. J. Biol. Macromol. 42 (2008) 455–462. [DOI] [PMID: 18423846]
8.	Luka, Z., Pakhomova, S., Loukachevitch, L.V., Newcomer, M.E. and Wagner, C. Folate in demethylation: the crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate. Biochem. Biophys. Res. Commun. 449 (2014) 392–398. [DOI] [PMID: 24858690]
9.	Augustin, P., Hromic, A., Pavkov-Keller, T., Gruber, K. and Macheroux, P. Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant. FEBS J. 283 (2016) 3587–3603. [DOI] [PMID: 27486859]

[EC 1.5.8.4 created 1972 as EC 1.5.99.2, transferred 2012 to EC 1.5.8.4, modified 2017]

1.7.1.16

Accepted name:

nitrobenzene nitroreductase

Reaction:

N-phenylhydroxylamine + 2 NADP⁺ + H₂O = nitrobenzene + 2 NADPH + 2 H⁺ (overall reaction)
(1a) N-phenylhydroxylamine + NADP⁺ = nitrosobenzene + NADPH + H⁺
(1b) nitrosobenzene + NADP⁺ + H₂O = nitrobenzene + NADPH + H⁺

Other name(s):

cnbA (gene name)

Systematic name:

N-phenylhydroxylamine:NADP⁺ oxidoreductase

Comments:

Contains FMN. The enzyme, characterized from Pseudomonas species, catalyses two successive reductions of nitrobenzene, via a nitrosobenzene intermediate. It is also active on 1-chloro-4-nitrobenzene.

Links to other databases:

References:

1.	Somerville, C.C., Nishino, S.F. and Spain, J.C. Purification and characterization of nitrobenzene nitroreductase from Pseudomonas pseudoalcaligenes JS45. J. Bacteriol. 177 (1995) 3837–3842. [DOI] [PMID: 7601851]
2.	Wu, J.F., Jiang, C.Y., Wang, B.J., Ma, Y.F., Liu, Z.P. and Liu, S.J. Novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in Comamonas sp. strain CNB-1. Appl. Environ. Microbiol. 72 (2006) 1759–1765. [DOI] [PMID: 16517619]

[EC 1.7.1.16 created 2017]

1.7.99.4

Transferred entry:

nitrate reductase, Now EC 1.7.1.1, nitrate reductase (NADH), EC 1.7.1.2, nitrate reductase [NAD(P)H], EC 1.7.1.3, nitrate reductase (NADPH), EC 1.7.5.1, nitrate reductase (quinone), EC 1.7.7.2, nitrate reductase (ferredoxin) and EC 1.9.6.1, nitrate reductase (cytochrome)

[EC 1.7.99.4 created 1972, modified 1976, deleted 2017]

*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]

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]

1.14.13.235

Accepted name:

indole-3-acetate monooxygenase

Reaction:

(indol-3-yl)acetate + NADH + H⁺ + O₂ = (2-hydroxy-1H-indol-3-yl)acetate + NAD⁺ + H₂O

Glossary:

(indol-3-yl)acetate =(1H-indol-3-yl)acetate = indole-3-acetate

Other name(s):

iacA (gene name)

Systematic name:

(indol-3-yl)acetate,NADH:oxygen oxidoreductase (2-hydroxylating)

Comments:

The enzyme, characterized from Pseudomonas putida strains, catalyses the first step in a pathway for degradation of the plant hormone indole-3-acetate. When acting on indole, the enzyme forms indoxyl, which reacts spontaneously with oxygen to form the blue dye indigo.

Links to other databases:

References:

1.	Leveau, J.H. and Lindow, S.E. Utilization of the plant hormone indole-3-acetic acid for growth by Pseudomonas putida strain 1290. Appl. Environ. Microbiol. 71 (2005) 2365–2371. [DOI] [PMID: 15870323]
2.	Scott, J.C., Greenhut, I.V. and Leveau, J.H. Functional characterization of the bacterial iac genes for degradation of the plant hormone indole-3-acetic acid. J Chem Ecol 39 (2013) 942–951. [DOI] [PMID: 23881445]

[EC 1.14.13.235 created 2017]

1.14.13.236

Accepted name:

toluene 4-monooxygenase

Reaction:

toluene + NADH + H⁺ + O₂ = 4-methylphenol + NAD⁺ + H₂O

Glossary:

4-methylphenol = p-cresol

Other name(s):

TMO

Systematic name:

toluene,NADH:oxygen oxidoreductase (4-hydroxylating)

Comments:

This bacterial enzyme belongs to a family of soluble diiron hydroxylases that includes toluene-, benzene-, xylene- and methane monooxygenases, phenol hydroxylases, and alkene epoxidases. The enzyme comprises a four-component complex that includes a hydroxylase, NADH-ferredoxin oxidoreductase, a Rieske-type [2Fe-2S] ferredoxin, and an effector protein.

Links to other databases:

References:

1.	Whited, G.M. and Gibson, D.T. Toluene-4-monooxygenase, a three-component enzyme system that catalyzes the oxidation of toluene to p-cresol in Pseudomonas mendocina KR1. J. Bacteriol. 173 (1991) 3010–3016. [DOI] [PMID: 2019563]
2.	Hemmi, H., Studts, J.M., Chae, Y.K., Song, J., Markley, J.L. and Fox, B.G. Solution structure of the toluene 4-monooxygenase effector protein (T4moD). Biochemistry 40 (2001) 3512–3524. [DOI] [PMID: 11297417]
3.	Schwartz, J.K., Wei, P.P., Mitchell, K.H., Fox, B.G. and Solomon, E.I. Geometric and electronic structure studies of the binuclear nonheme ferrous active site of toluene-4-monooxygenase: parallels with methane monooxygenase and insight into the role of the effector proteins in O₂ activation. J. Am. Chem. Soc. 130 (2008) 7098–7109. [DOI] [PMID: 18479085]
4.	Bailey, L.J., Acheson, J.F., McCoy, J.G., Elsen, N.L., Phillips, G.N., Jr. and Fox, B.G. Crystallographic analysis of active site contributions to regiospecificity in the diiron enzyme toluene 4-monooxygenase. Biochemistry 51 (2012) 1101–1113. [DOI] [PMID: 22264099]
5.	Hosseini, A., Brouk, M., Lucas, M.F., Glaser, F., Fishman, A. and Guallar, V. Atomic picture of ligand migration in toluene 4-monooxygenase. J. Phys. Chem. B 119 (2015) 671–678. [DOI] [PMID: 24798294]

[EC 1.14.13.236 created 2017]

*EC

1.14.14.30

Accepted name:

isobutylamine N-monooxygenase

Reaction:

(1) 2-methylpropan-1-amine + FADH₂ + O₂ = N-(2-methylpropyl)hydroxylamine + FAD + H₂O
(2) 2-methylpropan-1-amine + FMNH₂ + O₂ = N-(2-methylpropyl)hydroxylamine + FMN + H₂O

Glossary:

2-methylpropan-1-amine = isobutylamine
N-(2-methylpropyl)hydroxylamine = N-hydroxy-2-methylpropan-1-amine = isobutylhydroxylamine

Other name(s):

vlmH (gene name)

Systematic name:

2-methylpropan-1-amine,FADH₂:O₂ N-oxidoreductase

Comments:

The enzyme, characterized from the bacterium Streptomyces viridifaciens, is part of a two component system that also includes a flavin reductase, which provides reduced flavin mononucleotide for this enzyme. The enzyme, which is involved in the biosynthesis of the azoxy antibiotic valanimycin, has a similar activity with either FMNH₂ or FADH₂. It exhibits broad specificity, and also accepts propan-1-amine, butan-1-amine, butan-2-amine and benzylamine.

Links to other databases:

References:

1.	Parry, R.J. and Li, W. Purification and characterization of isobutylamine N-hydroxylase from the valanimycin producer Streptomyces viridifaciens MG456-hF10. Arch. Biochem. Biophys. 339 (1997) 47–54. [DOI] [PMID: 9056232]
2.	Parry, R.J., Li, W. and Cooper, H.N. Cloning, analysis, and overexpression of the gene encoding isobutylamine N-hydroxylase from the valanimycin producer, Streptomyces viridifaciens. J. Bacteriol. 179 (1997) 409–416. [DOI] [PMID: 8990292]
3.	Parry, R.J. and Li, W. An NADPH:FAD oxidoreductase from the valanimycin producer, Streptomyces viridifaciens. Cloning, analysis, and overexpression. J. Biol. Chem. 272 (1997) 23303–23311. [DOI] [PMID: 9287340]

[EC 1.14.14.30 created 2016, modified 2017]

1.14.14.44

Accepted name:

phenylacetaldehyde oxime monooxygenase

Reaction:

(E)-phenylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + O₂ = (R)-mandelonitrile + [oxidized NADPH—hemoprotein reductase] + 2 H₂O (overall reaction)
(1a) (E)-phenylacetaldehyde oxime = (Z)-phenylacetaldehyde oxime
(1b) (Z)-phenylacetaldehyde oxime = phenylacetonitrile + H₂O
(1c) phenylacetonitrile + [reduced NADPH—hemoprotein reductase] + O₂ = (R)-mandelonitrile + [oxidized NADPH—hemoprotein reductase] + H₂O

Glossary:

(R)-mandelonitrile = (2R)-hydroxy(phenyl)acetonitrile

Other name(s):

CYP71AN24 (gene name)

Systematic name:

(E)-phenylacetaldehyde oxime,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase

Comments:

This cytochrome P-450 (heme-thiolate) enzyme is involved in the biosynthesis of the cyanogenic glucosides (R)-prunasin and (R)-amygdalin. It catalyses three different activities - isomerization of the (E) isomer to the (Z) isomer, dehydration, and C-hydroxylation.

Links to other databases:

References:

Yamaguchi, T., Yamamoto, K. and Asano, Y. Identification and characterization of CYP79D16 and CYP71AN24 catalyzing the first and second steps in L-phenylalanine-derived cyanogenic glycoside biosynthesis in the Japanese apricot, Prunus mume Sieb. et Zucc. Plant Mol. Biol. 86 (2014) 215–223. [DOI] [PMID: 25015725]

[EC 1.14.14.44 created 2017]

1.14.14.45

Accepted name:

aromatic aldoxime N-monooxygenase

Reaction:

(1) (E)-indol-3-ylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + glutathione + O₂ = S-[(E)-N-hydroxy(indol-3-yl)acetimidoyl]-L-glutathione + [oxidized NADPH—hemoprotein reductase] + 2 H₂O (overall reaction)
(1a) (E)-indol-3-ylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + O₂ = 1-(1H-indol-3-yl)-2-aci-nitroethane + [oxidized NADPH—hemoprotein reductase] + H₂O
(1b) 1-(1H-indol-3-yl)-2-aci-nitroethane + glutathione = S-[(E)-N-hydroxy(indol-3-yl)acetimidoyl]-L-glutathione + H₂O (spontaneous)
(2) (E)-phenylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + glutathione + O₂ = S-[(Z)-N-hydroxy(phenyl)acetimidoyl]-L-glutathione + [oxidized NADPH—hemoprotein reductase] + 2 H₂O (overall reaction)
(2a) (E)-phenylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + O₂ = 1-aci-nitro-2-phenylethane + [oxidized NADPH—hemoprotein reductase] + H₂O
(2b) 1-aci-nitro-2-phenylethane + glutathione = S-[(Z)-N-hydroxy(phenyl)acetimidoyl]-L-glutathione + H₂O (spontaneous)

Other name(s):

CYP83B1 (gene name)

Systematic name:

(E)-indol-3-ylacetaldoxime,[reduced NADPH—hemoprotein reductase],glutathione:oxygen oxidoreductase (oxime-hydroxylating)

Comments:

This cytochrome P-450 (heme thiolate) enzyme is involved in the biosynthesis of glucosinolates in plants. The enzyme catalyses the N-hydroxylation of aromatic aldoximes derived from L-tryptophan, L-phenylalanine, and L-tyrosine, forming an aci-nitro intermediate that reacts non-enzymically with glutathione to produce an N-alkyl-thiohydroximate adduct, the committed precursor of glucosinolates. In the absence of glutathione, the enzyme is suicidal, probably due to interaction of the reactive aci-nitro compound with catalytic residues in the active site.

Links to other databases:

References:

1.	Bak, S., Tax, F.E., Feldmann, K.A., Galbraith, D.W. and Feyereisen, R. CYP83B1, a cytochrome P450 at the metabolic branch point in auxin and indole glucosinolate biosynthesis in Arabidopsis. Plant Cell 13 (2001) 101–111. [PMID: 11158532]
2.	Naur, P., Petersen, B.L., Mikkelsen, M.D., Bak, S., Rasmussen, H., Olsen, C.E. and Halkier, B.A. CYP83A1 and CYP83B1, two nonredundant cytochrome P450 enzymes metabolizing oximes in the biosynthesis of glucosinolates in Arabidopsis. Plant Physiol. 133 (2003) 63–72. [DOI] [PMID: 12970475]
3.	Geu-Flores, F., Møldrup, M.E., Böttcher, C., Olsen, C.E., Scheel, D. and Halkier, B.A. Cytosolic γ-glutamyl peptidases process glutathione conjugates in the biosynthesis of glucosinolates and camalexin in Arabidopsis. Plant Cell 23 (2011) 2456–2469. [DOI] [PMID: 21712415]

[EC 1.14.14.45 created 2017]

1.14.14.46

Accepted name:

pimeloyl-[acyl-carrier protein] synthase

Reaction:

a long-chain acyl-[acyl-carrier protein] + 2 reduced flavodoxin + 3 O₂ = pimeloyl-[acyl-carrier protein] + an n-alkanal + 2 oxidized flavodoxin + 3 H₂O (overall reaction)
(1a) a long-chain acyl-[acyl-carrier protein] + reduced flavodoxin + O₂ = a (7S)-7-hydroxy-long-chain-acyl-[acyl-carrier protein] + oxidized flavodoxin + H₂O
(1b) a (7S)-7-hydroxy-long-chain-acyl-[acyl-carrier protein] + reduced flavodoxin + O₂ = a (7R,8R)-7,8-dihydroxy-long-chain-acyl-[acyl-carrier protein] + oxidized flavodoxin + H₂O
(1c) a (7R,8R)-7,8-dihydroxy-long-chain-acyl-[acyl-carrier protein] + reduced flavodoxin + O₂ = a 7-oxoheptanoyl-[acyl-carrier protein] + an n-alkanal + oxidized flavodoxin + 2 H₂O
(1d) a 7-oxoheptanoyl-[acyl-carrier protein] + oxidized flavodoxin + H₂O = a pimeloyl-[acyl-carrier protein] + reduced flavodoxin + H⁺

Glossary:

a long-chain acyl-[acyl-carrier protein] = an acyl-[acyl-carrier protein] thioester where the acyl chain contains 13 to 22 carbon atoms.
palmitoyl-[acyl-carrier protein] = hexadecanoyl-[acyl-carrier protein]
pimeloyl-[acyl-carrier protein] = 6-carboxyhexanoyl-[acyl-carrier protein]

Other name(s):

bioI (gene name); P450BioI; CYP107H1

Systematic name:

acyl-[acyl-carrier protein],reduced-flavodoxin:oxygen oxidoreductase (pimeloyl-[acyl-carrier protein]-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein. The enzyme catalyses an oxidative C-C bond cleavage of long-chain acyl-[acyl-carrier protein]s of various lengths to generate pimeloyl-[acyl-carrier protein], an intermediate in the biosynthesis of biotin. The preferred substrate of the enzyme from the bacterium Bacillus subtilis is palmitoyl-[acyl-carrier protein] which then gives heptanal as the alkanal. The mechanism is similar to EC 1.14.15.6, cholesterol monooxygenase (side-chain-cleaving), followed by a hydroxylation step, which may occur spontaneously [2].

Links to other databases:

References:

1.	Stok, J.E. and De Voss, J. Expression, purification, and characterization of BioI: a carbon-carbon bond cleaving cytochrome P450 involved in biotin biosynthesis in Bacillus subtilis. Arch. Biochem. Biophys. 384 (2000) 351–360. [DOI] [PMID: 11368323]
2.	Cryle, M.J. and De Voss, J.J. Carbon-carbon bond cleavage by cytochrome p₄₅₀(BioI)(CYP107H1). Chem. Commun. (Camb.) (2004) 86–87. [DOI] [PMID: 14737344]
3.	Cryle, M.J. and Schlichting, I. Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex. Proc. Natl. Acad. Sci. USA 105 (2008) 15696–15701. [DOI] [PMID: 18838690]
4.	Cryle, M.J. Selectivity in a barren landscape: the P450(BioI)-ACP complex. Biochem. Soc. Trans. 38 (2010) 934–939. [DOI] [PMID: 20658980]

[EC 1.14.14.46 created 2013 as EC 1.14.15.12, transferred 2017 to EC 1.14.14.46]

1.14.14.47

Accepted name:

nitric-oxide synthase (flavodoxin)

Reaction:

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

Glossary:

nitric oxide = NO = nitrogen(II) oxide

Other name(s):

nitric oxide synthetase (ambiguous); NO synthase (ambiguous)

Systematic name:

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

Comments:

Binds heme (iron protoporphyrin IX) and tetrahydrobiopterin. The enzyme, found in bacteria and archaea, consist of only an oxygenase domain and functions together with bacterial ferredoxins or flavodoxins. The orthologous enzymes from plants and animals also contain a reductase domain and use only NADPH as the electron donor (cf. EC 1.14.13.39).

Links to other databases:

References:

1.	Pant, K., Bilwes, A.M., Adak, S., Stuehr, D.J. and Crane, B.R. Structure of a nitric oxide synthase heme protein from Bacillus subtilis. Biochemistry 41 (2002) 11071–11079. [DOI] [PMID: 12220171]
2.	Adak, S., Aulak, K.S. and Stuehr, D.J. Direct evidence for nitric oxide production by a nitric-oxide synthase-like protein from Bacillus subtilis. J. Biol. Chem. 277 (2002) 16167–16171. [DOI] [PMID: 11856757]
3.	Wang, Z.Q., Lawson, R.J., Buddha, M.R., Wei, C.C., Crane, B.R., Munro, A.W. and Stuehr, D.J. Bacterial flavodoxins support nitric oxide production by Bacillus subtilis nitric-oxide synthase. J. Biol. Chem. 282 (2007) 2196–2202. [DOI] [PMID: 17127770]
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.	Holden, J.K., Lim, N. and Poulos, T.L. Identification of redox partners and development of a novel chimeric bacterial nitric oxide synthase for structure activity analyses. J. Biol. Chem. 289 (2014) 29437–29445. [DOI] [PMID: 25194416]

[EC 1.14.14.47 created 2012 as EC 1.14.13.165, transferred 2017 to EC 1.14.14.47]

1.14.15.12

Transferred entry:

pimeloyl-[acyl-carrier protein] synthase. Now EC 1.14.14.46, pimeloyl-[acyl-carrier protein] synthase

[EC 1.14.15.12 created 2013, deleted 2017]

1.14.19.51

Accepted name:

(S)-corytuberine synthase

Reaction:

(S)-reticuline + [reduced NADPH—hemoprotein reductase] + O₂ = (S)-corytuberine + [oxidized NADPH—hemoprotein reductase] + 2 H₂O.

For diagram of corytuberine and magnoflorine biosynthesis, click here

Other name(s):

CYP80G2

Systematic name:

(S)-reticuline,NADPH:oxygen oxidoreductase (C-C phenol-coupling; (S)-corytuberine-forming)

Comments:

A cytochrome P-450 (heme-thiolate) protein. The enzyme is involved in the biosynthesis of the quaternary benzylisoquinoline alkaloid magnoflorine in the plant Coptis japonica. It is specific for (S)-reticuline.

Links to other databases:

References:

Ikezawa, N., Iwasa, K. and Sato, F. Molecular cloning and characterization of CYP80G2, a cytochrome P450 that catalyzes an intramolecular C-C phenol coupling of (S)-reticuline in magnoflorine biosynthesis, from cultured Coptis japonica cells. J. Biol. Chem. 283 (2008) 8810–8821. [DOI] [PMID: 18230623]

[EC 1.14.19.51 created 2017]

1.14.99.54

Accepted name:

lytic cellulose monooxygenase (C1-hydroxylating)

Reaction:

[(1→4)-β-D-glucosyl]_n+m + reduced acceptor + O₂ = [(1→4)-β-D-glucosyl]_m-1-(1→4)-D-glucono-1,5-lactone + [(1→4)-β-D-glucosyl]_n + acceptor + H₂O

Other name(s):

lytic polysaccharide monooxygenase (ambiguous); LPMO (ambiguous); LPMO9A

Systematic name:

cellulose, hydrogen-donor:oxygen oxidoreductase (D-glucosyl C1-hydroxylating)

Comments:

This copper-containing enzyme, found in fungi and bacteria, cleaves cellulose in an oxidative manner. The cellulose fragments that are formed contain a D-glucono-1,5-lactone residue at the reducing end, which hydrolyses quickly and spontaneously to the aldonic acid. The electrons are provided in vivo by the cytochrome b domain of EC 1.1.99.18, cellobiose dehydrogenase (acceptor) [1]. Ascorbate can serve as the electron donor in vitro.

Links to other databases:

References:

1.	Phillips, C.M., Beeson, W.T., Cate, J.H. and Marletta, M.A. Cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by Neurospora crassa. ACS Chem. Biol. 6 (2011) 1399–1406. [DOI] [PMID: 22004347]
2.	Beeson, W.T., Phillips, C.M., Cate, J.H. and Marletta, M.A. Oxidative cleavage of cellulose by fungal copper-dependent polysaccharide monooxygenases. J. Am. Chem. Soc. 134 (2012) 890–892. [DOI] [PMID: 22188218]
3.	Li, X., Beeson, W.T., 4th, Phillips, C.M., Marletta, M.A. and Cate, J.H. Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases. Structure 20 (2012) 1051–1061. [DOI] [PMID: 22578542]
4.	Bey, M., Zhou, S., Poidevin, L., Henrissat, B., Coutinho, P.M., Berrin, J.G. and Sigoillot, J.C. Cello-oligosaccharide oxidation reveals differences between two lytic polysaccharide monooxygenases (family GH61) from Podospora anserina. Appl. Environ. Microbiol. 79 (2013) 488–496. [DOI] [PMID: 23124232]
5.	Frommhagen, M., Sforza, S., Westphal, A.H., Visser, J., Hinz, S.W., Koetsier, M.J., van Berkel, W.J., Gruppen, H. and Kabel, M.A. Discovery of the combined oxidative cleavage of plant xylan and cellulose by a new fungal polysaccharide monooxygenase. Biotechnol. Biofuels 8:101 (2015). [DOI] [PMID: 26185526]
6.	Patel, I., Kracher, D., Ma, S., Garajova, S., Haon, M., Faulds, C.B., Berrin, J.G., Ludwig, R. and Record, E. Salt-responsive lytic polysaccharide monooxygenases from the mangrove fungus Pestalotiopsis sp. NCi6. Biotechnol Biofuels 9:108 (2016). [DOI] [PMID: 27213015]
7.	Courtade, G., Wimmer, R., Rohr, A.K., Preims, M., Felice, A.K., Dimarogona, M., Vaaje-Kolstad, G., Sorlie, M., Sandgren, M., Ludwig, R., Eijsink, V.G. and Aachmann, F.L. Interactions of a fungal lytic polysaccharide monooxygenase with β-glucan substrates and cellobiose dehydrogenase. Proc. Natl. Acad. Sci. USA 113 (2016) 5922–5927. [DOI] [PMID: 27152023]

[EC 1.14.99.54 created 2017]

1.14.99.55

Accepted name:

lytic starch monooxygenase

Reaction:

starch + reduced acceptor + O₂ = D-glucono-1,5-lactone-terminated malto-oligosaccharides + short-chain malto-oligosaccharides + acceptor + H₂O

Other name(s):

LPMO (ambiguous)

Systematic name:

starch, hydrogen-donor:oxygen oxidoreductase (D-glucosyl C1-hydroxylating)

Comments:

The enzyme cleaves starch in an oxidative manner. It releases fragments of starch with a D-glucono-1,5-lactone at the reducing end. The initially formed α-D-glucono-1,5-lactone at the reducing end of the shortend amylose chain quickly hydrolyses spontaneously to the aldonic acid. In vitro ascorbate has been found to be able to serve as reducing agent. The enzyme contains copper at the active site.

Links to other databases:

References:

1.	Vu, V.V., Beeson, W.T., Span, E.A., Farquhar, E.R. and Marletta, M.A. A family of starch-active polysaccharide monooxygenases. Proc. Natl. Acad. Sci. USA 111 (2014) 13822–13827. [DOI] [PMID: 25201969]
2.	Gudmundsson, M., Kim, S., Wu, M., Ishida, T., Momeni, M.H., Vaaje-Kolstad, G., Lundberg, D., Royant, A., Stahlberg, J., Eijsink, V.G., Beckham, G.T. and Sandgren, M. Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-ray photoreduction. J. Biol. Chem. 289 (2014) 18782–18792. [DOI] [PMID: 24828494]
3.	Lo Leggio, L., Simmons, T.J., Poulsen, J.C., Frandsen, K.E., Hemsworth, G.R., Stringer, M.A., von Freiesleben, P., Tovborg, M., Johansen, K.S., De Maria, L., Harris, P.V., Soong, C.L., Dupree, P., Tryfona, T., Lenfant, N., Henrissat, B., Davies, G.J. and Walton, P.H. Structure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase. Nat. Commun. 6:5961 (2015). [DOI] [PMID: 25608804]

[EC 1.14.99.55 created 2017]

1.14.99.56

Accepted name:

lytic cellulose monooxygenase (C4-dehydrogenating)

Reaction:

[(1→4)-β-D-glucosyl]_n+m + reduced acceptor + O₂ = 4-dehydro-β-D-glucosyl-[(1→4)-β-D-glucosyl]_n-1 + [(1→4)-β-D-glucosyl]_m + acceptor + H₂O

Systematic name:

cellulose, hydrogen-donor:oxygen oxidoreductase (D-glucosyl 4-dehydrogenating)

Comments:

This copper-containing enzyme, found in fungi and bacteria, cleaves cellulose in an oxidative manner. The cellulose fragments that are formed contain a 4-dehydro-D-glucose residue at the non-reducing end. Some enzymes also oxidize cellulose at the C-1 position of the reducing end forming a D-glucono-1,5-lactone residue [cf. EC 1.14.99.54, lytic cellulose monooxygenase (C1-hydroxylating)].

Links to other databases:

References:

1.	Beeson, W.T., Phillips, C.M., Cate, J.H. and Marletta, M.A. Oxidative cleavage of cellulose by fungal copper-dependent polysaccharide monooxygenases. J. Am. Chem. Soc. 134 (2012) 890–892. [DOI] [PMID: 22188218]
2.	Li, X., Beeson, W.T., 4th, Phillips, C.M., Marletta, M.A. and Cate, J.H. Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases. Structure 20 (2012) 1051–1061. [DOI] [PMID: 22578542]
3.	Forsberg, Z., Mackenzie, A.K., Sorlie, M., Rohr, A.K., Helland, R., Arvai, A.S., Vaaje-Kolstad, G. and Eijsink, V.G. Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases. Proc. Natl. Acad. Sci. USA 111 (2014) 8446–8451. [DOI] [PMID: 24912171]
4.	Borisova, A.S., Isaksen, T., Dimarogona, M., Kognole, A.A., Mathiesen, G., Varnai, A., Rohr, A.K., Payne, C.M., Sorlie, M., Sandgren, M. and Eijsink, V.G. Structural and functional characterization of a lytic polysaccharide monooxygenase with broad substrate specificity. J. Biol. Chem. 290 (2015) 22955–22969. [DOI] [PMID: 26178376]
5.	Patel, I., Kracher, D., Ma, S., Garajova, S., Haon, M., Faulds, C.B., Berrin, J.G., Ludwig, R. and Record, E. Salt-responsive lytic polysaccharide monooxygenases from the mangrove fungus Pestalotiopsis sp. NCi6. Biotechnol Biofuels 9:108 (2016). [DOI] [PMID: 27213015]

[EC 1.14.99.56 created 2017]

1.14.99.57

Accepted name:

heme oxygenase (mycobilin-producing)

Reaction:

(1) protoheme + 3 reduced acceptor + 3 O₂ = mycobilin a + Fe²⁺ + 3 acceptor + 3 H₂O
(2) protoheme + 3 reduced acceptor + 3 O₂ = mycobilin b + Fe²⁺ + 3 acceptor + 3 H₂O

For diagram of mycobilin biosynthesis, click here

Glossary:

mycobilin a = 8,12-bis(2-carboxyethyl)-19-formyl-3,7,13,18-tetramethyl-3,17-divinylbiladiene-ab-1,15(21H)-dione
mycobilin b = 8,12-bis(2-carboxyethyl)-19-formyl-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ab-1,15(21H)-dione

Other name(s):

mhuD (gene name)

Systematic name:

protoheme,donor:oxygen oxidoreductase (mycobilin-producing)

Comments:

The enzyme, characterized from the bacterium Mycobacterium tuberculosis, is involved in heme degradation and iron utilization. The enzyme binds two stacked protoheme molecules per monomer. Unlike the canonical heme oxygenases, the enzyme does not release carbon monoxide or formaldehyde. Instead, it forms unique products, named mycobilins, that retain the α-meso-carbon at the ring cleavage site as an aldehyde group. EC 1.6.2.4, NADPH-hemoprotein reductase, can act as electron donor in vitro.

Links to other databases:

References:

1.	Chim, N., Iniguez, A., Nguyen, T.Q. and Goulding, C.W. Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis. J. Mol. Biol. 395 (2010) 595–608. [DOI] [PMID: 19917297]
2.	Nambu, S., Matsui, T., Goulding, C.W., Takahashi, S. and Ikeda-Saito, M. A new way to degrade heme: the Mycobacterium tuberculosis enzyme MhuD catalyzes heme degradation without generating CO. J. Biol. Chem. 288 (2013) 10101–10109. [DOI] [PMID: 23420845]
3.	Graves, A.B., Morse, R.P., Chao, A., Iniguez, A., Goulding, C.W. and Liptak, M.D. Crystallographic and spectroscopic insights into heme degradation by Mycobacterium tuberculosis MhuD. Inorg. Chem. 53 (2014) 5931–5940. [DOI] [PMID: 24901029]

[EC 1.14.99.57 created 2017]

*EC

1.17.98.2

Accepted name:

bacteriochlorophyllide c C-7¹-hydroxylase

Reaction:

2 S-adenosyl-L-methionine + a bacteriochlorophyllide c + H₂O = a bacteriochlorophyllide e + 2 5′-deoxyadenosine + 2 L-methionine (overall reaction)
(1a) S-adenosyl-L-methionine + a bacteriochlorophyllide c + H₂O = a 7-(hydroxymethyl)bacteriochlorophyllide c + 5′-deoxyadenosine + L-methionine
(1b) S-adenosyl-L-methionine + a 7-(hydroxymethyl)bacteriochlorophyllide c + H₂O = a 7-(dihydroxymethyl)bacteriochlorophyllide c + 5′-deoxyadenosine + L-methionine
(1c) a 7-(dihydroxymethyl)bacteriochlorophyllide c = a bacteriochlorophyllide e + H₂O (spontaneous)

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

Other name(s):

bciD (gene name)

Systematic name:

bacteriochlorophyllide-c:S-adenosyl-L-methionine oxidoreductase (C-7¹-hydroxylating)

Comments:

The enzyme, found in green sulfur bacteria (Chlorobiaceae), is a radical S-adenosyl-L-methionine (AdoMet) enzyme and contains a [4Fe-4S] cluster. It catalyses two consecutive hydroxylation reactions of the C-7 methyl group of bacteriochlorophyllide c to form a geminal diol intermediate that spontaneously dehydrates to produce the formyl group of bacteriochlorophyllide e.

Links to other databases:

References:

1.	Harada, J., Mizoguchi, T., Satoh, S., Tsukatani, Y., Yokono, M., Noguchi, M., Tanaka, A. and Tamiaki, H. Specific gene bciD for C7-methyl oxidation in bacteriochlorophyll e biosynthesis of brown-colored green sulfur bacteria. PLoS One 8:e60026 (2013). [DOI] [PMID: 23560066]
2.	Thweatt, J.L., Ferlez, B.H., Golbeck, J.H. and Bryant, D.A. BciD is a radical S-adenosyl-L-methionine (SAM) enzyme that completes bacteriochlorophyllide e biosynthesis by oxidizing a methyl group into a formyl group at C-7. J. Biol. Chem. 292 (2017) 1361–1373. [DOI] [PMID: 27994052]

[EC 1.17.98.2 created 2016, modified 2017]

*EC

2.1.1.63

Accepted name:

methylated-DNA—[protein]-cysteine S-methyltransferase

Reaction:

(1) DNA (containing 6-O-methylguanine) + protein L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine
(2) DNA (containing 4-O-methylthymine) + protein L-cysteine = DNA (without 4-O-methylthymine) + protein S-methyl-L-cysteine

Other name(s):

ada (gene name); ogt (gene name); MGT1 (gene name); MGMT (gene name)

Systematic name:

DNA-6-O-methylguanine/DNA-4-O-methylthymine:[protein]-L-cysteine S-methyltransferase

Comments:

This protein is involved in the repair of methylated DNA. Unlike EC 3.2.2.20, DNA-3-methyladenine glycosidase I and EC 3.2.2.21, DNA-3-methyladenine glycosidase II, which remove the methylated base leaving an apurinic/apyrimidinic site, this enzyme transfers the methyl group from the methylated DNA to an internal cysteine residue, leaving an intact nucleotide. Since the methyl transfer is irreversible, the enzyme can only catalyse a single turnover.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 77271-19-3

References:

1.	Foote, R.S., Mitra, S. and Pal, B.C. Demethylation of O⁶-methylguanine in a synthetic DNA polymer by an inducible activity in Escherichia coli. Biochem. Biophys. Res. Commun. 97 (1980) 654–659. [DOI] [PMID: 7008792]
2.	Olsson, M. and Lindehl, T. Repair of alkylated DNA in Escherichia coli. Methyl group transfer from O⁶-methylguanine to a protein cysteine residue. J. Biol. Chem. 255 (1980) 10569–10571. [PMID: 7000780]
3.	McCarthy, T.V. and Lindahl, T. Methyl phosphotriesters in alkylated DNA are repaired by the Ada regulatory protein of E. coli. Nucleic Acids Res. 13 (1985) 2683–2698. [DOI] [PMID: 2987862]
4.	Potter, P.M., Wilkinson, M.C., Fitton, J., Carr, F.J., Brennand, J., Cooper, D.P. and Margison, G.P. Characterisation and nucleotide sequence of ogt, the O⁶-alkylguanine-DNA-alkyltransferase gene of E. coli. Nucleic Acids Res. 15 (1987) 9177–9193. [DOI] [PMID: 2825131]
5.	Rebeck, G.W., Smith, C.M., Goad, D.L. and Samson, L. Characterization of the major DNA repair methyltransferase activity in unadapted Escherichia coli and identification of a similar activity in Salmonella typhimurium. J. Bacteriol. 171 (1989) 4563–4568. [DOI] [PMID: 2670886]
6.	Koike, G., Maki, H., Takeya, H., Hayakawa, H. and Sekiguchi, M. Purification, structure, and biochemical properties of human O⁶-methylguanine-DNA methyltransferase. J. Biol. Chem. 265 (1990) 14754–14762. [PMID: 2394694]
7.	Sassanfar, M., Dosanjh, M.K., Essigmann, J.M. and Samson, L. Relative efficiencies of the bacterial, yeast, and human DNA methyltransferases for the repair of O⁶-methylguanine and O⁴-methylthymine. Suggestive evidence for O⁴-methylthymine repair by eukaryotic methyltransferases. J. Biol. Chem. 266 (1991) 2767–2771. [PMID: 1993655]
8.	Xiao, W., Derfler, B., Chen, J. and Samson, L. Primary sequence and biological functions of a Saccharomyces cerevisiae O⁶-methylguanine/O⁴-methylthymine DNA repair methyltransferase gene. EMBO J. 10 (1991) 2179–2186. [PMID: 2065659]

[EC 2.1.1.63 created 1982, modified 1983, modified 1999, modified 2003, modified 2017]

*EC

2.1.1.86

Transferred entry:

tetrahydromethanopterin S-methyltransferase. Now EC 7.2.1.4, tetrahydromethanopterin S-methyltransferase

[EC 2.1.1.86 created 1989, modified 2000, modified 2017, deleted 2024]

2.1.1.340

Accepted name:

3-aminomethylindole N-methyltransferase

Reaction:

2 S-adenosyl-L-methionine + 3-(aminomethyl)indole = 2 S-adenosyl-L-homocysteine + gramine (overall reaction)
(1a) S-adenosyl-L-methionine + 3-(aminomethyl)indole = S-adenosyl-L-homocysteine + (1H-indol-3-yl)-N-methylmethanamine
(1b) S-adenosyl-L-methionine + (1H-indol-3-yl)-N-methylmethanamine = S-adenosyl-L-homocysteine + gramine

For diagram of gramine biosynthesis, click here

Glossary:

3-(aminomethyl)indole = (1H-indol-3-yl)methanamine
gramine = (1H-indol-3-ylmethyl)dimethylamine = (1H-indol-3-yl)-N,N-dimethylmethanamine

Other name(s):

NMT (gene name)

Systematic name:

S-adenosyl-L-methionine:3-(aminomethyl)indole N-methyltransferase (gramine-forming)

Comments:

The enzyme, characterized from Hordeum vulgare (barley), catalyses two successive N-methylation reactions during the biosynthesis of gramine, a toxic indole alkaloid.

Links to other databases:

References:

1.	Leland, T.J. and Hanson, A.D. Induction of a specific N-methyltransferase enzyme by long-term heat stress during barley leaf growth. Plant Physiol. 79 (1985) 451–457. [PMID: 16664431]
2.	Larsson, K.A., Zetterlund, I., Delp, G. and Jonsson, L.M. N-Methyltransferase involved in gramine biosynthesis in barley: cloning and characterization. Phytochemistry 67 (2006) 2002–2008. [DOI] [PMID: 16930646]

[EC 2.1.1.340 created 2017]

2.1.1.341

Accepted name:

vanillate/3-O-methylgallate O-demethylase

Reaction:

(1) vanillate + tetrahydrofolate = protocatechuate + 5-methyltetrahydrofolate
(2) 3-O-methylgallate + tetrahydrofolate = gallate + 5-methyltetrahydrofolate

Glossary:

protocatechuate = 3,4-dihydroxybenzoate
vanillate = 4-hydroxy-3-methoxybenzoate
gallate = 3,4,5-trihydroxybenzoate

Other name(s):

ligM (gene name)

Systematic name:

vanillate:tetrahydrofolate O-methyltransferase

Comments:

The enzyme, characterized from the bacterium Sphingomonas sp. SYK6, is involved in the degradation of lignin. The enzyme has similar activities with vanillate and 3-O-methylgallate.

Links to other databases:

References:

1.	Nishikawa, S., Sonoki, T., Kasahara, T., Obi, T., Kubota, S., Kawai, S., Morohoshi, N. and Katayama, Y. Cloning and sequencing of the Sphingomonas (Pseudomonas) paucimobilis gene essential for the O demethylation of vanillate and syringate. Appl. Environ. Microbiol. 64 (1998) 836–842. [PMID: 9501423]
2.	Masai, E., Sasaki, M., Minakawa, Y., Abe, T., Sonoki, T., Miyauchi, K., Katayama, Y. and Fukuda, M. A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate. J. Bacteriol. 186 (2004) 2757–2765. [DOI] [PMID: 15090517]
3.	Abe, T., Masai, E., Miyauchi, K., Katayama, Y. and Fukuda, M. A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6. J. Bacteriol. 187 (2005) 2030–2037. [DOI] [PMID: 15743951]

[EC 2.1.1.341 created 2017]

2.1.1.342

Accepted name:

anaerobilin synthase

Reaction:

2 S-adenosyl-L-methionine + protoheme + 2 reduced flavodoxin = S-adenosyl-L-homocysteine + L-methionine + 5′-deoxyadenosine + anaerobilin + Fe²⁺ + 2 oxidized flavodoxin

For diagram of anaerobilin biosynthesis, click here

Glossary:

anaerobilin = (4Z,10Z,14E)-8,12-bis(2-carboxyethyl)-3,7,13,18-tetramethyl-1,2,17-trivinyl-23,24-dihydrobilin

Other name(s):

chuW (gene name)

Systematic name:

S-adenosyl-L-methionine:protoheme C-methyltransferase (anaerobilin-producing)

Comments:

The enzyme, studied from the bacterium Escherichia coli O157:H7, is a radical SAM (AdoMet) enzyme that is involved in heme degradation and iron utilization under anaerobic conditions. The enzyme uses two SAM molecules for the reaction. The first molecule is used to generate a 5′-deoxyadenosyl radical, which abstracts a hydrogen atom from the methyl group of the second SAM molecule. The newly formed methylene radical attacks the substrate, causing a rearrangement of the porphyrin ring that results in the liberation of iron.

Links to other databases:

References:

1.	LaMattina, J.W., Nix, D.B. and Lanzilotta, W.N. Radical new paradigm for heme degradation in Escherichia coli O157:H7. Proc. Natl. Acad. Sci. USA 113 (2016) 12138–12143. [DOI] [PMID: 27791000]
2.	LaMattina, J.W., Delrossi, M., Uy, K.G., Keul, N.D., Nix, D.B., Neelam, A.R. and Lanzilotta, W.N. Anaerobic heme degradation: ChuY Is an anaerobilin reductase that exhibits kinetic cooperativity. Biochemistry 56 (2017) 845–855. [DOI] [PMID: 28045510]

[EC 2.1.1.342 created 2017]

*EC

2.3.1.111

Accepted name:

mycocerosate synthase

Reaction:

(1) a long-chain acyl-[mycocerosic acid synthase] + 3 methylmalonyl-CoA + 6 NADPH + 6 H⁺ = a trimethylated-mycocerosoyl-[mycocerosate synthase] + 3 CoA + 3 CO₂ + 6 NADP⁺ + 3 H₂O
(2) a long-chain acyl-[mycocerosic acid synthase] + 4 methylmalonyl-CoA + 8 NADPH + 8 H⁺ = a tetramethylated-mycocerosoyl-[mycocerosate synthase] + 4 CoA + 4 CO₂ + 8 NADP⁺ + 4 H₂O

Glossary:

mycocerosic acid = a long-chain fatty acid with 3 or 4 methyl branches at positions 2,4,6 or 2,4,6,8, respectively. The carbon atoms bearing the methyl groups have the (R)-configuration.

Other name(s):

mas (gene name); mycocerosic acid synthase; acyl-CoA:methylmalonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing); long-chain acyl-CoA:methylmalonyl-CoA C-acyltransferase (mycocerosate-forming)

Systematic name:

long-chain acyl-[mycocerosic acid synthase]:methylmalonyl-CoA C-acyltransferase (mycocerosate-forming)

Comments:

The enzyme, characterized from mycobacteria, is loaded with a long-chain acyl moiety by EC 6.2.1.49, long-chain fatty acid adenylyltransferase FadD28, and elongates it by incorporation of three or four methylmalonyl (but not malonyl) residues, to form tri- or tetramethyl-branched fatty-acids, respectively, such as 2,4,6,8-tetramethyloctacosanoate (C₃₂-mycocerosate). Since the enzyme lacks a thioesterase domain, the product remains bound and requires additional enzyme(s) for removal. Even though the enzyme can accept C₆ to C₂₀ substrates in vitro, it prefers to act on C₁₄-C₂₀ substrates in vivo.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 95229-19-9

References:

1.	Rainwater, D.L. and Kollattukudy, P.E. Fatty acid biosynthesis in Mycobacterium tuberculosis var. bovis Bacillus* Calmette-Guérin. Purification and characterization of a novel fatty acid synthase, mycocerosic acid synthase, which elongates n-fatty acyl-CoA with methylmalonyl-CoA. J. Biol. Chem.* 260 (1985) 616–623. [PMID: 3880746]
2.	Mathur, M. and Kolattukudy, P.E. Molecular cloning and sequencing of the gene for mycocerosic acid synthase, a novel fatty acid elongating multifunctional enzyme, from Mycobacterium tuberculosis var. bovis Bacillus Calmette-Guerin. J. Biol. Chem. 267 (1992) 19388–19395. [PMID: 1527058]
3.	Trivedi, O.A., Arora, P., Vats, A., Ansari, M.Z., Tickoo, R., Sridharan, V., Mohanty, D. and Gokhale, R.S. Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid. Mol. Cell 17 (2005) 631–643. [DOI] [PMID: 15749014]
4.	Menendez-Bravo, S., Comba, S., Sabatini, M., Arabolaza, A. and Gramajo, H. Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli. Metab. Eng. 24 (2014) 97–106. [DOI] [PMID: 24831705]

[EC 2.3.1.111 created 1989, modified 2016, modified 2017]

2.3.1.264

Accepted name:

β-lysine N⁶-acetyltransferase

Reaction:

acetyl-CoA + (3S)-3,6-diaminohexanoate = CoA + (3S)-6-acetamido-3-aminohexanoate

Glossary:

(3S)-3,6-diaminohexanoate = β-L-lysine
(3S)-6-acetamido-3-aminohexanoate = N⁶-acetyl-β-L-lysine

Other name(s):

ablB (gene name)

Systematic name:

acetyl-CoA:(3S)-3,6-diaminohexanoate N⁶-acetyltransferase

Comments:

The enzyme is found in some methanogenic archaea and bacteria. In archaea it is induced under salt stress. The product, N⁶-acetyl-β-L-lysine, serves as a compatible solute, conferring high salt resistance on the producing organisms.

Links to other databases:

References:

1.	Pfluger, K., Baumann, S., Gottschalk, G., Lin, W., Santos, H. and Muller, V. Lysine-2,3-aminomutase and β-lysine acetyltransferase genes of methanogenic archaea are salt induced and are essential for the biosynthesis of N^ε-acetyl-β-lysine and growth at high salinity. Appl. Environ. Microbiol. 69 (2003) 6047–6055. [DOI] [PMID: 14532061]
2.	Muller, S., Hoffmann, T., Santos, H., Saum, S.H., Bremer, E. and Muller, V. Bacterial abl-like genes: production of the archaeal osmolyte N(ε)-acetyl-β-lysine by homologous overexpression of the yodP-kamA genes in Bacillus subtilis. Appl. Microbiol. Biotechnol. 91 (2011) 689–697. [DOI] [PMID: 21538109]

[EC 2.3.1.264 created 2017]

2.3.3.19

Accepted name:

2-phosphonomethylmalate synthase

Reaction:

acetyl-CoA + H₂O + 3-phosphonopyruvate = (R)-2-(phosphonomethyl)malate + CoA

Other name(s):

2-phosphinomethylmalic acid synthase; PMM synthase

Systematic name:

acetyl-CoA:3-phosphonopyruvate C-acetyltransferase

Comments:

The enzyme, isolated from several Streptomyces species, participate in the biosynthesis of certain phosphonate antibiotics. The enzyme is analogous to EC 2.3.3.1 (Si)-citrate synthase.

Links to other databases:

References:

1.	Shimotohno, K., Seto, H., Otake, N., Imai, S. and Satoh, A. Studies on the biosynthesis of bialaphos (SE-1293). 7. The absolute configuration of 2-phosphinomethylmalic acid, a biosynthetic intermediate of bialaphos. J. Antibiot. (Tokyo) 39 (1986) 1356–1359. [PMID: 3781934]
2.	Shimotohno, K.W., Seto, H., Otake, N., Imai, S. and Murakami, T. Studies on the biosynthesis of bialaphos (SF-1293). 8. Purification and characterization of 2-phosphinomethylmalic acid synthase from Streptomyces hygroscopicus SF-1293. J. Antibiot. (Tokyo) 41 (1988) 1057–1065. [PMID: 3170341]
3.	Eliot, A.C., Griffin, B.M., Thomas, P.M., Johannes, T.W., Kelleher, N.L., Zhao, H. and Metcalf, W.W. Cloning, expression, and biochemical characterization of Streptomyces rubellomurinus genes required for biosynthesis of antimalarial compound FR900098. Chem. Biol. 15 (2008) 765–770. [DOI] [PMID: 18721747]

[EC 2.3.3.19 created 2017]

2.4.1.57

Deleted entry:

phosphatidylinositol α-mannosyltransferase. Newer studies have shown that this is catalysed by two independent activities now covered by EC 2.4.1.345, phosphatidyl-myo-inositol α-mannosyl transferase and EC 2.4.1.346, phosphatidyl-myo-inositol dimannoside synthase

[EC 2.4.1.57 created 1972, modified 2003, deleted 2017]

*EC

2.4.1.86

Accepted name:

N-acetyl-β-D-glucosaminide β-(1,3)-galactosyltransferase

Reaction:

UDP-α-D-galactose + N-acetyl-β-D-glucosaminyl-R = UDP + β-D-galactosyl-(1→3)-N-acetyl-β-D-glucosaminyl-R

For diagram of lactotetraosylceramide biosynthesis, click here

Other name(s):

B3GALT1 (gene name); uridine diphosphogalactose-acetyl-glucosaminylgalactosylglucosylceramide galactosyltransferase; GalT-4; UDP-galactose:N-acetyl-D-glucosaminyl-1,3-D-galactosyl-1,4-D-glucosylceramide β-D-galactosyltransferase; UDP-galactose:N-acetyl-D-glucosaminyl-(1→3)-D-galactosyl-(1→4)-D-glucosylceramide 3-β-D-galactosyltransferase; UDP-galactose:N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosylceramide 3-β-D-galactosyltransferase; UDP-galactose:N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosyl(1↔1)ceramide 3-β-D-galactosyltransferase; UDP-galactose:N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide 3-β-D-galactosyltransferase; glucosaminylgalactosylglucosylceramide β-galactosyltransferase; UDP-α-D-galactose:N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide 3-β-D-galactosyltransferase

Systematic name:

UDP-α-D-galactose:N-acetyl-β-D-glucosaminyl-R 3-β-D-galactosyltransferase

Comments:

The enzyme transfers galactose from UDP-α-D-galactose to the 3-position of substrates with a non-reducing terminal N-acetyl-β-D-glucosamine (β-GlcNAc) residue. It can act on both glycolipids and glycoproteins, generating a structure known as the type 1 histo-blood group antigen precursor.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, CAS registry number: 9073-46-5

References:

1.	Basu, M. and Basu, S. Enzymatic synthesis of a tetraglycosylceramide by a galactosyltransferase from rabbit bone marrow. J. Biol. Chem. 247 (1972) 1489–1495. [PMID: 4335001]
2.	Basu, M., Presper, K.A., Basu, S., Hoffman, L.M. and Brooks, S.E. Differential activities of glycolipid glycosyltransferases in Tay-Sachs disease: studies in cultured cells from cerebrum. Proc. Natl. Acad. Sci. USA 76 (1979) 4270–4274. [DOI] [PMID: 291963]
3.	Amado, M., Almeida, R., Carneiro, F., Levery, S.B., Holmes, E.H., Nomoto, M., Hollingsworth, M.A., Hassan, H., Schwientek, T., Nielsen, P.A., Bennett, E.P. and Clausen, H. A family of human β3-galactosyltransferases. Characterization of four members of a UDP-galactose:β-N-acetyl-glucosamine/β-nacetyl-galactosamine β-1,3-galactosyltransferase family. J. Biol. Chem. 273 (1998) 12770–12778. [DOI] [PMID: 9582303]
4.	Amado, M., Almeida, R., Schwientek, T. and Clausen, H. Identification and characterization of large galactosyltransferase gene families: galactosyltransferases for all functions. Biochim. Biophys. Acta 1473 (1999) 35–53. [DOI] [PMID: 10580128]
5.	Bardoni, A., Valli, M. and Trinchera, M. Differential expression of β1,3galactosyltransferases in human colon cells derived from adenocarcinomas or normal mucosa. FEBS Lett. 451 (1999) 75–80. [DOI] [PMID: 10356986]

[EC 2.4.1.86 created 1976, modified 2017]

2.4.1.345

Accepted name:

phosphatidyl-myo-inositol α-mannosyltransferase

Reaction:

GDP-α-D-mannose + 1-phosphatidyl-1D-myo-inositol = GDP + 2-O-(α-D-mannosyl)-1-phosphatidyl-1D-myo-inositol

Glossary:

1-phosphatidyl-1D-myo-inositol = PtdIns

Other name(s):

mannosyltransferase PimA; PimA; guanosine diphosphomannose-phosphatidyl-inositol α-mannosyltransferase (ambiguous)

Systematic name:

GDP-α-D-mannose:1-phosphatidyl-1D-myo-inositol 2-α-D-mannosyltransferase (configuration-retaining)

Comments:

Requires Mg²⁺. The enzyme, found in Corynebacteriales, is involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs).

Links to other databases:

References:

1.	Kordulakova, J., Gilleron, M., Mikusova, K., Puzo, G., Brennan, P.J., Gicquel, B. and Jackson, M. Definition of the first mannosylation step in phosphatidylinositol mannoside synthesis. PimA is essential for growth of mycobacteria. J. Biol. Chem. 277 (2002) 31335–31344. [DOI] [PMID: 12068013]
2.	Gu, X., Chen, M., Wang, Q., Zhang, M., Wang, B. and Wang, H. Expression and purification of a functionally active recombinant GDP-mannosyltransferase (PimA) from Mycobacterium tuberculosis H37Rv. Protein Expr. Purif. 42 (2005) 47–53. [DOI] [PMID: 15939292]
3.	Giganti, D., Albesa-Jove, D., Urresti, S., Rodrigo-Unzueta, A., Martinez, M.A., Comino, N., Barilone, N., Bellinzoni, M., Chenal, A., Guerin, M.E. and Alzari, P.M. Secondary structure reshuffling modulates glycosyltransferase function at the membrane. Nat. Chem. Biol. 11 (2015) 16–18. [DOI] [PMID: 25402770]
4.	Rodrigo-Unzueta, A., Martinez, M.A., Comino, N., Alzari, P.M., Chenal, A. and Guerin, M.E. Molecular basis of membrane association by the phosphatidylinositol mannosyltransferase PimA enzyme from Mycobacteria. J. Biol. Chem. 291 (2016) 13955–13963. [DOI] [PMID: 27189944]

[EC 2.4.1.345 created 2017]

2.4.1.346

Accepted name:

phosphatidyl-myo-inositol dimannoside synthase

Reaction:

(1) GDP-α-D-mannose + 2-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol = GDP + 2,6-di-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol
(2) GDP-α-D-mannose + 2-O-(6-O-acyl-α-D-mannosyl)-1-phosphatidyl-1D-myo-inositol = GDP + 2-O-(6-O-acyl-α-D-mannosyl)-6-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol

Glossary:

1-phosphatidyl-1D-myo-inositol = PtdIns

Other name(s):

mannosyltransferase PimB; PimB; guanosine diphosphomannose-phosphatidyl-inositol α-mannosyltransferase (ambiguous)

Systematic name:

GDP-α-D-mannose:2-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol 6-α-D-mannosyltransferase (configuration-retaining)

Comments:

Requires Mg²⁺. The enzyme, found in Corynebacteriales, is involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs).

Links to other databases:

References:

1.	Guerin, M.E., Kaur, D., Somashekar, B.S., Gibbs, S., Gest, P., Chatterjee, D., Brennan, P.J. and Jackson, M. New insights into the early steps of phosphatidylinositol mannoside biosynthesis in mycobacteria: PimB′ is an essential enzyme of Mycobacterium smegmatis. J. Biol. Chem. 284 (2009) 25687–25696. [DOI] [PMID: 19638342]
2.	Mishra, A.K., Batt, S., Krumbach, K., Eggeling, L. and Besra, G.S. Characterization of the Corynebacterium glutamicum Δ pimB′ Δ mgtA double deletion mutant and the role of Mycobacterium tuberculosis orthologues Rv2188c and Rv0557 in glycolipid biosynthesis. J. Bacteriol. 191 (2009) 4465–4472. [DOI] [PMID: 19395496]
3.	Batt, S.M., Jabeen, T., Mishra, A.K., Veerapen, N., Krumbach, K., Eggeling, L., Besra, G.S. and Futterer, K. Acceptor substrate discrimination in phosphatidyl-myo-inositol mannoside synthesis: structural and mutational analysis of mannosyltransferase Corynebacterium glutamicum PimB′. J. Biol. Chem. 285 (2010) 37741–37752. [DOI] [PMID: 20843801]

[EC 2.4.1.346 created 2017]

*EC

2.4.99.2

Transferred entry:

β-D-galactosyl-(1→3)-N-acetyl-β-D-galactosaminide α-2,3-sialyltransferase. Now EC 2.4.3.2, β-D-galactosyl-(1→3)-N-acetyl-β-D-galactosaminide α-2,3-sialyltransferase

[EC 2.4.99.2 created 1976, modified 1986, deleted 2022]

2.5.1.140

Accepted name:

N-(2-amino-2-carboxyethyl)-L-glutamate synthase

Reaction:

O-phospho-L-serine + L-glutamate = N-[(2S)-2-amino-2-carboxyethyl]-L-glutamate + phosphate

Other name(s):

SbnA; ACEGA synthase

Systematic name:

O-phospho-L-serine:L-glutamate N-(2S)-2-amino-2-carboxyethyltransferase

Comments:

The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of the siderophore staphyloferrin B.

Links to other databases:

References:

1.	Beasley, F.C., Cheung, J. and Heinrichs, D.E. Mutation of L-2,3-diaminopropionic acid synthase genes blocks staphyloferrin B synthesis in Staphylococcus aureus. BMC Microbiol. 11:199 (2011). [DOI] [PMID: 21906287]
2.	Kobylarz, M.J., Grigg, J.C., Takayama, S.J., Rai, D.K., Heinrichs, D.E. and Murphy, M.E. Synthesis of L-2,3-diaminopropionic acid, a siderophore and antibiotic precursor. Chem. Biol. 21 (2014) 379–388. [DOI] [PMID: 24485762]

[EC 2.5.1.140 created 2017]

*EC

2.6.1.82

Accepted name:

putrescine—2-oxoglutarate transaminase

Reaction:

putrescine + 2-oxoglutarate = 4-aminobutanal + L-glutamate

For diagram of arginine catabolism, click here

Glossary:

putrescine = butane-1,4-diamine
1-pyrroline = 3,4-dihydro-2H-pyrrole

Other name(s):

putrescine-α-ketoglutarate transaminase; YgjG; putrescine:α-ketoglutarate aminotransferase; PAT (ambiguous); putrescine transaminase (ambiguous); putrescine aminotransferase (ambiguous); butane-1,4-diamine:2-oxoglutarate aminotransferase

Systematic name:

putrescine:2-oxoglutarate aminotransferase

Comments:

A pyridoxal 5′-phosphate protein [3]. The product, 4-aminobutanal, spontaneously cyclizes to form 1-pyrroline, which may be the actual substrate for EC 1.2.1.19, aminobutyraldehyde dehydrogenase. Cadaverine and spermidine can also act as substrates [3]. Forms part of the arginine-catabolism pathway [2]. cf. EC 2.6.1.113, putrescine—pyruvate transaminase.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 98982-73-1

References:

1.	Prieto-Santos, M.I., Martin-Checa, J., Balaña-Fouce, R. and Garrido-Pertierra, A. A pathway for putrescine catabolism in Escherichia coli. Biochim. Biophys. Acta 880 (1986) 242–244. [DOI] [PMID: 3510672]
2.	Samsonova, N.N., Smirnov, S.V., Novikova, A.E. and Ptitsyn, L.R. Identification of Escherichia coli K12 YdcW protein as a γ-aminobutyraldehyde dehydrogenase. FEBS Lett. 579 (2005) 4107–4112. [DOI] [PMID: 16023116]
3.	Samsonova, N.N., Smirnov, S.V., Altman, I.B. and Ptitsyn, L.R. Molecular cloning and characterization of Escherichia coli K12 ygjG gene. BMC Microbiol. 3 (2003) 2. [DOI] [PMID: 12617754]

[EC 2.6.1.82 created 2006, modified 2017, modified 2021]

2.6.1.113

Accepted name:

putrescine—pyruvate transaminase

Reaction:

putrescine + pyruvate = 4-aminobutanal + alanine

Other name(s):

spuC (gene name)

Systematic name:

putrescine:pyruvate aminotransferase

Comments:

A pyridoxal 5′-phosphate protein. The enzyme, studied in the bacterium Pseudomonas aeruginosa, participates in a putrescine degradation pathway. cf. EC 2.6.1.82, putrescine—2-oxoglutarate aminotransferase.

Links to other databases:

References:

1.	Lu, C.D., Itoh, Y., Nakada, Y. and Jiang, Y. Functional analysis and regulation of the divergent spuABCDEFGH-spuI operons for polyamine uptake and utilization in Pseudomonas aeruginosa PAO1. J. Bacteriol. 184 (2002) 3765–3773. [DOI] [PMID: 12081945]

[EC 2.6.1.113 created 2017]

2.7.1.217

Accepted name:

3-dehydrotetronate 4-kinase

Reaction:

(1) ATP + 3-dehydro-L-erythronate = ADP + 3-dehydro-4-phospho-L-erythronate
(2) ATP + 3-dehydro-D-erythronate = ADP + 3-dehydro-4-phospho-D-erythronate

For diagram of erythronate and threonate catabolism, click here

Glossary:

L-erythronate = (2S,3S)-2,3,4-trihydroxybutanoate
D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate

Other name(s):

otnK (gene name)

Systematic name:

ATP:3-dehydrotetronate 4-phosphotransferase

Comments:

The enzyme, characterized from bacteria, is involved in D-erythronate and L-threonate catabolism.

Links to other databases:

References:

[EC 2.7.1.217 created 2017]

2.7.7.95

Transferred entry:

mycocerosic acid adenylyltransferase. Now EC 6.2.1.49, long-chain fatty acid adenylyltransferase FadD28

[EC 2.7.7.95 created 2016, deleted 2017]

*EC

2.8.1.4

Accepted name:

tRNA uracil 4-sulfurtransferase

Reaction:

ATP + [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + uracil in tRNA + 2 reduced ferredoxin [iron-sulfur] cluster = AMP + diphosphate + 4-thiouracil in tRNA + [ThiI sulfur-carrier protein]-L-cysteine + 2 oxidized ferredoxin [iron-sulfur] cluster

Other name(s):

thiI (gene name); transfer ribonucleate sulfurtransferase (ambiguous); RNA sulfurtransferase (ambiguous); ribonucleate sulfurtransferase (ambiguous); transfer RNA sulfurtransferase (ambiguous); transfer RNA thiolase (ambiguous); L-cysteine:tRNA sulfurtransferase (incorrect); tRNA sulfurtransferase (ambiguous)

Systematic name:

[ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine:uracil in tRNA sulfurtransferase

Comments:

The enzyme, found in bacteria and archaea, is activated by EC 2.8.1.7, cysteine desulfurase, which transfers a sulfur atom to an internal L-cysteine residue, forming a cysteine persulfide. The activated enzyme then transfers the sulfur to a uridine in a tRNA chain in a reaction that requires ATP. The enzyme from the bacterium Escherichia coli forms 4-thiouridine only at position 8 of tRNA. The enzyme also participates in the biosynthesis of the thiazole moiety of thiamine, but different domains are involved in the two processes.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9055-57-6

References:

1.	Abrell, J.W., Kaufman, E.E. and Lipsett, M.N. The biosynthesis of 4-thiouridylate. Separation and purification of two enzymes in the transfer ribonucleic acid-sulfurtransferase system. J. Biol. Chem. 246 (1971) 294–301. [PMID: 5541999]
2.	Hayward, R.S. and Weiss, S.B. RNA thiolase: the enzymatic transfer of sulfur from cysteine to sRNA in Escherichia coli extracts. Proc. Natl. Acad. Sci. USA 55 (1966) 1161–1168. [DOI] [PMID: 5334200]
3.	Lipsett, M.N. and Peterkofsky, A. Enzymatic thiolation of E. coli sRNA. Proc. Natl. Acad. Sci. USA 55 (1966) 1169–1174. [DOI] [PMID: 5334201]
4.	Wong, T., Weiss, S.B., Eliceiri, G.L. and Bryant, J. Ribonucleic acid sulfurtransferase from Bacillus subtilis W168. Sulfuration with β-mercaptopyruvate and properties of the enzyme system. Biochemistry 9 (1970) 2376–2386. [PMID: 4987417]
5.	Kambampati, R. and Lauhon, C.T. Evidence for the transfer of sulfane sulfur from IscS to ThiI during the in vitro biosynthesis of 4-thiouridine in Escherichia coli tRNA. J. Biol. Chem. 275 (2000) 10727–10730. [DOI] [PMID: 10753862]
6.	Mueller, E.G., Palenchar, P.M. and Buck, C.J. The role of the cysteine residues of ThiI in the generation of 4-thiouridine in tRNA. J. Biol. Chem. 276 (2001) 33588–33595. [DOI] [PMID: 11443125]
7.	Lauhon, C.T., Erwin, W.M. and Ton, G.N. Substrate specificity for 4-thiouridine modification in Escherichia coli. J. Biol. Chem. 279 (2004) 23022–23029. [DOI] [PMID: 15037613]
8.	Neumann, P., Lakomek, K., Naumann, P.T., Erwin, W.M., Lauhon, C.T. and Ficner, R. Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification. Nucleic Acids Res. 42 (2014) 6673–6685. [DOI] [PMID: 24705700]
9.	Liu, Y., Vinyard, D.J., Reesbeck, M.E., Suzuki, T., Manakongtreecheep, K., Holland, P.L., Brudvig, G.W. and Soll, D. A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes. Proc. Natl. Acad. Sci. USA 113 (2016) 12703–12708. [DOI] [PMID: 27791189]

[EC 2.8.1.4 created 1984, modified 2017]

2.8.1.15

Accepted name:

tRNA-5-methyluridine⁵⁴ 2-sulfurtransferase

Reaction:

ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluracil⁵⁴ in tRNA + H₂O = AMP + diphosphate + 5-methyl-2-thiouracil⁵⁴ in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly

Other name(s):

TtuA

Systematic name:

[TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH:tRNA (5-methyluridine⁵⁴-2-O)-sulfurtransferase

Comments:

The enzyme, found in thermophilic bacteria and archaea, modifies the ribothymidine (5-methyluridine) residue at position 54 of tRNAs. Contains zinc and an [4Fe-4S] cluster. Some organisms, such as the archaeon Pyrococcus horikoshii, do not have a TtuB sulfur-carrier protein, and appear to use sulfide as the sulfur source.

Links to other databases:

References:

1.	Shigi, N., Sakaguchi, Y., Suzuki, T. and Watanabe, K. Identification of two tRNA thiolation genes required for cell growth at extremely high temperatures. J. Biol. Chem. 281 (2006) 14296–14306. [DOI] [PMID: 16547008]
2.	Shigi, N., Suzuki, T., Terada, T., Shirouzu, M., Yokoyama, S. and Watanabe, K. Temperature-dependent biosynthesis of 2-thioribothymidine of Thermus thermophilus tRNA. J. Biol. Chem. 281 (2006) 2104–2113. [DOI] [PMID: 16317006]
3.	Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Katsura, K., Terada, T., Shirouzu, M., Sekine, S., Shigi, N. and Yokoyama, S. Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA. Proteins 81 (2013) 1232–1244. [DOI] [PMID: 23444054]
4.	Chen, M., Narai, S., Omura, N., Shigi, N., Chimnaronk, S., Tanaka, Y. and Yao, M. Crystallographic study of the 2-thioribothymidine-synthetic complex TtuA-TtuB from Thermus thermophilus. Acta Crystallogr. F Struct. Biol. Commun. 72 (2016) 777–781. [DOI] [PMID: 27710943]

[EC 2.8.1.15 created 2017]

3.2.1.203

Accepted name:

carboxymethylcellulase

Reaction:

Endohydrolysis of (1→4)-β-D-glucosidic linkages in (carboxymethyl)cellulose.

Other name(s):

CMCase

Systematic name:

4-β-D-(carboxymethyl)glucan 4-(carboxymethyl)glucanohydrolase

Comments:

The enzyme from the acidophilic bacterium Alicyclobacillus acidocaldarius is an endo-cleaving hydrolase that cleaves β(1→4)-linked residues. However, it is specific for (carboxymethyl)cellulose and does not act on cellulosic substrates such as avicel.

Links to other databases:

References:

1.	Morana, A., Esposito, A., Maurelli, L., Ruggiero, G., Ionata, E., Rossi, M. and La Cara, F. A novel thermoacidophilic cellulase from Alicyclobacillus acidocaldarius. Protein Pept. Lett. 15 (2008) 1017–1021. [PMID: 18991780]

[EC 3.2.1.203 created 2017]

3.5.1.120

Transferred entry:

2-aminomuconate deaminase (2-hydroxymuconate-forming). Now EC 3.5.99.11, 2-aminomuconate deaminase (2-hydroxymuconate-forming)

[EC 3.5.1.120 created 2016, deleted 2017]

3.5.99.11

Accepted name:

2-aminomuconate deaminase (2-hydroxymuconate-forming)

Reaction:

2-aminomuconate + H₂O = (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NH₃

Glossary:

2-aminomuconate = (2Z,4E)-2-aminohexa-2,4-dienedioate
(2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (2Z,4E)-2-hydroxymuconate

Other name(s):

cnbZ (gene name)

Systematic name:

2-aminomuconate aminohydrolase [(2Z,4E)-2-hydroxyhexa-2,4-dienedioate-forming]

Comments:

The enzyme, characterized from the bacterium Comamonas testosteroni CNB-1, converts 2-aminomuconate to 2-hydroxyhexa-2,4-dienedioate, unlike the enzymes from Pseudomonas, which produce (3E)-2-oxohex-3-enedioate (see EC 3.5.99.5, 2-aminomuconate deaminase). The enzyme also acts on 2-amino-5-chloromuconate.

Links to other databases:

References:

1.	Liu, L., Wu, J.F., Ma, Y.F., Wang, S.Y., Zhao, G.P. and Liu, S.J. A novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with Comamonas sp. strain CNB-1. J. Bacteriol. 189 (2007) 2677–2682. [DOI] [PMID: 17259310]

[EC 3.5.99.11 created 2016 as EC 3.5.1.120, transferred 2017 to EC 3.5.99.11]

3.13.1.5

Accepted name:

carbon disulfide hydrolase

Reaction:

carbon disulfide + 2 H₂O = CO₂ + 2 hydrogen sulfide (overall reaction)
(1a) carbon disulfide + H₂O = carbonyl sulfide + hydrogen sulfide
(1b) carbonyl sulfide + H₂O = CO₂ + hydrogen sulfide

Other name(s):

CS2 hydrolase (misleading); carbon disulfide lyase; CS2-converting enzyme; carbon disulphide-lyase (decarboxylating)

Systematic name:

carbon-disulfide hydrogen-sulfide-lyase (decarboxylating)

Comments:

The enzyme contains Zn²⁺. The hyperthermophilic archaeon Acidianus sp. A1-3 obtains energy by the conversion of carbon disulfide to hydrogen sulfide, with carbonyl sulfide as an intermediate.

Links to other databases:

References:

Smeulders, M.J., Barends, T.R., Pol, A., Scherer, A., Zandvoort, M.H., Udvarhelyi, A., Khadem, A.F., Menzel, A., Hermans, J., Shoeman, R.L., Wessels, H.J., van den Heuvel, L.P., Russ, L., Schlichting, I., Jetten, M.S. and Op den Camp, H.J. Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon. Nature 478 (2011) 412–416. [DOI] [PMID: 22012399]

[EC 3.13.1.5 created 2013 as EC 4.4.1.27, transferred 2017 to EC 3.13.1.5]

4.1.1.104

Accepted name:

3-dehydro-4-phosphotetronate decarboxylase

Reaction:

(1) 3-dehydro-4-phospho-L-erythronate = glycerone phosphate + CO₂
(2) 3-dehydro-4-phospho-D-erythronate = glycerone phosphate + CO₂

For diagram of erythronate and threonate catabolism, click here

Glossary:

L-erythronate = (2S,3S)-2,3,4-trihydroxybutanoate
D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate

Other name(s):

otnC (gene name)

Systematic name:

3-dehydro-4-phosphotetronate carboxy-lyase

Comments:

The enzyme, characterized from bacteria, is involved in D-erythronate and L-threonate catabolism.

Links to other databases:

References:

[EC 4.1.1.104 created 2017]

4.1.2.59

Accepted name:

dihydroneopterin phosphate aldolase

Reaction:

7,8-dihydroneopterin 3′-phosphate = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde phosphate

Other name(s):

H₂NMP aldolase

Systematic name:

7,8-dihydroneopterin 3′-phosphate glycolaldehyde phosphate-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]

Comments:

The enzyme participates in methanopterin biosynthesis the archaeon Pyrococcus furiosus. The enzyme is specific for 7,8-dihydroneopterin 3′-phosphate. cf. EC 4.1.2.25, dihydroneopterin aldolase and EC 4.1.2.60, dihydroneopterin triphosphate aldolase.

Links to other databases:

References:

de Crecy-Lagard, V., Phillips, G., Grochowski, L.L., El Yacoubi, B., Jenney, F., Adams, M.W., Murzin, A.G. and White, R.H. Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate. ACS Chem. Biol. 7 (2012) 1807–1816. [DOI] [PMID: 22931285]

[EC 4.1.2.59 created 2017]

4.1.2.60

Accepted name:

dihydroneopterin triphosphate aldolase

Reaction:

7,8-dihydroneopterin 3′-triphosphate = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde triphosphate

Other name(s):

PTPS-III

Systematic name:

7,8-dihydroneopterin 3′-triphosphate glycolaldehyde phosphate-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]

Comments:

The enzyme, which participates in a pathway for folate biosynthesis, is found in the Stramenopiles, a large group that includes oomycetes, various microalgae and brown algae, as well as in several bacterial phyla. It provides a bypass mechanism compensating for the lack of EC 4.1.2.25, dihydroneopterin aldolase. In the malaria parasite Plasmodium falciparum the enzyme is bifunctional and also catalyses the activity of EC 4.2.3.12, 6-pyruvoyltetrahydropterin synthase. cf. EC 4.1.2.59, dihydroneopterin phosphate aldolase.

Links to other databases:

References:

1.	Dittrich, S., Mitchell, S.L., Blagborough, A.M., Wang, Q., Wang, P., Sims, P.F. and Hyde, J.E. An atypical orthologue of 6-pyruvoyltetrahydropterin synthase can provide the missing link in the folate biosynthesis pathway of malaria parasites. Mol. Microbiol. 67 (2008) 609–618. [DOI] [PMID: 18093090]
2.	Hyde, J.E., Dittrich, S., Wang, P., Sims, P.F., de Crecy-Lagard, V. and Hanson, A.D. Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms. Trends Parasitol. 24 (2008) 502–508. [DOI] [PMID: 18805734]
3.	Pribat, A., Jeanguenin, L., Lara-Nunez, A., Ziemak, M.J., Hyde, J.E., de Crecy-Lagard, V. and Hanson, A.D. 6-pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria. J. Bacteriol. 191 (2009) 4158–4165. [DOI] [PMID: 19395485]

[EC 4.1.2.60 created 2017]

4.4.1.27

Transferred entry:

carbon disulfide lyase. Now EC 3.13.1.5, carbon disulfide hydrolase

[EC 4.4.1.27 created 2013, deleted 2017]

4.99.1.10

Accepted name:

magnesium dechelatase

Reaction:

(1) chlorophyll a + 2 H⁺ = pheophytin a + Mg²⁺
(2) chlorophyllide a + 2 H⁺ = pheophorbide a + Mg²⁺

For diagram of chlorophyll catabolism, click here

Other name(s):

SGR (gene name); SGRL (gene name); Mg-dechelatase

Systematic name:

chlorophyll a magnesium lyase

Comments:

Inhibited by Ca²⁺, Mg²⁺ and especially Hg²⁺. SGR has very low activity with chlorophyllide a and none with chlorophyll b. It acts on chlorophyll a both in its free form and in protein complex. SGRL, on the other hand, is more active with chlorophyllide a than with chlorophyll a. The magnesium formed is scavenged by MCS (metal-chelating substance).

Links to other databases:

References:

1.	Tang, L., Okazawa, A., Fukusaki, E. and Kobayashi, A. Removal of magnesium by Mg-dechelatase is a major step in the chlorophyll-degrading pathway in Ginkgo biloba in the process of autumnal tints. Z. Naturforsch. C 55 (2000) 923–926. [PMID: 11204197]
2.	Costa, M.A., Civello, P.M., Chaves, A.R. and Martínez, G.A. Characterization of Mg-dechelatase activity obtained from Fragaria x ananassa fruit. Plant Physiol. Biochem. 40 (2002) 111–118.
3.	Wang, T., Quisenberry, S.S., Ni, X. and Tolmay, V. Enzymatic chlorophyll degradation in wheat near-isogenic lines elicited by cereal aphid (Homoptera: Aphididae) feeding. J. Econ. Entomol. 97 (2004) 661–667. [PMID: 15154496]
4.	Suzuki, T., Kunieda, T., Murai, F., Morioka, S. and Shioi, Y. Mg-dechelation activity in radish cotyledons with artificial and native substrates, Mg-chlorophyllin a and chlorophyllide a. Plant Physiol. Biochem. 43 (2005) 459–464. [DOI] [PMID: 15890522]
5.	Kunieda, T., Amano, T. and Shioi, Y. Search for chlorophyll degradation enzyme, Mg-dechelatase, from extracts of Chenopodium album with native and artificial substrates. Plant Sci. 169 (2005) 177–183.
6.	Shimoda, Y., Ito, H. and Tanaka, A. Arabidopsis STAY-GREEN, Mendel’s green cotyledon gene, encodes magnesium-dechelatase. Plant Cell 28 (2016) 2147–2160. [DOI] [PMID: 27604697]

[EC 4.99.1.10 created 2017]

4.99.1.11

Accepted name:

sirohydrochlorin nickelchelatase

Reaction:

Ni-sirohydrochlorin + 2 H⁺ = sirohydrochlorin + Ni²⁺

Other name(s):

cfbA (gene name)

Systematic name:

Ni-sirohydrochlorin nickel-lyase (sirohydrochlorin-forming)

Comments:

The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, participates in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F₄₃₀, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase. It catalyses the insertion of the nickel ion into sirohydrochlorin.

Links to other databases:

References:

1.	Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F₄₃₀ in methanogenic and methanotrophic archaea. Science 354 (2016) 339–342. [DOI] [PMID: 27846569]

[EC 4.99.1.11 created 2017]

5.1.3.41

Accepted name:

fructoselysine 3-epimerase

Reaction:

N⁶-(D-fructosyl)-L-lysine = N⁶-(D-psicosyl)-L-lysine

Other name(s):

frlC (gene name)

Systematic name:

D-fructosyl-L-lysine 3-epimerase

Comments:

The enzyme, characterized from the bacterium Escherichia coli, is involved in the catabolism of fructoseamines, amino acid sugar complexes that are formed non-enzymically.

Links to other databases:

References:

1.	Wiame, E. and Van Schaftingen, E. Fructoselysine 3-epimerase, an enzyme involved in the metabolism of the unusual Amadori compound psicoselysine in Escherichia coli. Biochem. J. 378 (2004) 1047–1052. [DOI] [PMID: 14641112]

[EC 5.1.3.41 created 2017]

5.3.1.35

Accepted name:

2-dehydrotetronate isomerase

Reaction:

(1) 2-dehydro-L-erythronate = 3-dehydro-L-erythronate
(2) 2-dehydro-D-erythronate = 3-dehydro-D-erythronate

For diagram of erythronate and threonate catabolism, click here

Glossary:

L-erythronate = (2S,3S)-2,3,4-trihydroxybutanoate
D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate

Other name(s):

otnI (gene name)

Systematic name:

2-dehydrotetronate isomerase

Comments:

The enzyme, characterized from bacteria, is involved in D-erythronate and L-threonate catabolism.

Links to other databases:

References:

[EC 5.3.1.35 created 2017]

*EC

5.4.3.3

Accepted name:

lysine 5,6-aminomutase

Reaction:

(1) (3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate
(2) D-lysine = (2R,5S)-2,5-diaminohexanoate

For diagram of lysine catabolism, click here

Other name(s):

β-lysine 5,6-aminomutase; β-lysine mutase; L-β-lysine 5,6-aminomutase; D-lysine 5,6-aminomutase; D-α-lysine mutase; adenosylcobalamin-dependent D-lysine 5,6-aminomutase

Systematic name:

(3S)-3,6-diaminohexanoate 5,6-aminomutase

Comments:

This enzyme is a member of the ‘AdoMet radical’ (radical SAM) family. It requires pyridoxal 5′-phosphate and adenosylcobalamin for activity. A 5′-deoxyadenosyl radical is generated during the reaction cycle by reductive cleavage of adenosylcobalamin, which is regenerated at the end of the reaction.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9075-69-8

References:

1.	Stadtman, T.C. and Tasi, L. A cobamide coenzyme dependent migration of the ε-amino group of D-lysine. Biochem. Biophys. Res. Commun. 28 (1967) 920–926. [DOI] [PMID: 4229021]
2.	Stadtman, T.C. and Renz, P. Anaerobic degradation of lysine. V. Some properties of the cobamide coenzyme-dependent β-lysine mutase of Clostridium sticklandii. Arch. Biochem. Biophys. 125 (1968) 226–239. [DOI] [PMID: 5649516]
3.	Morley, C.G.D. and Stadtman, T.C. Studies on the fermentation of D-α-lysine. Purification and properties of an adenosine triphosphate regulated B₁₂-coenzyme-dependent D-α-lysine mutase complex from Clostridium sticklandii. Biochemistry 9 (1970) 4890–4900. [PMID: 5480154]
4.	Retey, J., Kunz, F., Arigoni, D. and Stadtman, T.C. Zur Kenntnis der β-Lysin-Mutase-Reaktion: mechanismus und sterischer Verlauf. Helv. Chim. Acta 61 (1978) 2989–2998.
5.	Chang, C.H. and Frey, P.A. Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-lysine 5, 6-aminomutase from Clostridium sticklandii. J. Biol. Chem. 275 (2000) 106–114. [DOI] [PMID: 10617592]
6.	Tang, K.H., Harms, A. and Frey, P.A. Identification of a novel pyridoxal 5′-phosphate binding site in adenosylcobalamin-dependent lysine 5,6-aminomutase from Porphyromonas gingivalis. Biochemistry 41 (2002) 8767–8776. [DOI] [PMID: 12093296]
7.	Tang, K.H., Mansoorabadi, S.O., Reed, G.H. and Frey, P.A. Radical triplets and suicide inhibition in reactions of 4-thia-D- and 4-thia-L-lysine with lysine 5,6-aminomutase. Biochemistry 48 (2009) 8151–8160. [DOI] [PMID: 19634897]
8.	Berkovitch, F., Behshad, E., Tang, K.H., Enns, E.A., Frey, P.A. and Drennan, C.L. A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase. Proc. Natl. Acad. Sci. USA 101 (2004) 15870–15875. [DOI] [PMID: 15514022]

[EC 5.4.3.3 created 1972 (EC 5.4.3.4 created 1972, incorporated 2017), modified 2017]

5.4.3.4

Transferred entry:

D-lysine 5,6-aminomutase. Now included in EC 5.4.3.3, lysine 5,6-aminomutase

[EC 5.4.3.4 created 1972, modified 2003, deleted 2017]

6.2.1.49

Accepted name:

long-chain fatty acid adenylyltransferase FadD28

Reaction:

ATP + a long-chain fatty acid + holo-[mycocerosate synthase] = AMP + diphosphate + a long-chain acyl-[mycocerosate synthase] (overall reaction)
(1a) ATP + a long-chain fatty acid = diphosphate + a long-chain acyl-adenylate ester
(1b) a long-chain acyl-adenylate ester + holo-[mycocerosate synthase] = AMP + a long-chain acyl-[mycocerosate synthase]

Other name(s):

fadD28 (gene name)

Systematic name:

long-chain fatty acid:holo-[mycocerosate synthase] ligase (AMP-forming)

Comments:

The enzyme, found in certain mycobacteria, activates long-chain fatty acids by adenylation and transfers them to EC 2.3.1.111, mycocerosate synthase. The enzyme participates in the biosynthesis of the virulent lipids dimycocerosates (DIM) and dimycocerosyl triglycosyl phenolphthiocerol (PGL).

Links to other databases:

References:

1.	Fitzmaurice, A.M. and Kolattukudy, P.E. Open reading frame 3, which is adjacent to the mycocerosic acid synthase gene, is expressed as an acyl coenzyme A synthase in Mycobacterium bovis BCG. J. Bacteriol. 179 (1997) 2608–2615. [DOI] [PMID: 9098059]
2.	Goyal, A., Yousuf, M., Rajakumara, E., Arora, P., Gokhale, R.S. and Sankaranarayanan, R. Crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of FadD28, a fatty-acyl AMP ligase from Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (2006) 350–352. [DOI] [PMID: 16582482]
3.	Arora, P., Goyal, A., Natarajan, V.T., Rajakumara, E., Verma, P., Gupta, R., Yousuf, M., Trivedi, O.A., Mohanty, D., Tyagi, A., Sankaranarayanan, R. and Gokhale, R.S. Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis. Nat. Chem. Biol. 5 (2009) 166–173. [DOI] [PMID: 19182784]
4.	Menendez-Bravo, S., Comba, S., Sabatini, M., Arabolaza, A. and Gramajo, H. Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli. Metab. Eng. 24 (2014) 97–106. [DOI] [PMID: 24831705]
5.	Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040–1050. [DOI] [PMID: 25561717]

[EC 6.2.1.49 created 2016 as EC 2.7.7.95, transferred 2017 to EC 6.2.1.49]

*EC

6.3.2.5

Accepted name:

phosphopantothenate—cysteine ligase (CTP)

Reaction:

CTP + (R)-4′-phosphopantothenate + L-cysteine = CMP + diphosphate + N-[(R)-4′-phosphopantothenoyl]-L-cysteine

For diagram of coenzyme A biosynthesis (late stages), click here

Other name(s):

phosphopantothenoylcysteine synthetase (ambiguous); phosphopantothenate—cysteine ligase (ambiguous)

Systematic name:

(R)-4′-phosphopantothenate:L-cysteine ligase

Comments:

A key enzyme in the production of coenzyme A. The bacterial enzyme requires CTP, in contrast to the eukaryotic enzyme, EC 6.3.2.51, which requires ATP. Cysteine can be replaced by some of its derivatives.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9023-50-1

References:

1.	Brown, G.M. The metabolism of pantothenic acid. J. Biol. Chem. 234 (1959) 370–378. [PMID: 13630913]
2.	Strauss, E., Kinsland, C., Ge, Y., McLafferty, F.W. and Begley, T.P. Phosphopantothenoylcysteine synthetase from Escherichia coli. Identification and characterization of the last unidentified Coenzyme A biosynthetic enzymes in bacteria. J. Biol. Chem. 276 (2001) 13513–13516. [DOI] [PMID: 11278255]
3.	Kupke, T. Molecular characterization of the 4′-phosphopantothenoylcysteine synthetase domain of bacterial Dfp flavoproteins. J. Biol. Chem. 277 (2002) 36137–36145. [DOI] [PMID: 12140293]

[EC 6.3.2.5 created 1961, modified 2003, modified 2017]

6.3.2.50

Accepted name:

tenuazonic acid synthetase

Reaction:

ATP + L-isoleucine + acetoacetyl-CoA = AMP + diphosphate + tenuazonic acid + CoA

Glossary:

tenuazonic acid = (5S)-3-acetyl-5-[(2S)-butan-2-yl]-4-hydroxy-1,5-dihydro-2H-pyrrol-2-one

Other name(s):

TAS1 (gene name)

Systematic name:

L-isoleucine:acetoacetyl-CoA ligase (tenuazonic acid-forming)

Comments:

This fungal enzyme, isolated from Magnaporthe oryzae, is an non-ribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) hybrid protein that consists of condensation (C), adenylation (A) and peptidyl-carrier protein (PCP) domains in the NRPS portion and a ketosynthase (KS) domain in the PKS portion. ATP is required for activation of isoleucine, which is then condensed with acetoacetyl-CoA. Cyclization and release from the enzyme are catalysed by the KS domain.

Links to other databases:

References:

1.	Yun, C.S., Motoyama, T. and Osada, H. Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS-PKS hybrid enzyme. Nat. Commun. 6:8758 (2015). [DOI] [PMID: 26503170]

[EC 6.3.2.50 created 2017]

6.3.2.51

Accepted name:

phosphopantothenate—cysteine ligase (ATP)

Reaction:

ATP + (R)-4′-phosphopantothenate + L-cysteine = AMP + diphosphate + N-[(R)-4′-phosphopantothenoyl]-L-cysteine

For diagram of the late stages of CoA biosynthesis, click here

Other name(s):

phosphopantothenoylcysteine synthetase (ambiguous); PPCS (gene name)

Systematic name:

(R)-4′-phosphopantothenate:L-cysteine ligase (ATP-utilizing)

Comments:

A key enzyme in the production of coenzyme A. The eukaryotic enzyme requires ATP, in contrast to the bacterial enzyme, EC 6.3.2.5, phosphopantothenate—cysteine ligase (CTP), which requires CTP.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9023-50-1

References:

1.	Daugherty, M. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J. Biol. Chem. 277 (2002) 21431–21439. [DOI] [PMID: 11923312]
2.	Manoj, N., Strauss, E., Begley, T.P. and Ealick, S.E. Structure of human phosphopantothenoylcysteine synthetase at 2.3 Å Resolution. Structure 11 (2003) 927–936. [DOI] [PMID: 12906824]
3.	Kupke, T., Hernandez-Acosta, P. and Culianez-Macia, F.A. 4′-phosphopantetheine and coenzyme A biosynthesis in plants. J. Biol. Chem. 278 (2003) 38229–38237. [DOI] [PMID: 12860978]

[EC 6.3.2.51 created 2017]

6.3.3.7

Accepted name:

Ni-sirohydrochlorin a,c-diamide reductive cyclase

Reaction:

ATP + Ni-sirohydrochlorin a,c-diamide + 3 reduced electron acceptor + H₂O = ADP + phosphate + 15,17³-seco-F₄₃₀-17³-acid + 3 electron acceptor

Other name(s):

cfbC (gene name); cfbD (gene name)

Systematic name:

Ni-sirohydrochlorin a,c-diamide reductive cyclo-ligase (ADP-forming)

Comments:

Links to other databases:

References:

1.	Pfaltz, A., Kobelt, A., Huster, R. and Thauer, R.K. Biosynthesis of coenzyme F₄₃₀ in methanogenic bacteria. Identification of 15,17³-seco-F₄₃₀-17³-acid as an intermediate. Eur. J. Biochem. 170 (1987) 459–467. [PMID: 3691535]
2.	Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F₄₃₀ in methanogenic and methanotrophic archaea. Science 354 (2016) 339–342. [DOI] [PMID: 27846569]

[EC 6.3.3.7 created 2017]

6.3.5.12

Accepted name:

Ni-sirohydrochlorin a,c-diamide synthase

Reaction:

2 ATP + Ni-sirohydrochlorin + 2 L-glutamine + 2 H₂O = 2 ADP + 2 phosphate + Ni-sirohydrochlorin a,c-diamide + 2 L-glutamate

Other name(s):

cfbB (gene name)

Systematic name:

Ni-sirohydrochlorin:L-glutamine amido-ligase (ADP-forming)

Comments:

Links to other databases:

References:

1.	Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F₄₃₀ in methanogenic and methanotrophic archaea. Science 354 (2016) 339–342. [DOI] [PMID: 27846569]

[EC 6.3.5.12 created 2017]

6.4.1.9

Accepted name:

coenzyme F₄₃₀ synthetase

Reaction:

ATP + 15,17³-seco-F₄₃₀-17³-acid = ADP + phosphate + coenzyme F₄₃₀

Other name(s):

cfbE (gene name)

Systematic name:

15,17³-seco-F₄₃₀-17³-acid cyclo-ligase (ADP-forming)

Comments:

The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, catalyses the last step in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F₄₃₀, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase.

Links to other databases: