Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Richard Cammack, Ron Caspi, Masaaki Kotera, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

An asterisk before'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.


Contents

*EC 1.1.1.219 dihydroflavonol 4-reductase (31 August 2016)
*EC 1.1.1.290 4-phosphoerythronate dehydrogenase (31 August 2016)
EC 1.1.1.395 3α-hydroxy bile acid-CoA-ester 3-dehydrogenase (31 August 2016)
EC 1.1.1.396 bacteriochlorophyllide a dehydrogenase (31 August 2016)
EC 1.1.1.397 β-methylindole-3-pyruvate reductase (31 August 2016)
EC 1.1.1.398 2-glutathionyl-2-methylbut-3-en-1-ol dehydrogenase (31 August 2016)
EC 1.1.1.399 2-oxoglutarate reductase (31 August 2016)
EC 1.1.1.400 2-methyl-1,2-propanediol dehydrogenase (31 August 2016)
EC 1.1.1.401 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD+) (31 August 2016)
EC 1.1.1.402 D-erythritol 1-phosphate dehydrogenase (31 August 2016)
EC 1.1.1.403 D-threitol dehydrogenase (NAD+) (31 August 2016)
EC 1.1.2.9 1-butanol dehydrogenase (cytochrome c) (31 August 2016)
EC 1.1.5.11 1-butanol dehydrogenase (quinone) (31 August 2016)
*EC 1.2.1.50 long-chain acyl-protein thioester reductase (31 August 2016)
EC 1.2.1.98 2-hydroxy-2-methylpropanal dehydrogenase (31 August 2016)
EC 1.2.3.15 (methyl)glyoxal oxidase (31 August 2016)
*EC 1.3.1.75 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) (31 August 2016)
EC 1.3.3.15 coproporphyrinogen III oxidase (coproporphyrin-forming) (31 August 2016)
EC 1.3.7.13 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (ferredoxin) (31 August 2016)
EC 1.3.7.14 3,8-divinyl chlorophyllide a reductase (31 August 2016)
EC 1.3.7.15 chlorophyllide a reductase (31 August 2016)
EC 1.3.98.3 coproporphyrinogen dehydrogenase (31 August 2016)
EC 1.3.99.22 transferred, now EC 1.3.98.3 (31 August 2016)
EC 1.3.99.35 transferred, now EC 1.3.7.15 (31 August 2016)
EC 1.7.2.7 hydrazine synthase (31 August 2016)
EC 1.7.2.8 hydrazine dehydrogenase (31 August 2016)
EC 1.7.99.8 transferred, now EC 1.7.2.8 (31 August 2016)
EC 1.8.99.3 deleted (31 August 2016)
EC 1.14.11.51 DNA N6-methyladenine demethylase (31 August 2016)
EC 1.14.11.52 validamycin A dioxygenase (31 August 2016)
EC 1.14.11.53 mRNA N6-methyladenine demethylase (31 August 2016)
EC 1.14.13.13 transferred, now EC 1.14.15.18 (31 August 2016)
EC 1.14.13.100 transferred, now EC 1.14.14.29 (31 August 2016)
*EC 1.14.13.141 cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] (31 August 2016)
EC 1.14.13.218 5-methylphenazine-1-carboxylate 1-monooxygenase (31 August 2016)
EC 1.14.13.219 resorcinol 4-hydroxylase (NADPH) (31 August 2016)
EC 1.14.13.220 resorcinol 4-hydroxylase (NADH) (31 August 2016)
EC 1.14.13.221 cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] (31 August 2016)
*EC 1.14.14.3 bacterial luciferase (31 August 2016)
*EC 1.14.14.18 heme oxygenase (biliverdin-producing) (31 August 2016)
EC 1.14.14.27 resorcinol 4-hydroxylase (FADH2) (31 August 2016)
EC 1.14.14.28 long-chain alkane monooxygenase (31 August 2016)
EC 1.14.14.29 25/26-hydroxycholesterol 7α-hydroxylase (31 August 2016)
EC 1.14.15.18 calcidiol 1-monooxygenase (31 August 2016)
EC 1.14.15.19 C-19 steroid 1α-hydroxylase (31 August 2016)
EC 1.14.15.20 heme oxygenase (biliverdin-producing, ferredoxin) (31 August 2016)
EC 2.1.1.325 juvenile hormone-III synthase (31 August 2016)
EC 2.1.1.326 N-acetyl-demethylphosphinothricin P-methyltransferase (31 August 2016)
*EC 2.3.1.161 lovastatin nonaketide synthase (31 August 2016)
EC 2.3.1.252 mycolipanoate synthase (31 August 2016)
EC 2.4.1.338 validoxylamine A glucosyltransferase (31 August 2016)
EC 2.4.1.339 β-1,2-mannobiose phosphorylase (31 August 2016)
EC 2.4.1.340 1,2-β-oligomannan phosphorylase (31 August 2016)
EC 2.4.1.341 α-1,2-colitosyltransferase (31 August 2016)
EC 2.4.2.58 hydroxyproline O-arabinosyltransferase (31 August 2016)
EC 2.5.1.132 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate synthase (31 August 2016)
EC 2.6.1.68 deleted, covered by EC 2.6.1.13 and EC 2.6.1.36 (31 August 2016)
EC 2.7.1.209 L-erythrulose 4-kinase (31 August 2016)
EC 2.7.1.210 D-erythrulose 4-kinase (31 August 2016)
EC 2.8.3.24 (R)-2-hydroxy-4-methylpentanoate CoA-transferase (31 August 2016)
EC 3.1.3.101 validoxylamine A 7'-phosphate phosphatase (31 August 2016)
EC 3.1.3.102 FMN hydrolase (31 August 2016)
EC 3.3.2.15 trans-2,3-dihydro-3-hydroxyanthranilic acid synthase (31 August 2016)
EC 3.5.1.120 2-aminomuconate deaminase (2-hydroxymuconate-forming) (31 August 2016)
EC 3.5.4.42 N-isopropylammelide isopropylaminohydrolase (31 August 2016)
EC 3.5.99.4 transferred, now EC 3.5.4.42 (31 August 2016)
*EC 3.6.1.9 nucleotide diphosphatase (31 August 2016)
EC 3.6.1.19 transferred, now included in *EC 3.6.1.9 (31 August 2016)
*EC 4.2.1.106 bile-acid 7α-dehydratase (31 August 2016)
EC 4.2.1.164 dTDP-4-dehydro-2,6-dideoxy-D-glucose 3-dehydratase (31 August 2016)
EC 4.2.1.165 chlorophyllide a 31-hydratase (31 August 2016)
EC 4.2.1.166 phosphinomethylmalate isomerase (31 August 2016)
EC 4.2.1.167 (R)-2-hydroxyglutaryl-CoA dehydratase (31 August 2016)
*EC 4.2.3.152 2-epi-5-epi-valiolone synthase (31 August 2016)
EC 4.2.3.154 demethyl-4-deoxygadusol synthase (31 August 2016)
EC 4.2.3.155 2-epi-valiolone synthase (31 August 2016)
EC 4.3.1.31 L-tryptophan ammonia lyase (31 August 2016)
EC 4.99.1.9 coproporphyrin ferrochelatase (31 August 2016)
*EC 5.1.1.14 nocardicin A epimerase (31 August 2016)
EC 5.1.3.38 D-erythrulose 1-phosphate 3-epimerase (31 August 2016)
EC 5.1.3.39 L-erythrulose 4-phosphate epimerase (31 August 2016)
EC 5.3.1.33 L-erythrulose 1-phosphate isomerase (31 August 2016)
EC 5.3.1.34 D-erythrulose 4-phosphate isomerase (31 August 2016)
EC 5.3.3.20 2-hydroxyisobutanoyl-CoA mutase (31 August 2016)
*EC 6.3.2.47 dapdiamide synthase (31 August 2016)

*EC 1.1.1.219

Accepted name: dihydroflavonol 4-reductase

Reaction: a (2R,3S,4S)-leucoanthocyanidin + NADP+ = a (2R,3R)-dihydroflavonol + NADPH + H+

For diagram of reaction click here.

Other name(s): dihydrokaempferol 4-reductase; dihydromyricetin reductase; NADPH-dihydromyricetin reductase; dihydroquercetin reductase; DFR (gene name), dihydroflavanol 4-reductase (incorrect)

Systematic name: (2R,3S,4S)-leucoanthocyanidin:NADP+ 4-oxidoreductase

Comments: This plant enzyme, involved in the biosynthesis of anthocyanidins, is known to act on (+)-dihydrokaempferol, (+)-taxifolin, and (+)-dihydromyricetin, although some enzymes may act only on a subset of these compounds. Each dihydroflavonol is reduced to the corresponding cis-flavan-3,4-diol. NAD+ can act instead of NADP+, but more slowly.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 83682-99-9

References:

1. Heller, W., Forkmann, G., Britsch, L. and Grisebach, H. Enzymatic reduction of (+)-dihydroflavonols to flavan-3,4-cis- diols with flower extracts from Matthiola incana and its role in anthocyanin biosynthesis. Planta 165 (1985) 284-287.

2. Stafford, H.A. and Lester, H.H. Flavan-3-ol biosynthesis the conversion of (+)-dihydromyricetin to its flavan-3,4-diol (leucodelphinidin) and to (+)-gallocatechin by reductases extracted from tissue-cultures of Ginkgo biloba and Pseudotsuga-menziesii. Plant Physiol. 78 (1985) 791-794. [PMID: 16664326]

3. Fischer, D., Stich, K., Britsch, L. and Grisebach, H. Purification and characterization of (+)-dihydroflavonol (3-hydroxyflavanone) 4-reductase from flowers of Dahlia variabilis. Arch. Biochem. Biophys. 264 (1988) 40-47. [PMID: 3293532]

4. Li, H., Qiu, J., Chen, F., Lv, X., Fu, C., Zhao, D., Hua, X. and Zhao, Q. Molecular characterization and expression analysis of dihydroflavonol 4-reductase (DFR) gene in Saussurea medusa. Mol. Biol. Rep. 39 (2012) 2991-2999. [PMID: 21701830]

[EC 1.1.1.219 created 1989, modified 2016]

*EC 1.1.1.290

Accepted name: 4-phosphoerythronate dehydrogenase

Reaction: 4-phospho-D-erythronate + NAD+ = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + NADH + H+

For diagram of reaction click here.

Other name(s): PdxB; PdxB 4PE dehydrogenase; 4-O-phosphoerythronate dehydrogenase

Systematic name: 4-phospho-D-erythronate:NAD+ 2-oxidoreductase

Comments: This enzyme catalyses a step in a bacterial pathway for the biosynthesis of pyridoxal 5'-phosphate. The enzyme contains a tightly-bound NAD(H) cofactor that is not re-oxidized by free NAD+. In order to re-oxidize the cofactor and restore enzyme activity, the enzyme catalyses the reduction of a 2-oxo acid (such as 2-oxoglutarate, oxaloacetate, or pyruvate) to the respective (R)-hydroxy acid [6]. cf. EC 1.1.1.399, 2-oxoglutarate reductase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 125858-75-5

References:

1. Lam, H.M. and Winkler, M.E. Metabolic relationships between pyridoxine (vitamin B6) and serine biosynthesis in Escherichia coli K-12. J. Bacteriol. 172 (1990) 6518-6528. [PMID: 2121717]

2. Pease, A.J., Roa, B.R., Luo, W. and Winkler, M.E. Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12. J. Bacteriol. 184 (2002) 1359-1369. [PMID: 11844765]

3. Zhao, G. and Winkler, M.E. A novel α-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria. J. Bacteriol. 178 (1996) 232-239. [PMID: 8550422]

4. Grant, G.A. A new family of 2-hydroxyacid dehydrogenases. Biochem. Biophys. Res. Commun. 165 (1989) 1371-1374. [PMID: 2692566]

5. Schoenlein, P.V., Roa, B.B. and Winkler, M.E. Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12. J. Bacteriol. 171 (1989) 6084-6092. [PMID: 2681152]

6. Rudolph, J., Kim, J. and Copley, S.D. Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates. Biochemistry 49 (2010) 9249-9255. [PMID: 20831184]

[EC 1.1.1.290 created 2006, modified 2016]

EC 1.1.1.395

Accepted name: 3α-hydroxy bile acid-CoA-ester 3-dehydrogenase

Reaction: a 3α-hydroxy bile acid CoA ester + NAD+ = a 3-oxo bile acid CoA ester + NADH + H+

Other name(s): baiA1 (gene name); baiA2 (gene name); baiA3 (gene name)

Systematic name: 3α-hydroxy-bile-acid-CoA-ester:NAD+ 3-oxidoreductase

Comments: This bacterial enzyme is involved in the 7-dehydroxylation process associated with bile acid degradation. The enzyme has very little activity with unconjugated bile acid substrates. It has similar activity with choloyl-CoA, chenodeoxycholoyl-CoA, deoxycholoyl-CoA, and lithocholoyl-CoA.

References:

1. Mallonee, D.H., Lijewski, M.A. and Hylemon, P.B. Expression in Escherichia coli and characterization of a bile acid-inducible 3α-hydroxysteroid dehydrogenase from Eubacterium sp. strain VPI 12708. Curr. Microbiol. 30 (1995) 259-263. [PMID: 7766153]

2. Bhowmik, S., Jones, D.H., Chiu, H.P., Park, I.H., Chiu, H.J., Axelrod, H.L., Farr, C.L., Tien, H.J., Agarwalla, S. and Lesley, S.A. Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe. Proteins 82 (2014) 216-229. [PMID: 23836456]

[EC 1.1.1.395 created 2016]

EC 1.1.1.396

Accepted name: bacteriochlorophyllide a dehydrogenase

Reaction: (1) 3-deacetyl-3-(1-hydroxyethyl)bacteriochlorophyllide a + NAD+ = bacteriochlorophyllide a + NADH + H+
(2) 3-devinyl-3-(1-hydroxyethyl)chlorophyllide a + NAD+ = 3-acetyl-3-devinylchlorophyllide a + NADH + H+

For diagram of reaction click here.

Other name(s): bchC (gene name)

Systematic name: 3-deacetyl-3-hydroxyethylbacteriochlorophyllide-a:NAD+ oxidoreductase (bacteriochlorophyllide a-forming)

Comments: The enzyme, together with EC 1.3.7.15, chlorophyllide-a reductase, and EC 4.2.1.165, chlorophyllide-a 31-hydratase, is involved in the conversion of chlorophyllide a to bacteriochlorophyllide a. The enzymes can act in multiple orders, resulting in the formation of different intermediates, but the final product of the cumulative action of the three enzymes is always bacteriochlorophyllide a. The enzyme oxidizes a hydroxyl group on ring A, converting it to an oxo group.

References:

1. Wellington, C.L. and Beatty, J.T. Promoter mapping and nucleotide sequence of the bchC bacteriochlorophyll biosynthesis gene from Rhodobacter capsulatus. Gene 83 (1989) 251-261. [PMID: 2555268]

2. McGlynn, P. and Hunter, C.N. Genetic analysis of the bchC and bchA genes of Rhodobacter sphaeroides. Mol. Gen. Genet. 236 (1993) 227-234. [PMID: 8437569]

3. Lange, C., Kiesel, S., Peters, S., Virus, S., Scheer, H., Jahn, D. and Moser, J. Broadened substrate specificity of 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC) indicates a new route for the biosynthesis of bacteriochlorophyll a. J. Biol. Chem. 290 (2015) 19697-19709. [PMID: 26088139]

[EC 1.1.1.396 created 2016]

EC 1.1.1.397

Accepted name: β-methylindole-3-pyruvate reductase

Reaction: (2S,3R)-2-hydroxy-3-(indol-3-yl)butanoate + NAD+ = (R)-3-(indol-3-yl)-2-oxobutanoate + NADH + H+

Glossary: (R)-3-(indol-3-yl)-2-oxobutanoate = (R)-β-methylindole-3-pyruvate
(2S,3R)-2-hydroxy-3-(indol-3-yl)butanoate = indolmycenate

Other name(s): ind2 (gene name)

Systematic name: (2S,3R)-2-hydroxy-3-(indol-3-yl)butanoate:NAD+ oxidoreductase

Comments: The enzyme, characterized from the bacterium Streptomyces griseus, participates in the biosynthesis of indolmycin, an antibacterial drug that inhibits the bacterial tryptophan—tRNA ligase (EC 6.1.1.2).

References:

1. Du, Y.L., Alkhalaf, L.M. and Ryan, K.S. In vitro reconstitution of indolmycin biosynthesis reveals the molecular basis of oxazolinone assembly. Proc. Natl. Acad. Sci. USA 112 (2015) 2717-2722. [PMID: 25730866]

[EC 1.1.1.397 created 2016]

EC 1.1.1.398

Accepted name: 2-glutathionyl-2-methylbut-3-en-1-ol dehydrogenase

Reaction: 2-(glutathione-S-yl)-2-methylbut-3-en-1-ol + 2 NAD+ + H2O = 2-(glutathione-S-yl)-2-methylbut-3-enoate + 2 NADH + 2 H+ (overall reaction)
(1a) 2-(glutathione-S-yl)-2-methylbut-3-en-1-ol + NAD+ = 2-(glutathione-S-yl)-2-methylbut-3-enal + NADH + H+
(1b) 2-(glutathione-S-yl)-2-methylbut-3-enal + NAD+ + H2O = 2-(glutathione-S-yl)-2-methylbut-3-enoate + NADH + H+

Other name(s): isoH (gene name); 4-hydroxy-3-glutathionyl-3-methylbut-1-ene dehydrogenase

Systematic name: 2-(glutathione-S-yl)-2-methylbut-3-en-1-ol:NAD+ oxidoreductase

Comments: The enzyme, characterized from the bacterium Rhodococcus sp. AD45, is involved in isoprene degradation.

References:

1. van Hylckama Vlieg, J.E., Kingma, J., Kruizinga, W. and Janssen, D.B. Purification of a glutathione S-transferase and a glutathione conjugate-specific dehydrogenase involved in isoprene metabolism in Rhodococcus sp. strain AD45. J. Bacteriol. 181 (1999) 2094-2101. [PMID: 10094686]

[EC 1.1.1.398 created 2016]

EC 1.1.1.399

Accepted name: 2-oxoglutarate reductase

Reaction: (R)-2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH + H+

Other name(s): serA (gene name)

Systematic name: (R)-2-hydroxyglutarate,NAD+ 2-oxidireductase

Comments: The enzyme catalyses a reversible reaction. The enzyme from the bacterium Peptoniphilus asaccharolyticus is specific for (R)-2-hydroxyglutarate [1,2]. The SerA enzyme from the bacterium Escherichia coli can also accept (S)-2-hydroxyglutarate with a much higher Km, and also catalyses the activity of EC 1.1.1.95, phosphoglycerate dehydrogenase [3].

References:

1. Lerud, R.F. and Whiteley, H.R. Purification and properties of α-ketoglutarate reductase from Micrococcus aerogenes. J. Bacteriol. 106 (1971) 571-577. [PMID: 4396793]

2. Johnson, W.M. and Westlake, D.W. Purification and characterization of glutamic acid dehydrogenase and α-ketoglutaric acid reductase from Peptococcus aerogenes. Can. J. Microbiol. 18 (1972) 881-892. [PMID: 4338318]

3. Zhao, G. and Winkler, M.E. A novel α-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria. J. Bacteriol. 178 (1996) 232-239. [PMID: 8550422]

[EC 1.1.1.399 created 2016]

EC 1.1.1.400

Accepted name: 2-methyl-1,2-propanediol dehydrogenase

Reaction: 2-methylpropane-1,2-diol + NAD+ = 2-hydroxy-2-methylpropanal + NADH + H+

Other name(s): mpdB (gene name)

Systematic name: 2-methylpropane-1,2-diol:NAD+ 1-oxidoreductase

Comments: This bacterial enzyme is involved in the degradation pathways of the alkene 2-methylpropene and the fuel oxygenate methyl tert-butyl ether (MTBE), a widely occurring groundwater contaminant.

References:

1. Lopes Ferreira, N., Labbe, D., Monot, F., Fayolle-Guichard, F. and Greer, C.W. Genes involved in the methyl tert-butyl ether (MTBE) metabolic pathway of Mycobacterium austroafricanum IFP 2012. Microbiology 152 (2006) 1361-1374. [PMID: 16622053]

2. Kottegoda, S., Waligora, E. and Hyman, M. Metabolism of 2-methylpropene (isobutylene) by the aerobic bacterium Mycobacterium sp. strain ELW1. Appl. Environ. Microbiol. 81 (2015) 1966-1976. [PMID: 25576605]

[EC 1.1.1.400 created 2016]

EC 1.1.1.401

Accepted name: 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD+)

Reaction: 2-dehydro-3-deoxy-L-rhamnonate + NAD+ = 2,4-didehydro-3-deoxy-L-rhamnonate + NADH + H+

Other name(s): 2-keto-3-deoxy-L-rhamnonate dehydrogenase

Systematic name: 2-dehydro-3-deoxy-L-rhamnonate:NAD+ 4-oxidoreductase

Comments: The enzyme, characterized from the bacteria Sphingomonas sp. SKA58 and Sulfobacillus thermosulfidooxidans, is involved in the non-phosphorylative degradation pathway for L-rhamnose. It does not show any detectable activity with NADP+ or with other aldoses.

References:

1. Watanabe, S. and Makino, K. Novel modified version of nonphosphorylated sugar metabolism – an alternative L-rhamnose pathway of Sphingomonas sp. FEBS J. 276 (2009) 1554-1567. [PMID: 19187228]

2. Bae, J., Kim, S.M. and Lee, S.B. Identification and characterization of 2-keto-3-deoxy-L-rhamnonate dehydrogenase belonging to the MDR superfamily from the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans: implications to L-rhamnose metabolism in archaea. Extremophiles 19 (2015) 469-478. [PMID: 25617114]

[EC 1.1.1.401 created 2016]

EC 1.1.1.402

Accepted name: D-erythritol 1-phosphate dehydrogenase

Reaction: D-erythritol 1-phosphate + NADP+ = D-erythrulose 1-phosphate + NADPH + H+

Other name(s): eryB (gene name)

Systematic name: D-erythritol-1-phosphate 2-oxidoreductase

Comments: The enzyme, characterized from the pathogenic bacterium Brucella abortus, which causes brucellosis in livestock, participates in erythritol catabolism.

References:

1. Sperry, J.F. and Robertson, D.C. Erythritol catabolism by Brucella abortus. J. Bacteriol. 121 (1975) 619-630. [PMID: 163226]

2. Sangari, F.J., Aguero, J. and Garcia-Lobo, J.M. The genes for erythritol catabolism are organized as an inducible operon in Brucella abortus. Microbiology 146 (2000) 487-495. [PMID: 10708387]

3. Barbier, T., Collard, F., Zuniga-Ripa, A., Moriyon, I., Godard, T., Becker, J., Wittmann, C., Van Schaftingen, E. and Letesson, J.J. Erythritol feeds the pentose phosphate pathway via three new isomerases leading to D-erythrose-4-phosphate in Brucella. Proc. Natl. Acad. Sci. USA 111 (2014) 17815-17820. [PMID: 25453104]

[EC 1.1.1.402 created 2016]

EC 1.1.1.403

Accepted name: D-threitol dehydrogenase (NAD+)

Reaction: D-threitol + NAD+ = D-erythrulose + NADH + H+

Other name(s): dthD (gene name)

Systematic name: D-threitol:NAD+ oxidoreductase

Comments: The enzyme, characterized from the bacterium Mycobacterium smegmatis, participates in the degradation of D-threitol.

References:

1. Huang, H., Carter, M.S., Vetting, M.W., Al-Obaidi, N., Patskovsky, Y., Almo, S.C. and Gerlt, J.A. A general strategy for the discovery of metabolic pathways: D-threitol, L-threitol, and erythritol utilization in Mycobacterium smegmatis. J. Am. Chem. Soc. 137 (2015) 14570-14573. [PMID: 26560079]

[EC 1.1.1.403 created 2016]

EC 1.1.2.9

Accepted name: 1-butanol dehydrogenase (cytochrome c)

Reaction: butan-1-ol + 2 ferricytochrome c = butanal + 2 ferrocytochrome c + 2 H+

Other name(s): BDH

Systematic name: butan-1-ol:ferricytochrome c oxidoreductase

Comments: This periplasmic quinoprotein alcohol dehydrogenase, characterized from the bacterium Thauera butanivorans, is involved in butane degradation. It contains both pyrroloquinoline quinone (PQQ) and heme c prosthetic groups. cf. EC 1.1.5.11, 1-butanol dehydrogenase (quinone).

References:

1. Vangnai, A.S. and Arp, D.J. An inducible 1-butanol dehydrogenase, a quinohaemoprotein, is involved in the oxidation of butane by 'Pseudomonas butanovora'. Microbiology 147 (2001) 745-756. [PMID: 11238982]

2. Vangnai, A.S., Arp, D.J. and Sayavedra-Soto, L.A. Two distinct alcohol dehydrogenases participate in butane metabolism by Pseudomonas butanovora. J. Bacteriol. 184 (2002) 1916-1924. [PMID: 11889098]

3. Vangnai, A.S., Sayavedra-Soto, L.A. and Arp, D.J. Roles for the two 1-butanol dehydrogenases of Pseudomonas butanovora in butane and 1-butanol metabolism. J. Bacteriol. 184 (2002) 4343-4350. [PMID: 12142403]

[EC 1.1.2.9 created 2016]

EC 1.1.5.11

Accepted name: 1-butanol dehydrogenase (quinone)

Reaction: butan-1-ol + a quinone = butanal + a quinol

Other name(s): BOH

Systematic name: butan-1-ol:quinone oxidoreductase

Comments: This periplasmic quinoprotein alcohol dehydrogenase, characterized from the bacterium Thauera butanivorans, is involved in butane degradation. It contains a pyrroloquinoline quinone (PQQ) prosthetic group. cf. EC 1.1.2.9, 1-butanol dehydrogenase (cytochrome c).

References:

1. Vangnai, A.S., Arp, D.J. and Sayavedra-Soto, L.A. Two distinct alcohol dehydrogenases participate in butane metabolism by Pseudomonas butanovora. J. Bacteriol. 184 (2002) 1916-1924. [PMID: 11889098]

2. Vangnai, A.S., Sayavedra-Soto, L.A. and Arp, D.J. Roles for the two 1-butanol dehydrogenases of Pseudomonas butanovora in butane and 1-butanol metabolism. J. Bacteriol. 184 (2002) 4343-4350. [PMID: 12142403]

[EC 1.1.5.11 created 2016]

*EC 1.2.1.50

Accepted name: long-chain acyl-protein thioester reductase

Reaction: a long-chain aldehyde + [protein]-L-cysteine + NADP+ = a [protein]-S-(long-chain fatty acyl)-L-cysteine + NADPH + H+

Other name(s): luxC (gene name); acyl-CoA reductase; acyl coenzyme A reductase; long-chain-aldehyde:NADP+ oxidoreductase (acyl-CoA-forming); long-chain-fatty-acyl-CoA reductase

Systematic name: long-chain-aldehyde:NADP+ oxidoreductase (protein thioesther-forming)

Comments: Together with a transferase component (EC 3.1.2.2 and EC 3.1.2.14) and a synthetase component (EC 6.2.1.19), this enzyme forms a multienzyme fatty acid reductase complex that produces the long-chain aldehyde substrate of the bacterial luciferase enzyme (EC 1.14.14.3). The enzyme is acylated by receiving an acyl group from EC 6.2.1.19, and catalyses the reduction of the acyl group, releasing the aldehyde product. The enzyme is also able to accept the acyl group from a long-chain acyl-CoA.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 50936-56-6

References:

1. Riendeau, D., Rodrigues, A. and Meighen, E. Resolution of the fatty acid reductase from Photobacterium phosphoreum into acyl protein synthetase and acyl-CoA reductase activities. Evidence for an enzyme complex. J. Biol. Chem. 257 (1982) 6908-6915. [PMID: 7085612]

2. Wall, L. and Meighen, E.A. Subunit structure of the fatty-acid reductase complex from Photobacterium phosphoreum. Biochemistry 25 (1986) 4315-4321.

3. Lin, J.W., Chao, Y.F. and Weng, S.F. Nucleotide sequence of the luxC gene encoding fatty acid reductase of the lux operon from Photobacterium leiognathi. Biochem. Biophys. Res. Commun. 191 (1993) 314-318. [PMID: 8447834]

[EC 1.2.1.50 created 1986, modified 2016]

EC 1.2.1.98

Accepted name: 2-hydroxy-2-methylpropanal dehydrogenase

Reaction: 2-hydroxy-2-methylpropanal + NAD+ + H2O = 2-hydroxyisobutanoate + NADH + H+

Other name(s): mpdC (gene name)

Systematic name: 2-hydroxy-2-methylpropanal:NAD+ oxidoreductase

Comments: This bacterial enzyme is involved in the degradation pathways of the alkene 2-methylpropene and the fuel oxygenate methyl tert-butyl ether (MTBE), a widely occurring groundwater contaminant.

References:

1. Lopes Ferreira, N., Labbe, D., Monot, F., Fayolle-Guichard, F. and Greer, C.W. Genes involved in the methyl tert-butyl ether (MTBE) metabolic pathway of Mycobacterium austroafricanum IFP 2012. Microbiology 152 (2006) 1361-1374. [PMID: 16622053]

[EC 1.2.1.98 created 2016]

EC 1.2.3.15

Accepted name: (methyl)glyoxal oxidase

Reaction: (1) glyoxal + H2O + O2 = glyoxylate + H2O2
(2) 2-oxopropanal + H2O + O2 = pyruvate + H2O2

Glossary: 2-oxopropanal = methylglyoxal

Other name(s): glx1 (gene name); glx2 (gene name)

Systematic name: (methyl)glyoxal:oxygen oxidoreductase

Comments: The enzyme, originally characterized from the white rot fungus Phanerochaete chrysosporium, utilizes a free radical-coupled copper complex for catalysis.

References:

1. Kersten, P.J. and Kirk, T.K. Involvement of a new enzyme, glyoxal oxidase, in extracellular H2O2 production by Phanerochaete chrysosporium. J. Bacteriol. 169 (1987) 2195-2201. [PMID: 3553159]

2. Kersten, P.J. and Cullen, D. Cloning and characterization of cDNA encoding glyoxal oxidase, a H2O2-producing enzyme from the lignin-degrading basidiomycete Phanerochaete chrysosporium. Proc. Natl. Acad. Sci. USA 90 (1993) 7411-7413. [PMID: 8346264]

3. Kersten, P.J., Witek, C., vanden Wymelenberg, A. and Cullen, D. Phanerochaete chrysosporium glyoxal oxidase is encoded by two allelic variants: structure, genomic organization, and heterologous expression of glx1 and glx2. J. Bacteriol. 177 (1995) 6106-6110. [PMID: 7592374]

4. Whittaker, M.M., Kersten, P.J., Nakamura, N., Sanders-Loehr, J., Schweizer, E.S. and Whittaker, J.W. Glyoxal oxidase from Phanerochaete chrysosporium is a new radical-copper oxidase. J. Biol. Chem. 271 (1996) 681-687. [PMID: 8557673]

[EC 1.2.3.15 created 2016]

*EC 1.3.1.75

Accepted name: 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH)

Reaction: protochlorophyllide a + NADP+ = 3,8-divinyl protochlorophyllide a + NADPH + H+

For diagram of reaction click here.

Other name(s): DVR (gene name); bciA (gene name); [4-vinyl]chlorophyllide a reductase; 4VCR; chlorophyllide-a:NADP+ oxidoreductase; divinyl chlorophyllide a 8-vinyl-reductase; plant-type divinyl chlorophyllide a 8-vinyl-reductase

Systematic name: protochlorophyllide-a:NADP+ C-81-oxidoreductase

Comments: The enzyme, found in higher plants, green algae, and some phototrophic bacteria, is involved in the production of monovinyl versions of (bacterio)chlorophyll pigments from their divinyl precursors. It can also act on 3,8-divinyl chlorophyllide a. cf. EC 1.3.7.13, 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (ferredoxin).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Tripathy, B.C. and Rebeiz, C.A. Chloroplast biogenesis 60. Conversion of divinyl protochlorophyllide to monovinyl protochlorophyllide in green(ing) barley, a dark monovinyl/light divinyl plant species. Plant Physiol. 87 (1988) 89-94. [PMID: 16666133]

2. Parham, R. and Rebeiz, C.A. Chloroplast biogenesis: [4-vinyl] chlorophyllide a reductase is a divinyl chlorophyllide a-specific, NADPH-dependent enzyme. Biochemistry 31 (1992) 8460-8464. [PMID: 1390630]

3. Parham, R. and Rebeiz, C.A. Chloroplast biogenesis 72: a [4-vinyl]chlorophyllide a reductase assay using divinyl chlorophyllide a as an exogenous substrate. Anal. Biochem. 231 (1995) 164-169. [PMID: 8678296]

4. Kolossov, V.L. and Rebeiz, C.A. Chloroplast biogenesis 84: solubilization and partial purification of membrane-bound [4-vinyl]chlorophyllide a reductase from etiolated barley leaves. Anal. Biochem. 295 (2001) 214-219. [PMID: 11488624]

5. Nagata, N., Tanaka, R., Satoh, S. and Tanaka, A. Identification of a vinyl reductase gene for chlorophyll synthesis in Arabidopsis thaliana and implications for the evolution of Prochlorococcus species. Plant Cell 17 (2005) 233-240. [PMID: 15632054]

6. Chew, A.G. and Bryant, D.A. Characterization of a plant-like protochlorophyllide a divinyl reductase in green sulfur bacteria. J. Biol. Chem. 282 (2007) 2967-2975. [PMID: 17148453]

[EC 1.3.1.75 created 2003, modified 2016]

EC 1.3.3.15

Accepted name: coproporphyrinogen III oxidase (coproporphyrin-forming)

Reaction: coproporphyrinogen III + 3 O2 = coproporphyrin III + 3 H2O2

Other name(s): hemY (gene name)

Systematic name: coproporphyrinogen-III:oxygen oxidoreductase (coproporphyrin-forming)

Comments: Contains FAD. The enzyme, present in Gram-positive bacteria, participates in heme biosynthesis. It can also catalyse the reaction of EC 1.3.3.4, protoporphyrinogen oxidase, at a lower level.

References:

1. Hansson, M. and Hederstedt, L. Bacillus subtilis HemY is a peripheral membrane protein essential for protoheme IX synthesis which can oxidize coproporphyrinogen III and protoporphyrinogen IX. J. Bacteriol. 176 (1994) 5962-5970. [PMID: 7928957]

2. Corrigall, A.V., Siziba, K.B., Maneli, M.H., Shephard, E.G., Ziman, M., Dailey, T.A., Dailey, H.A., Kirsch, R.E. and Meissner, P.N. Purification of and kinetic studies on a cloned protoporphyrinogen oxidase from the aerobic bacterium Bacillus subtilis. Arch. Biochem. Biophys. 358 (1998) 251-256. [PMID: 9784236]

3. Qin, X., Sun, L., Wen, X., Yang, X., Tan, Y., Jin, H., Cao, Q., Zhou, W., Xi, Z. and Shen, Y. Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis. J. Struct. Biol. 170 (2010) 76-82. [PMID: 19944166]

4. Dailey, H.A., Gerdes, S., Dailey, T.A., Burch, J.S. and Phillips, J.D. Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin. Proc. Natl. Acad. Sci. USA 112 (2015) 2210-2215. [PMID: 25646457]

[EC 1.3.3.15 created 2016]

EC 1.3.7.13

Accepted name: 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (ferredoxin)

Reaction: protochlorophyllide a + 2 oxidized ferredoxin [iron-sulfur] cluster = 3,8-divinyl protochlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+

For diagram of reaction click here.

Other name(s): bciB (gene name); cyano-type divinyl chlorophyllide a 8-vinyl-reductase

Systematic name: protochlorophyllide-a:ferredoxin C-81-oxidoreductase

Comments: The enzyme, found in many phototrophic bacteria, land plants, and some green and red algae, is involved in the production of monovinyl versions of (bacterio)chlorophyll pigments from their divinyl precursors. Binds two [4Fe-4S] clusters and an FAD cofactor. It can also act on 3,8-divinyl chlorophyllide a, 3,8-divinyl chlorophyll a, and chlorophyll c2. cf. EC 1.3.1.75, 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH).

References:

1. Chew, A.G. and Bryant, D.A. Characterization of a plant-like protochlorophyllide a divinyl reductase in green sulfur bacteria. J. Biol. Chem. 282 (2007) 2967-2975. [PMID: 17148453]

2. Saunders, A.H., Golbeck, J.H. and Bryant, D.A. Characterization of BciB: a ferredoxin-dependent 8-vinyl-protochlorophyllide reductase from the green sulfur bacterium Chloroherpeton thalassium. Biochemistry 52 (2013) 8442-8451. [PMID: 24151992]

3. Ito, H. and Tanaka, A. Evolution of a new chlorophyll metabolic pathway driven by the dynamic changes in enzyme promiscuous activity. Plant Cell Physiol 55 (2014) 593-603. [PMID: 24399236]

[EC 1.3.7.13 created 2016]

EC 1.3.7.14

Accepted name: 3,8-divinyl chlorophyllide a reductase

Reaction: bacteriochlorophyllide g + 2 oxidized ferredoxin [iron-sulfur] cluster + ADP + phosphate = 3,8-divinyl chlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + ATP + H2O + 2 H+

For diagram of reaction click here.

Systematic name: bacteriochlorophyllide-g:ferredoxin C-81-oxidoreductase

Comments: The enzyme, found only in bacteriochlorophyll b-producing bacteria, catalyses the introduction of a C-8 ethylidene group. The enzyme contains a [4Fe-4S] cluster, and structurally resembles the Fe protein/MoFe protein complex of nitrogenase. It is very similar to EC 1.3.7.15, chlorophyllide a reductase, and is composed of three subunits. Two of them form the catalytic component, while the third one functions as an ATP-dependent reductase component that catalyses the electron transfer from ferredoxin to the catalytic component.

References:

1. Tsukatani, Y., Yamamoto, H., Harada, J., Yoshitomi, T., Nomata, J., Kasahara, M., Mizoguchi, T., Fujita, Y. and Tamiaki, H. An unexpectedly branched biosynthetic pathway for bacteriochlorophyll b capable of absorbing near-infrared light. Sci Rep 3 (2013) 1217. [PMID: 23386973]

2. Tsukatani, Y., Harada, J., Nomata, J., Yamamoto, H., Fujita, Y., Mizoguchi, T. and Tamiaki, H. Rhodobacter sphaeroides mutants overexpressing chlorophyllide a oxidoreductase of Blastochloris viridis elucidate functions of enzymes in late bacteriochlorophyll biosynthetic pathways. Sci Rep 5 (2015) 9741. [PMID: 25978726]

[EC 1.3.7.14 created 2016]

EC 1.3.7.15

Accepted name: chlorophyllide a reductase

Reaction: (1) 3-deacetyl-3-vinylbacteriochlorophyllide a + 2 oxidized ferredoxin [iron-sulfur] cluster + ADP + phosphate = chlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + ATP + H2O + 2 H+
(2) bacteriochlorophyllide a + 2 oxidized ferredoxin [iron-sulfur] cluster + ADP + phosphate = 3-acetyl-3-devinylchlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + ATP + H2O + 2 H+
(3) 3-deacetyl-3-(1-hydroxyethyl)bacteriochlorophyllide a + 2 oxidized ferredoxin [iron-sulfur] cluster + ADP + phosphate = 3-devinyl-3-(1-hydroxyethyl)chlorophyllide a + 2 reduced ferredoxin [iron-sulfur] cluster + ATP + H2O + 2 H+

For diagram of reaction click here.

Other name(s): bchX (gene name); bchY (gene name); bchZ (gene name); COR

Systematic name: bacteriochlorophyllide-a:ferredoxin 7,8-oxidoreductase

Comments: The enzyme, together with EC 1.1.1.396, bacteriochlorophyllide-a dehydrogenase, and EC 4.2.1.165, chlorophyllide-a 31-hydratase, is involved in the conversion of chlorophyllide a to bacteriochlorophyllide a. These enzymes can act in multiple orders, resulting in the formation of different intermediates, but the final product of the cumulative action of the three enzymes is always bacteriochlorophyllide a. This enzyme catalyses a trans-reduction of the B-ring; the product has the (7R,8R)-configuration. In addition, the enzyme has a latent activity of EC 1.3.7.13, 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (ferredoxin) [4]. The enzyme contains a [4Fe-4S] cluster, and structurally resembles the Fe protein/MoFe protein complex of nitrogenase (EC 1.18.6.1), which catalyses an ATP-driven reduction.

References:

1. Nomata, J., Mizoguchi, T., Tamiaki, H. and Fujita, Y. A second nitrogenase-like enzyme for bacteriochlorophyll biosynthesis: reconstitution of chlorophyllide a reductase with purified X-protein (BchX) and YZ-protein (BchY-BchZ) from Rhodobacter capsulatus. J. Biol. Chem. 281 (2006) 15021-15028. [PMID: 16571720]

2. Tsukatani, Y., Yamamoto, H., Harada, J., Yoshitomi, T., Nomata, J., Kasahara, M., Mizoguchi, T., Fujita, Y. and Tamiaki, H. An unexpectedly branched biosynthetic pathway for bacteriochlorophyll b capable of absorbing near-infrared light. Sci Rep 3 (2013) 1217. [PMID: 23386973]

3. Lange, C., Kiesel, S., Peters, S., Virus, S., Scheer, H., Jahn, D. and Moser, J. Broadened substrate specificity of 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC) indicates a new route for the biosynthesis of bacteriochlorophyll a. J. Biol. Chem. 290 (2015) 19697-19709. [PMID: 26088139]

4. Harada, J., Mizoguchi, T., Tsukatani, Y., Yokono, M., Tanaka, A. and Tamiaki, H. Chlorophyllide a oxidoreductase works as one of the divinyl reductases specifically involved in bacteriochlorophyll a biosynthesis. J. Biol. Chem. 289 (2014) 12716-12726. [PMID: 24637023]

[EC 1.3.7.15 created 1965 as EC 1.3.99.35, modified 2012, transferred 2016 to EC 1.3.7.15]

EC 1.3.98.3

Accepted name: coproporphyrinogen dehydrogenase

Reaction: coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine

For diagram of reaction click here.

Other name(s): oxygen-independent coproporphyrinogen-III oxidase; HemN; coproporphyrinogen III oxidase

Systematic name: coproporphyrinogen-III:S-adenosyl-L-methionine oxidoreductase (decarboxylating)

Comments: This enzyme differs from EC 1.3.3.3, coproporphyrinogen oxidase, by using S-adenosyl-L-methionine (AdoMet) instead of oxygen as oxidant. It occurs mainly in bacteria, whereas eukaryotes use the oxygen-dependent oxidase. The reaction starts by using an electron from the reduced form of the enzyme's [4Fe-4S] cluster to split AdoMet into methionine and the radical 5'-deoxyadenosin-5'-yl. This radical initiates attack on the 2-carboxyethyl groups, leading to their conversion into vinyl groups. This conversion, —·CH-CH2-COO- → —CH=CH2 + CO2 + e- replaces the electron initially used.

References:

1. Layer, G., Verfürth, K., Mahlitz, E. and Jahn, D. Oxygen-independent coproporphyrinogen-III oxidase HemN from Escherichia coli. J. Biol. Chem. 277 (2002) 34136-34142. [PMID: 12114526]

2. Layer, G., Moser, J., Heinz, D.W., Jahn, D. and Schubert, W.D. Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of radical SAM enzymes. EMBO J. 22 (2003) 6214-6224. [PMID: 14633981]

[EC 1.3.98.3 created 2004 as EC 1.3.99.22, transferred 2016 to EC 1.3.98.3]

[EC 1.3.99.22 Transferred entry: coproporphyrinogen dehydrogenase. Now EC 1.3.98.3, coproporphyrinogen dehydrogenase (EC 1.3.99.22 created 2004, deleted 2016)]

[EC 1.3.99.35 Transferred entry: chlorophyllide a reductase. Now EC 1.3.7.15, chlorophyllide a reductase (EC 1.3.99.35 created 2014, deleted 2016)]

EC 1.7.2.7

Accepted name: hydrazine synthase

Reaction: hydrazine + H2O + 3 ferricytochrome c = nitric oxide + ammonium + 3 ferrocytochrome c

Other name(s): HZS

Systematic name: hydrazine:ferricytochrome-c oxidoreductase

Comments: The enzyme, characterized from anaerobic ammonia oxidizers (anammox bacteria), is one of only two enzymes that are known to form an N-N bond (the other being EC 1.7.1.14, nitric oxide reductase [NAD(P)+, nitrous oxide-forming]). The enzyme from the bacterium Candidatus Kuenenia stuttgartiensis is heterotrimeric and contains multiple c-type cytochromes.

References:

1. Kartal, B., Maalcke, W.J., de Almeida, N.M., Cirpus, I., Gloerich, J., Geerts, W., Op den Camp, H.J., Harhangi, H.R., Janssen-Megens, E.M., Francoijs, K.J., Stunnenberg, H.G., Keltjens, J.T., Jetten, M.S. and Strous, M. Molecular mechanism of anaerobic ammonium oxidation. Nature 479 (2011) 127-130. [PMID: 21964329]

[EC 1.7.2.7 created 2016]

EC 1.7.2.8

Accepted name: hydrazine dehydrogenase

Reaction: hydrazine + 4 ferricytochrome c = N2 + 4 ferrocytochrome c

Other name(s): HDH

Systematic name: hydrazine:ferricytochrome c oxidoreductase

Comments: The enzyme, which is involved in the pathway of anaerobic ammonium oxidation in anammox bacteria, has been purified from the bacterium Candidatus Kuenenia stuttgartiensis. The electrons derived from hydrazine are eventually transferred to the quinone pool.

References:

1. Schalk, J., de Vries, S., Kuenen, J.G. and Jetten, M.S. Involvement of a novel hydroxylamine oxidoreductase in anaerobic ammonium oxidation. Biochemistry 39 (2000) 5405-5412. [PMID: 10820012]

2. Jetten, M.S., Wagner, M., Fuerst, J., van Loosdrecht, M., Kuenen, G. and Strous, M. Microbiology and application of the anaerobic ammonium oxidation ('anammox') process. Curr. Opin. Biotechnol. 12 (2001) 283-288. [PMID: 11404106]

3. Kartal, B., Maalcke, W.J., de Almeida, N.M., Cirpus, I., Gloerich, J., Geerts, W., Op den Camp, H.J., Harhangi, H.R., Janssen-Megens, E.M., Francoijs, K.J., Stunnenberg, H.G., Keltjens, J.T., Jetten, M.S. and Strous, M. Molecular mechanism of anaerobic ammonium oxidation. Nature 479 (2011) 127-130. [PMID: 21964329]

4. Kartal, B., de Almeida, N.M., Maalcke, W.J., Op den Camp, H.J., Jetten, M.S. and Keltjens, J.T. How to make a living from anaerobic ammonium oxidation. FEMS Microbiol. Rev. 37 (2013) 428-461. [PMID: 23210799]

[EC 1.7.2.8 created 2003 as EC 1.7.99.8, modified 2010, transferred 2016 to EC 1.7.2.8]

[EC 1.7.99.8 Transferred entry: hydrazine oxidoreductase, now classified as EC 1.7.2.8, hydrazine dehydrogenase. (EC 1.7.99.8 created 2003, modified 2010, deleted 2016)]

[EC 1.8.99.3 Deleted entry: hydrogensulfite reductase, now known to be an in vitro artifact of EC 1.8.99.5, dissimilatory sulfite reductase (EC 1.8.99.3 created 1986, deleted 2016)]

EC 1.14.11.51

Accepted name: DNA N6-methyladenine demethylase

Reaction: N6-methyladenine in DNA + 2-oxoglutarate + O2 = adenine in DNA + formaldehyde + succinate + CO2

Other name(s): ALKBH1

Systematic name: DNA-N6-methyladenosine,2-oxoglutarate:oxygen oxidoreductase (formaldehyde-forming)

Comments: Contains iron(II). Catalyses oxidative demethylation of DNA N6-methyladenine, a prevalent modification in LINE-1 transposons, which are specifically enriched on the human X chromosome.

References:

1. Wu, T.P., Wang, T., Seetin, M.G., Lai, Y., Zhu, S., Lin, K., Liu, Y., Byrum, S.D., Mackintosh, S.G., Zhong, M., Tackett, A., Wang, G., Hon, L.S., Fang, G., Swenberg, J.A. and Xiao, A.Z. DNA methylation on N-adenine in mammalian embryonic stem cells. Nature 532 (2016) 329-333. [PMID: 27027282]

[EC 1.14.11.51 created 2016]

EC 1.14.11.52

Accepted name: validamycin A dioxygenase

Reaction: validamycin A + 2-oxoglutarate + O2 = validamycin B + succinate + CO2

For diagram of reaction click here.

Glossary: validamycin A = (1R,2R,3S,4S,6R)-2,3-dihydroxy-6-(hydroxymethyl)-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl β-D-glucopyranoside
validamycin B = (1R,2R,3S,4S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl β-D-glucopyranoside

Other name(s): vldW (gene name)

Systematic name: validamycin-A,2-oxoglutarate:oxygen oxidoreductase (6'-hydroxylating)

Comments: The enzyme was characterized from the bacterium Streptomyces hygroscopicus subsp. limoneus. Requires Fe2+.

References:

1. Almabruk, K.H., Asamizu, S., Chang, A., Varghese, S.G. and Mahmud, T. The α-ketoglutarate/Fe(II)-dependent dioxygenase VldW is responsible for the formation of validamycin B. Chembiochem 13 (2012) 2209-2211. [PMID: 22961651]

[EC 1.14.11.52 created 2016]

EC 1.14.11.53

Accepted name: mRNA N6-methyladenine demethylase

Reaction: N6-methyladenine in mRNA + 2-oxoglutarate + O2 = adenine in mRNA + formaldehyde + succinate + CO2

Other name(s): ALKBH5; FTO

Systematic name: mRNA-N6-methyladenosine,2-oxoglutarate:oxygen oxidoreductase (formaldehyde-forming)

Comments: Contains iron(II). Catalyses oxidative demethylation of mRNA N6-methyladenine. The FTO enzyme from human can also demethylate N3-methylthymine from single stranded DNA and N3-methyluridine from single stranded RNA [1,2] with low activity [3].

References:

1. Jia, G., Yang, C.G., Yang, S., Jian, X., Yi, C., Zhou, Z. and He, C. Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO. FEBS Lett. 582 (2008) 3313-3319. [PMID: 18775698]

2. Han, Z., Niu, T., Chang, J., Lei, X., Zhao, M., Wang, Q., Cheng, W., Wang, J., Feng, Y. and Chai, J. Crystal structure of the FTO protein reveals basis for its substrate specificity. Nature 464 (2010) 1205-1209. [PMID: 20376003]

3. Jia, G., Fu, Y., Zhao, X., Dai, Q., Zheng, G., Yang, Y., Yi, C., Lindahl, T., Pan, T., Yang, Y.G. and He, C. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7 (2011) 885-887. [PMID: 22002720]

4. Zheng, G., Dahl, J.A., Niu, Y., Fedorcsak, P., Huang, C.M., Li, C.J., Vagbo, C.B., Shi, Y., Wang, W.L., Song, S.H., Lu, Z., Bosmans, R.P., Dai, Q., Hao, Y.J., Yang, X., Zhao, W.M., Tong, W.M., Wang, X.J., Bogdan, F., Furu, K., Fu, Y., Jia, G., Zhao, X., Liu, J., Krokan, H.E., Klungland, A., Yang, Y.G. and He, C. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49 (2013) 18-29. [PMID: 23177736]

5. Feng, C., Liu, Y., Wang, G., Deng, Z., Zhang, Q., Wu, W., Tong, Y., Cheng, C. and Chen, Z. Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition. J. Biol. Chem. 289 (2014) 11571-11583. [PMID: 24616105]

6. Xu, C., Liu, K., Tempel, W., Demetriades, M., Aik, W., Schofield, C.J. and Min, J. Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. J. Biol. Chem. 289 (2014) 17299-17311. [PMID: 24778178]

7. Aik, W., Scotti, J.S., Choi, H., Gong, L., Demetriades, M., Schofield, C.J. and McDonough, M.A. Structure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. Nucleic Acids Res. 42 (2014) 4741-4754. [PMID: 24489119]

[EC 1.14.11.53 created 2016]

[EC 1.14.13.13 Transferred entry: calcidiol 1-monooxygenase, Now classified as EC 1.14.15.18, calcidiol 1-monooxygenase (EC 1.14.13.13 created 1976, deleted 2016)]

[EC 1.14.13.100 Transferred entry: 25/26-hydroxycholesterol 7α-hydroxylase. Now classified as EC 1.14.14.29, 25/26-hydroxycholesterol 7α-hydroxylase (EC 1.14.13.100 created 2005, modified 2013 (EC 1.14.13.60 created 1999, incorporated 2013), deleted 2016)]

*EC 1.14.13.141

Accepted name: cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming]

Reaction: cholest-4-en-3-one + 3 NADH + 3 H+ + 3 O2 = (25S)-3-oxocholest-4-en-26-oate + 3 NAD+ + 4 H2O (overall reaction)
(1a) cholest-4-en-3-one + NADH + H+ + O2 = (25S)-26-hydroxycholest-4-en-3-one + NAD+ + H2O
(1b) (25S)-26-hydroxycholest-4-en-3-one + NADH + H+ + O2 = (25S)-26-oxocholest-4-en-3-one + NAD+ + 2 H2O
(1c) (25S)-26-oxocholest-4-en-3-one + NADH + H+ + O2 = (25S)-3-oxocholest-4-en-26-oate + NAD+ + H2O

Other name(s): CYP125; CYP125A1; cholest-4-en-3-one 27-monooxygenase (misleading); cholest-4-en-3-one,NADH:oxygen oxidoreductase (26-hydroxylating); cholest-4-en-3-one 26-monooxygenase (ambiguous)

Systematic name: cholest-4-en-3-one,NADH:oxygen oxidoreductase [(25S)-3-oxocholest-4-en-26-oate forming]

Comments: This enzyme, found in several bacterial pathogens, is involved in degradation of the host's cholesterol. It catalyses the hydroxylation of the C-26 carbon, followed by oxidation of the alcohol to the carboxylic acid via the aldehyde intermediate, initiating the degradation of the alkyl side-chain of cholesterol [4]. The products are exclusively in the (25S) configuration. It is a two-component system consisting of a P-450 (heme thiolate) oxygenase (Cyp125) and a ferredoxin reductase (most likely KshB, which is also a part of EC 1.14.13.142 , 3-ketosteroid 9α-monooxygenase). The enzyme also accepts cholesterol as a substrate. cf. EC 1.14.13.221, cholest-4-en-3-one 27-monooxygenase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Rosloniec, K.Z., Wilbrink, M.H., Capyk, J.K., Mohn, W.W., Ostendorf, M., van der Geize, R., Dijkhuizen, L. and Eltis, L.D. Cytochrome P450 125 (CYP125) catalyses C26-hydroxylation to initiate sterol side-chain degradation in Rhodococcus jostii RHA1. Mol. Microbiol. 74 (2009) 1031-1043. [PMID: 19843222]

2. McLean, K.J., Lafite, P., Levy, C., Cheesman, M.R., Mast, N., Pikuleva, I.A., Leys, D. and Munro, A.W. The Structure of Mycobacterium tuberculosis CYP125: molecular basis for cholesterol binding in a P450 needed for host infection. J. Biol. Chem. 284 (2009) 35524-35533. [PMID: 19846552]

3. Capyk, J.K., Kalscheuer, R., Stewart, G.R., Liu, J., Kwon, H., Zhao, R., Okamoto, S., Jacobs, W.R., Jr., Eltis, L.D. and Mohn, W.W. Mycobacterial cytochrome P450 125 (cyp125) catalyzes the terminal hydroxylation of C27 steroids. J. Biol. Chem. 284 (2009) 35534-35542. [PMID: 19846551]

4. Ouellet, H., Guan, S., Johnston, J.B., Chow, E.D., Kells, P.M., Burlingame, A.L., Cox, J.S., Podust, L.M. and de Montellano, P.R. Mycobacterium tuberculosis CYP125A1, a steroid C27 monooxygenase that detoxifies intracellularly generated cholest-4-en-3-one. Mol. Microbiol. 77 (2010) 730-742. [PMID: 20545858]

[EC 1.14.13.141 created 2012, modified 2016]

EC 1.14.13.218

Accepted name: 5-methylphenazine-1-carboxylate 1-monooxygenase

Reaction: 5-methylphenazine-1-carboxylate + NADH + O2 = pyocyanin + NAD+ + CO2 + H2O

Glossary: pyocyanin = 6-methylphenazin-6-ium-1-olate

Other name(s): phzS (gene name)

Systematic name: 5-methylphenazine-1-carboxylate,NADH:oxygen oxidoreductase (1-hydroxylating, decarboxylating)

Comments: The enzyme, characterized from the bacterium Pseudomonas aeruginosa, is involved in the biosynthesis of pyocyanin, a toxin produced and secreted by the organism. It can also act on phenazine-1-carboxylate, converting it into 1-hydroxyphenazine.

References:

1. Mavrodi, D.V., Bonsall, R.F., Delaney, S.M., Soule, M.J., Phillips, G. and Thomashow, L.S. Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PAO1. J. Bacteriol. 183 (2001) 6454-6465. [PMID: 11591691]

2. Parsons, J.F., Greenhagen, B.T., Shi, K., Calabrese, K., Robinson, H. and Ladner, J.E. Structural and functional analysis of the pyocyanin biosynthetic protein PhzM from Pseudomonas aeruginosa. Biochemistry 46 (2007) 1821-1828. [PMID: 17253782]

3. Greenhagen, B.T., Shi, K., Robinson, H., Gamage, S., Bera, A.K., Ladner, J.E. and Parsons, J.F. Crystal structure of the pyocyanin biosynthetic protein PhzS. Biochemistry 47 (2008) 5281-5289. [PMID: 18416536]

[EC 1.14.13.218 created 2016]

EC 1.14.13.219

Accepted name: resorcinol 4-hydroxylase (NADPH)

Reaction: resorcinol + NADPH + H+ + O2 = hydroxyquinol + NADP+ + H2O

Glossary: resorcinol = 1,3-dihydroxybenzene
hydroxyquinol = 1,2,4-trihydroxybenzene

Systematic name: resorcinol,NADPH:oxygen oxidoreductase (4-hydroxylating)

Comments: The enzyme, characterized from the bacterium Corynebacterium glutamicum, is a single-component hydroxylase. The enzyme has no activity with NADH. cf. EC 1.14.13.220, resorcinol 4-hydroxylase (NADH), and EC 1.14.14.27, resorcinol 4-hydroxylase (FADH2).

References:

1. Huang, Y., Zhao, K.X., Shen, X.H., Chaudhry, M.T., Jiang, C.Y. and Liu, S.J. Genetic characterization of the resorcinol catabolic pathway in Corynebacterium glutamicum. Appl. Environ. Microbiol. 72 (2006) 7238-7245. [PMID: 16963551]

[EC 1.14.13.219 created 2016]

EC 1.14.13.220

Accepted name: resorcinol 4-hydroxylase (NADH)

Reaction: resorcinol + NADH + H+ + O2 = hydroxyquinol + NAD+ + H2O

Glossary: resorcinol = 1,3-dihydroxybenzene
hydroxyquinol = 1,2,4-trihydroxybenzene

Other name(s): tsdB (gene name)

Systematic name: resorcinol,NADH:oxygen oxidoreductase (4-hydroxylating)

Comments: The enzyme, characterized from the bacterium Rhodococcus jostii RHA1, is a single-component hydroxylase. The enzyme has no activity with NADPH. cf. EC 1.14.13.219, resorcinol 4-hydroxylase (NADPH), and EC 1.14.14.27, resorcinol 4-hydroxylase (FADH2).

References:

1. Kasai, D., Araki, N., Motoi, K., Yoshikawa, S., Iino, T., Imai, S., Masai, E. and Fukuda, M. γ-Resorcylate catabolic-pathway genes in the soil actinomycete Rhodococcus jostii RHA1. Appl. Environ. Microbiol. 81 (2015) 7656-7665. [PMID: 26319878]

[EC 1.14.13.220 created 2016]

EC 1.14.13.221

Accepted name: cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming]

Reaction: cholest-4-en-3-one + 3 NADPH + 3 H+ + 3 O2 = (25R)-3-oxocholest-4-en-26-oate + 3 NADP+ + 4 H2O (overall reaction)
(1a) cholest-4-en-3-one + NADPH + H+ + O2 = (25R)-26-hydroxycholest-4-en-3-one + NADP+ + H2O
(1b) (25R)-26-hydroxycholest-4-en-3-one + NADPH + H+ + O2 = (25R)-26-oxocholest-4-en-3-one + NADP+ + 2 H2O
(1c) (25R)-26-oxocholest-4-en-3-one + NADPH + H+ + O2 = (25R)-3-oxocholest-4-en-26-oate + NADP+ + H2O

Other name(s): CYP142

Systematic name: cholest-4-en-3-one,NADPH:oxygen oxidoreductase [(25R)-3-oxocholest-4-en-26-oate forming]

Comments: This enzyme, found in several bacterial pathogens, is involved in degradation of the host cholesterol. It catalyses the hydroxylation of the C-26 carbon, followed by oxidation of the alcohol to the carboxylic acid via the aldehyde intermediate, initiating the degradation of the alkyl side-chain of cholesterol. The products are exclusively in the (25R) conformation. The enzyme also accepts cholesterol as a substrate. cf. EC 1.14.13.141, cholest-4-en-3-one 26-monooxygenase. The enzyme can receive electrons from ferredoxin reductase in vitro, its natural electron donor is not known yet.

References:

1. Driscoll, M.D., McLean, K.J., Levy, C., Mast, N., Pikuleva, I.A., Lafite, P., Rigby, S.E., Leys, D. and Munro, A.W. Structural and biochemical characterization of Mycobacterium tuberculosis CYP142: evidence for multiple cholesterol 27-hydroxylase activities in a human pathogen. J. Biol. Chem. 285 (2010) 38270-38282. [PMID: 20889498]

2. Johnston, J.B., Ouellet, H. and Ortiz de Montellano, P.R. Functional redundancy of steroid C26-monooxygenase activity in Mycobacterium tuberculosis revealed by biochemical and genetic analyses. J. Biol. Chem. 285 (2010) 36352-36360. [PMID: 20843794]

[EC 1.14.13.221 created 2016]

*EC 1.14.14.3

Accepted name: bacterial luciferase

Reaction: a long-chain aldehyde + FMNH2 + O2 = a long-chain fatty acid + FMN + H2O +

Other name(s): aldehyde monooxygenase; luciferase; Vibrio fischeri luciferase; alkanal,reduced-FMN:oxygen oxidoreductase (1-hydroxylating, luminescing); alkanal,FMNH2:oxygen oxidoreductase (1-hydroxylating, luminescing); alkanal monooxygenase (FMN); aldehyde,FMNH2:oxygen oxidoreductase (1-hydroxylating, luminescing)

Systematic name: long-chain-aldehyde,FMNH2:oxygen oxidoreductase (1-hydroxylating, luminescing)

Comments: The reaction sequence starts with the incorporation of a molecule of oxygen into reduced FMN bound to the enzyme, forming luciferase peroxyflavin. The peroxyflavin interacts with an aliphatic long-chain aldehyde, producing a highly fluorescent species believed to be luciferase hydroxyflavin. The enzyme is highly specific for reduced FMN and for long-chain aliphatic aldehydes with eight carbons or more. The highest efficiency is achieved with tetradecanal. cf. EC 1.13.12.18, dinoflagellate luciferase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9014-00-0

References:

1. Hastings, J.W. and Nealson, K.H. Bacterial bioluminescence. Annu. Rev. Microbiol. 31 (1977) 549-595. [PMID: 199107]

2. Hastings, J.W. Bacterial bioluminescence light emission in the mixed function oxidation of reduced flavin and fatty aldehyde. Crit. Rev. Biochem. 5 (1978) 163-184. [PMID: 363350]

3. Hastings, J.W. and Presswood, R.P. Bacterial luciferase: FMNH2-aldehyde oxidase. Methods Enzymol. 53 (1978) 558-570. [PMID: 309549]

4. Nealson, K.H. and Hastings, J.W. Bacterial bioluminescence: its control and ecological significance. Microbiol. Rev. 43 (1979) 496-518. [PMID: 396467]

5. Suzuki, K., Kaidoh, T., Katagiri, M. and Tsuchiya, T. O2 incorporation into a long-chain fatty-acid during bacterial luminescence. Biochim. Biophys. Acta 722 (1983) 297-301.

6. Kurfurst, M., Ghisla, S. and Hastings, J.W. Characterization and postulated structure of the primary emitter in the bacterial luciferase reaction. Proc. Natl. Acad. Sci. USA 81 (1984) 2990-2994. [PMID: 16593462]

[EC 1.14.14.3 created 1981, modified 2016]

*EC 1.14.14.18

Accepted name: heme oxygenase (biliverdin-producing)

Reaction: protoheme + 3 [reduced NADPH—hemoprotein reductase] + 3 O2 = biliverdin + Fe2+ + CO + 3 [oxidized NADPH—hemoprotein reductase] + 3 H2O

For diagram of reaction click here.

Other name(s): ORP33 proteins; haem oxygenase (ambiguous); heme oxygenase (decyclizing) (ambiguous); heme oxidase (ambiguous); haem oxidase (ambiguous); heme oxygenase (ambiguous); heme,hydrogen-donor:oxygen oxidoreductase (α-methene-oxidizing, hydroxylating)

Systematic name: protoheme,NADPH—hemoprotein reductase:oxygen oxidoreductase (α-methene-oxidizing, hydroxylating)

Comments: This mammalian enzyme participates in the degradation of heme. The terminal oxygen atoms that are incorporated into the carbonyl groups of pyrrole rings A and B of biliverdin are derived from two separate oxygen molecules [4]. The third oxygen molecule provides the oxygen atom that converts the α-carbon to CO. The enzyme requires NAD(P)H and EC 1.6.2.4, NADPH—hemoprotein reductase. cf. EC 1.14.15.20, heme oxygenase (biliverdin-producing, ferredoxin).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9059-22-7

References:

1. Maines, M.D., Ibrahim, N.G. and Kappas, K. Solubilization and partial purification of heme oxygenase from rat liver. J. Biol. Chem. 252 (1977) 5900-5903. [PMID: 18477]

2. Sunderman, F.W., Jr., Downs, J.R., Reid, M.C. and Bibeau, L.M. Gas-chromatographic assay for heme oxygenase activity. Clin. Chem. 28 (1982) 2026-2032. [PMID: 6897023]

3. Yoshida, T., Takahashi, S. and Kikuchi, J. Partial purification and reconstitution of the heme oxygenase system from pig spleen microsomes. J. Biochem. (Tokyo) 75 (1974) 1187-1191. [PMID: 4370250]

4. Noguchi, M., Yoshida, T. and Kikuchi, G. Specific requirement of NADPH-cytochrome c reductase for the microsomal heme oxygenase reaction yielding biliverdin IX α. FEBS Lett. 98 (1979) 281-284. [PMID: 105935]

5. Lad, L., Schuller, D.J., Shimizu, H., Friedman, J., Li, H., Ortiz de Montellano, P.R. and Poulos, T.L. Comparison of the heme-free and-bound crystal structures of human heme oxygenase-1. J. Biol. Chem. 278 (2003) 7834-7843. [PMID: 12500973]

[EC 1.14.14.18 created 1972 as EC 1.14.99.3, modified 2006, transferred 2015 to EC 1.14.14.18, modified 2016]

EC 1.14.14.27

Accepted name: resorcinol 4-hydroxylase (FADH2)

Reaction: resorcinol + FADH2 + O2 = hydroxyquinol + FAD + H2O

Glossary: resorcinol = 1,3-dihydroxybenzene
hydroxyquinol = 1,2,4-trihydroxybenzene

Other name(s): graA (gene name)

Systematic name: resorcinol,FADH2:oxygen oxidoreductase (4-hydroxylating)

Comments: The enzyme, characterized from the bacterium Rhizobium sp. strain MTP-10005, uses FADH2 as a substrate rather than a cofactor. FADH2 is provided by a dedicated EC 1.5.1.36, flavin reductase (NADH). The enzyme participates in the degradation of γ-resorcylate and resorcinol. cf. EC 1.14.13.220, resorcinol 4-hydroxylase (NADH), and EC 1.14.13.219, resorcinol 4-hydroxylase (NADPH).

References:

1. Ohta, Y. and Ribbons, D.W. Bacterial metabolism of resorcinylic compounds: purification and properties of orcinol hydroxylase and resorcinol hydroxylase from Pseudomonas putida ORC. Eur. J. Biochem. 61 (1976) 259-269. [PMID: 1280]

2. Yoshida, M., Oikawa, T., Obata, H., Abe, K., Mihara, H. and Esaki, N. Biochemical and genetic analysis of the γ-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in Rhizobium sp. strain MTP-10005: identification and functional analysis of its gene cluster. J. Bacteriol. 189 (2007) 1573-1581. [PMID: 17158677]

[EC 1.14.14.27 created 2016]

EC 1.14.14.28

Accepted name: long-chain alkane monooxygenase

Reaction: a long-chain alkane + FMNH2 + O2 = a long-chain primary alcohol + FMN + H2O

Systematic name: long-chain-alkane,FMNH2:oxygen oxidoreductase

Comments: The enzyme, characterized from the bacterium Geobacillus thermodenitrificans NG80-2, is capable of converting alkanes ranging from C15 to C36 into their corresponding primary alcohols [1,2]. The FMNH2 cofactor is provided by an FMN reductase [3].

References:

1. Feng, L., Wang, W., Cheng, J., Ren, Y., Zhao, G., Gao, C., Tang, Y., Liu, X., Han, W., Peng, X., Liu, R. and Wang, L. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc. Natl. Acad. Sci. USA 104 (2007) 5602-5607. [PMID: 17372208]

2. Li, L., Liu, X., Yang, W., Xu, F., Wang, W., Feng, L., Bartlam, M., Wang, L. and Rao, Z. Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-chain alkane hydroxylase. J. Mol. Biol. 376 (2008) 453-465. [PMID: 18164311]

3. Dong, Y., Yan, J., Du, H., Chen, M., Ma, T. and Feng, L. Engineering of LadA for enhanced hexadecane oxidation using random- and site-directed mutagenesis. Appl. Microbiol. Biotechnol. 94 (2012) 1019-1029. [PMID: 22526792]

[EC 1.14.14.28 created 2016]

EC 1.14.14.29

Accepted name: 25/26-hydroxycholesterol 7α-hydroxylase

Reaction: (1) cholest-5-ene-3β,25-diol + [reduced NADPH—hemoprotein reductase] + O2 = cholest-5-ene-3β,7α,25-triol + [oxidized NADPH—hemoprotein reductase] + H2O
(2) (25R)-cholest-5-ene-3β,26-diol + [reduced NADPH—hemoprotein reductase] + O2 = (25R)-cholest-5-ene-3β,7α,26-triol + [oxidized NADPH—hemoprotein reductase] + H2O

For diagram of reaction click here.

Other name(s): 25-hydroxycholesterol 7α-monooxygenase; CYP7B1; CYP7B1 oxysterol 7α-hydroxylase; 27-hydroxycholesterol 7-monooxygenase; 27-hydroxycholesterol 7α-hydroxylase; cholest-5-ene-3β,25-diol,NADPH:oxygen oxidoreductase (7α-hydroxylating); 25-hydroxycholesterol 7α-hydroxylase

Systematic name: cholest-5-ene-3β,25/26-diol,[NADPH—hemoprotein reductase]:oxygen oxidoreductase (7α-hydroxylating)

Comments: A P-450 (heme-thiolate) protein. Unlike EC 1.14.14.26, 24-hydroxycholesterol 7α-monooxygenase, which is specific for its oxysterol substrate, this enzyme can also metabolize the oxysterols 24,25-epoxycholesterol, 22-hydroxycholesterol and 24-hydroxycholesterol, but to a lesser extent [2]. The direct electron donor to the enzyme is EC 1.6.2.4, NADPH—hemoprotein reductase.

References:

1. Kumiko, O.M., Budai, K. and Javitt, N.B. Cholesterol and 27-hydroxycholesterol 7α-hydroxylation: evidence for two different enzymes. J. Lipid Res. 34 (1993) 581-588.

2. Toll, A., Wikvall, K., Sudjana-Sugiaman, E., Kondo, K.H. and Björkhem, I. 7α hydroxylation of 25-hydroxycholesterol in liver microsomes. Evidence that the enzyme involved is different from cholesterol 7α-hydroxylase. Eur. J. Biochem. 224 (1994) 309-316. [PMID: 7925343]

3. Li-Hawkins, J., Lund, E.G., Bronson, A.D. and Russell, D.W. Expression cloning of an oxysterol 7α-hydroxylase selective for 24-hydroxycholesterol. J. Biol. Chem. 275 (2000) 16543-16549. [PMID: 10748047]

4. Ren, S., Marques, D., Redford, K., Hylemon, P.B., Gil, G., Vlahcevic, Z.R. and Pandak, W.M. Regulation of oxysterol 7α-hydroxylase (CYP7B1) in the rat. Metabolism 52 (2003) 636-642. [PMID: 12759897]

5. Russell, D.W. The enzymes, regulation, and genetics of bile acid synthesis. Annu. Rev. Biochem. 72 (2003) 137-174. [PMID: 12543708]

[EC 1.14.14.29 created 2005 as EC 1.14.13.100, modified 2013 (EC 1.14.13.60 created 1999, incorporated 2013), transferred 2016 to EC 1.14.14.29]

EC 1.14.15.18

Accepted name: calcidiol 1-monooxygenase

Reaction: calcidiol + 2 reduced adrenodoxin + 2 H+ + O2 = calcitriol + 2 oxidized adrenodoxin + H2O

For diagram of reaction click here.

Glossary: calcidiol = 25-hydroxyvitamin D3 = (3S,5Z,7E)-9,10-seco-5,7,10(19)-cholestatriene-3,25-diol
calcitriol = 1α,25-dihydroxyvitamin D3 = (1S,3R,5Z,7E)-9,10-seco-5,7,10(19)-cholestatriene-1,3,25-triol

Other name(s): 25-hydroxycholecalciferol 1-hydroxylase; 25-hydroxycholecalciferol 1-monooxygenase; 1-hydroxylase-25-hydroxyvitamin D3; 25-hydroxy D3-1α-hydroxylase; 25-hydroxycholecalciferol 1α-hydroxylase; 25-hydroxyvitamin D3 1α-hydroxylase

Systematic name: calcidiol,adrenodoxin:oxygen oxidoreductase (1-hydroxylating)

References:

1. Gray, R.W., Omdahl, J.L., Ghazarian, J.G. and De Luca, H.F. 25-Hydroxycholecalciferol-1-hydroxylase. Subcellular location and properties. J. Biol. Chem. 247 (1972) 7528-7532. [PMID: 4404596]

[EC 1.14.15.18 created 1976 as EC 1.14.13.13, transferred 2016 to EC 1.14.15.18]

EC 1.14.15.19

Accepted name: C-19 steroid 1α-hydroxylase

Reaction: testosterone + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = 1α-hydroxytestosterone + H2O + 2 oxidized ferredoxin [iron-sulfur] cluster

Other name(s): CYP260A1

Systematic name: testosterone,reduced-ferredoxin:oxygen oxidoreductase (1α-hydroxylating)

Comments: The enzyme, characterized from the bacterium Sorangium cellulosum, is a class I cytochrome P-450, and uses ferredoxin as its electron donor [1]. It was shown to act on several C-19 steroid substrates, including testosterone, androstenedione, testosterone-acetate and 11-oxoandrostenedione [2].

References:

1. Ewen, K.M., Hannemann, F., Khatri, Y., Perlova, O., Kappl, R., Krug, D., Huttermann, J., Muller, R. and Bernhardt, R. Genome mining in Sorangium cellulosum So ce56: identification and characterization of the homologous electron transfer proteins of a myxobacterial cytochrome P450. J. Biol. Chem. 284 (2009) 28590-28598. [PMID: 19696019]

2. Khatri, Y., Ringle, M., Lisurek, M., von Kries, J.P., Zapp, J. and Bernhardt, R. Substrate hunting for the myxobacterial CYP260A1 revealed new 1α-hydroxylated products from C-19 steroids. Chembiochem 17 (2016) 90-101. [PMID: 26478560]

[EC 1.14.15.19 created 2016]

EC 1.14.15.20

Accepted name: heme oxygenase (biliverdin-producing, ferredoxin)

Reaction: protoheme + 6 reduced ferredoxin [iron-sulfur] cluster + 3 O2 + 6 H+ = biliverdin + Fe2+ + CO + 6 oxidized ferredoxin [iron-sulfur] cluster + 3 H2O

Other name(s): HO1 (gene name); HY1 (gene name); HO3 (gene name); HO4 (gene name); pbsA1 (gene name)

Systematic name: protoheme,reduced ferredoxin:oxygen oxidoreductase (α-methene-oxidizing, hydroxylating)

Comments: The enzyme, found in plants, algae, and cyanobacteria, participates in the biosynthesis of phytochromobilin and phytobilins. The terminal oxygen atoms that are incorporated into the carbonyl groups of pyrrole rings A and B of biliverdin are derived from two separate oxygen molecules. The third oxygen molecule provides the oxygen atom that converts the α-carbon to CO. Unlike this enzyme, which uses ferredoxin as its electron donor, the electron source for the related mammalian enzyme (EC 1.14.14.18) is EC 1.6.2.4, NADPH—hemoprotein reductase.

References:

1. Montgomery, B.L. and Lagarias, J.C. Phytochrome ancestry: sensors of bilins and light. Trends Plant Sci 7 (2002) 357-366. [PMID: 12167331]

2. Sugishima, M., Migita, C.T., Zhang, X., Yoshida, T. and Fukuyama, K. Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme. Eur. J. Biochem. 271 (2004) 4517-4525. [PMID: 15560792]

3. Dammeyer, T. and Frankenberg-Dinkel, N. Function and distribution of bilin biosynthesis enzymes in photosynthetic organisms. Photochem Photobiol Sci 7 (2008) 1121-1130. [PMID: 18846276]

[EC 1.14.15.20 created 2016]

EC 2.1.1.325

Accepted name: juvenile hormone-III synthase

Reaction: (1) S-adenosyl-L-methionine + (2E,6E)-farnesoate = S-adenosyl-L-homocysteine + methyl (2E,6E)-farnesoate
(2) S-adenosyl-L-methionine + juvenile hormone III acid = S-adenosyl-L-homocysteine + juvenile hormone III

Glossary: juvenile hormone III = methyl (2E,6E,10R)-10,11-epoxy-3,7,11-trimethyldodeca-2,6-dienoate
juvenile hormone III acid = (2E,6E,10R)-10,11-epoxy-3,7,11-trimethyldodeca-2,6-dienoate

Other name(s): farnesoic acid methyltransferase; juvenile hormone acid methyltransferase; JHAMT

Systematic name: S-adenosyl-L-methionine:(2E,6E)-farnesoate O-methyltransferase

Comments: The enzyme, found in insects, is involved in the synthesis of juvenile hormone III, a sesquiterpenoid that regulates several processes including embryonic development, metamorphosis, and reproduction, in many insect species.

References:

1. Shinoda, T. and Itoyama, K. Juvenile hormone acid methyltransferase: a key regulatory enzyme for insect metamorphosis. Proc. Natl. Acad. Sci. USA 100 (2003) 11986-11991. [PMID: 14530389]

2. Defelipe, L.A., Dolghih, E., Roitberg, A.E., Nouzova, M., Mayoral, J.G., Noriega, F.G. and Turjanski, A.G. Juvenile hormone synthesis: "esterify then epoxidize" or "epoxidize then esterify"? Insights from the structural characterization of juvenile hormone acid methyltransferase. Insect Biochem. Mol. Biol. 41 (2011) 228-235. [PMID: 21195763]

3. Van Ekert, E., Heylen, K., Rouge, P., Powell, C.A., Shatters, R.G., Jr., Smagghe, G. and Borovsky, D. Aedes aegypti juvenile hormone acid methyl transferase, the ultimate enzyme in the biosynthetic pathway of juvenile hormone III, exhibits substrate control. J. Insect Physiol. 64 (2014) 62-73. [PMID: 24657668]

4. Van Ekert, E., Shatters, R.G., Jr., Rouge, P., Powell, C.A., Smagghe, G. and Borovsky, D. Cloning and expressing a highly functional and substrate specific farnesoic acid o-methyltransferase from the Asian citrus psyllid (Diaphorina citri Kuwayama). FEBS Open Bio 5 (2015) 264-275. [PMID: 25893162]

[EC 2.1.1.325 created 2016]

EC 2.1.1.326

Accepted name: N-acetyl-demethylphosphinothricin P-methyltransferase

Reaction: 2 S-adenosyl-L-methionine + N-acetyl-demethylphosphinothricin + reduced acceptor = S-adenosyl-L-homocysteine + 5'-deoxyadenosine + L-methionine + N-acetyl-phosphinothricin + oxidized acceptor

Glossary: N-acetyl-demethylphosphinothricin = (2S)-2-acetamido-4-phosphinatobutanoate

Other name(s): phpK (gene name); bcpD (gene name); P-methylase

Systematic name: S-adenosyl-L-methionine:N-acetyl-demethylphosphinothricin P-methyltransferase

Comments: The enzyme was originally characterized from bacteria that produce the tripeptides bialaphos and phosalacine, which inhibit plant and bacterial glutamine synthetases. It is a radical S-adenosyl-L-methionine (SAM) enzyme that contains a [4Fe-4S] center and a methylcob(III)alamin cofactor. According to the proposed mechanism, the reduced iron-sulfur center donates an electron to SAM, resulting in homolytic cleavage of the carbon-sulfur bond to form a 5'-deoxyadenosyl radical that abstracts the hydrogen atom from the P-H bond of the substrate, forming a phosphinate-centered radical. This radical reacts with methylcob(III)alamin to produce the methylated product and cob(II)alamin, which is reduced by an unknown donor to cob(I)alamin. A potential route for restoring the latter back to methylcob(III)alamin is a nucleophilic attack on a second SAM molecule. The enzyme acts in vivo on N-acetyl-demethylphosphinothricin-L-alanyl-L-alanine or N-acetyl-demethylphosphinothricin-L-alanyl-L-leucine, the intermediates in the biosynthesis of bialaphos and phosalacine, respectively. This transformation produces the only example of a carbon-phosphorus-carbon linkage known to occur in nature.

References:

1. Kamigiri, K., Hidaka, T., Imai, S., Murakami, T. and Seto, H. Studies on the biosynthesis of bialaphos (SF-1293) 12. C-P bond formation mechanism of bialaphos: discovery of a P-methylation enzyme. J. Antibiot. (Tokyo) 45 (1992) 781-787. [PMID: 1624380]

2. Hidaka, T., Hidaka, M., Kuzuyama, T. and Seto, H. Sequence of a P-methyltransferase-encoding gene isolated from a bialaphos-producing Streptomyces hygroscopicus. Gene 158 (1995) 149-150. [PMID: 7789803]

3. Werner, W.J., Allen, K.D., Hu, K., Helms, G.L., Chen, B.S. and Wang, S.C. In vitro phosphinate methylation by PhpK from Kitasatospora phosalacinea. Biochemistry 50 (2011) 8986-8988. [PMID: 21950770]

4. Allen, K.D. and Wang, S.C. Spectroscopic characterization and mechanistic investigation of P-methyl transfer by a radical SAM enzyme from the marine bacterium Shewanella denitrificans OS217. Biochim. Biophys. Acta 1844 (2014) 2135-2144. [PMID: 25224746]

5. Hu, K., Werner, W.J., Allen, K.D. and Wang, S.C. Investigation of enzymatic C-P bond formation using multiple quantum HCP nuclear magnetic resonance spectroscopy. Magn. Reson. Chem. 53 (2015) 267-272. [PMID: 25594737]

[EC 2.1.1.326 created 2016]

*EC 2.3.1.161

Accepted name: lovastatin nonaketide synthase

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

For diagram of reaction click here.

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

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

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

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

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 235426-97-8

References:

1. Ma, S.M., Li, J.W., Choi, J.W., Zhou, H., Lee, K.K., Moorthie, V.A., Xie, X., Kealey, J.T., Da Silva, N.A., Vederas, J.C. and Tang, Y. Complete reconstitution of a highly reducing iterative polyketide synthase. Science 326 (2009) 589-592. [PMID: 19900898]

2. Kennedy, J., Auclair, K., Kendrew, S.G., Park, C., Vederas, J.C. and Hutchinson, C.R. Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science 284 (1999) 1368-1372. [PMID: 10334994]

3. Auclair, K., Sutherland, A., Kennedy, J., Witter, D.J., van der Heever, J.P., Hutchinson, C.R. and Vederas, J.C. Lovastatin nonaketide synthase catalyses an intramolecular Diels-Alder reaction of a substrate analogue. J. Am. Chem. Soc. 122 (2000) 11519-11520.

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

EC 2.3.1.252

Accepted name: mycolipanoate synthase

Reaction: a long-chain acyl-CoA + 3 (R)-methylmalonyl-CoA + 6 NADPH + 6 H+ + holo-[mycolipanoate synthase] = mycolipanoyl-[mycolipanoate synthase] + 4 CoA + 3 CO2 + 6 NADP+ + 3 H2O

Glossary: mycolipanoic acid = (2S,4S,6S)-2,4,6-trimethyl-very-long-chain fatty acid

Other name(s): msl3 (gene name); Pks3/4; mycolipanoic acid synthase

Systematic name: long-chain acyl-CoA:methylmalonyl-CoA C-acyltransferase (mycolipanoate-forming)

Comments: This mycobacterial enzyme accepts long-chain fatty acyl groups from their CoA esters and extends them by incorporation of three methylmalonyl (but not malonyl) residues, forming trimethyl-branched fatty-acids such as (2S,4S,6S)-2,4,6-trimethyltetracosanoate (C27-mycolipanoate). Since the enzyme lacks a thioesterase domain, the product remains bound to the enzyme and requires additional enzyme(s) for removal.

References:

1. Sirakova, T.D., Thirumala, A.K., Dubey, V.S., Sprecher, H. and Kolattukudy, P.E. The Mycobacterium tuberculosis pks2 gene encodes the synthase for the hepta- and octamethyl-branched fatty acids required for sulfolipid synthesis. J. Biol. Chem. 276 (2001) 16833-16839. [PMID: 11278910]

2. Dubey, V.S., Sirakova, T.D. and Kolattukudy, P.E. Disruption of msl3 abolishes the synthesis of mycolipanoic and mycolipenic acids required for polyacyltrehalose synthesis in Mycobacterium tuberculosis H37Rv and causes cell aggregation. Mol. Microbiol. 45 (2002) 1451-1459. [PMID: 12207710]

[EC 2.3.1.252 created 2016]

EC 2.4.1.338

Accepted name: validoxylamine A glucosyltransferase

Reaction: UDP-α-D-glucose + validoxylamine A = UDP + validamycin A

For diagram of reaction click here.

Glossary: validoxylamine A = (1S,2S,3R,6S)-4-(hydroxymethyl)-6-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}cyclohex-4-ene-1,2,3-triol

Other name(s): vldK (gene name); valG (gene name)

Systematic name: UDP-α-D-glucose:validoxylamine-A D-glucosyltransferase

Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus subsp. limoneus, catalyses the ultimate step in the biosynthesis of the antifungal agent validamycin A.

References:

1. Bai, L., Li, L., Xu, H., Minagawa, K., Yu, Y., Zhang, Y., Zhou, X., Floss, H.G., Mahmud, T. and Deng, Z. Functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine A. Chem. Biol. 13 (2006) 387-397. [PMID: 16632251]

2. Xu, H., Minagawa, K., Bai, L., Deng, Z. and Mahmud, T. Catalytic analysis of the validamycin glycosyltransferase (ValG) and enzymatic production of 4''-epi-validamycin A. J Nat Prod 71 (2008) 1233-1236. [PMID: 18563934]

[EC 2.4.1.338 created 2016]

EC 2.4.1.339

Accepted name: β-1,2-mannobiose phosphorylase

Reaction: β-D-mannopyranosyl-(1→2)-D-mannopyranose + phosphate = D-mannopyranose + α-D-mannose 1-phosphate

Systematic name: β-D-mannopyranosyl-(1→2)-D-mannopyranose:phosphate α-D-mannosyltransferase

Comments: The enzyme, originally characterized from the thermophilic anaerobic bacterium Thermoanaerobacter sp. X514, catalyses a reversible reaction. cf. EC 2.4.1.340, 1,2-β-oligomannan phosphorylase.

References:

1. Chiku, K., Nihira, T., Suzuki, E., Nishimoto, M., Kitaoka, M., Ohtsubo, K. and Nakai, H. Discovery of two β-1,2-mannoside phosphorylases showing different chain-length specificities from Thermoanaerobacter sp. X-514. PLoS One 9 (2014) e114882. [PMID: 25500577]

2. Tsuda, T., Nihira, T., Chiku, K., Suzuki, E., Arakawa, T., Nishimoto, M., Kitaoka, M., Nakai, H. and Fushinobu, S. Characterization and crystal structure determination of β-1,2-mannobiose phosphorylase from Listeria innocua. FEBS Lett. 589 (2015) 3816-3821. [PMID: 26632508]

[EC 2.4.1.339 created 2016]

EC 2.4.1.340

Accepted name: 1,2-β-oligomannan phosphorylase

Reaction: [(1→2)-β-D-mannosyl]n + phosphate = [(1→2)-β-D-mannosyl]n-1 + α-D-mannose 1-phosphate

Systematic name: (1→2)-β-D-mannan:phosphate β-D-mannosyl transferase (conformation-inverting)

Comments: The enzyme, originally characterized from the thermophilic anaerobic bacterium Thermoanaerobacter sp. X514, catalyses a reversible reaction. In the synthetic direction it produces oligosaccharides with a degree of polymerization (DP) of 3, 4 and 5. The phosphorolysis reaction proceeds to completion, although activity is highest when the substrate has at least three residues. cf. EC 2.4.1.339, β-1,2-mannobiose phosphorylase.

References:

1. Chiku, K., Nihira, T., Suzuki, E., Nishimoto, M., Kitaoka, M., Ohtsubo, K. and Nakai, H. Discovery of two β-1,2-mannoside phosphorylases showing different chain-length specificities from Thermoanaerobacter sp. X-514. PLoS One 9 (2014) e114882. [PMID: 25500577]

[EC 2.4.1.340 created 2016]

EC 2.4.1.341

Accepted name: α-1,2-colitosyltransferase

Reaction: GDP-β-L-colitose + β-D-galactopyranosyl-(1→3)-N-acetyl-D-glucosamine = GDP + α-L-colitosyl-(1→2)-β-D-galactosyl-(1→3)-N-acetyl-D-glucosamine

Glossary: β-D-galactopyranosyl-(1→3)-N-acetyl-D-glucosamine = lacto-N-biose

Other name(s): wbgN (gene name)

Systematic name: GDP-β-L-colitose:β-D-galactopyranosyl-(1→3)-N-acetyl-D-glucosamine L-colitosyltransferase (configuration-inverting)

Comments: The enzyme, characterized from the bacterium Escherichia coli O55:H7, participates in the biosynthesis of an O-antigen. The reaction involves anomeric inversion, and does not require any metal ions. The enzyme is highly specific towards the acceptor, exclusively recognizing lacto-N-biose, but can accept GDP-L-fucose as the donor with almost the same activity as with GDP-β-L-colitose.

References:

1. Wu, Z., Zhao, G., Li, T., Qu, J., Guan, W., Wang, J., Ma, C., Li, X., Zhao, W., Wang, P.G. and Li, L. Biochemical characterization of an α1,2-colitosyltransferase from Escherichia coli O55:H7. Glycobiology (2015) . [PMID: 26703456]

[EC 2.4.1.341 created 2016]

EC 2.4.2.58

Accepted name: hydroxyproline O-arabinosyltransferase

Reaction: UDP-β-L-arabinofuranose + [protein]-trans-4-hydroxy-L-proline = UDP + [protein]-O-(β-L-arabinofuranosyl)-trans-4-hydroxy-L-proline

Glossary: trans-4-hydroxy-L-proline = (2S,4R)-4-hydroxyproline = (4R)-4-hydroxy-L-proline

Other name(s): HPAT

Systematic name: UDP-β-L-arabinofuranose:[protein]-trans-4-hydroxy-L-proline L-arabinofuranosyl transferase (configuration-retaining)

Comments: The enzyme, found in plants and mosses, catalyses the O-arabinosylation of hydroxyprolines in hydroxyproline-rich glycoproteins. The enzyme acts on the first hydroxyproline in the motif Val-hydroxyPro-hydroxyPro-Ser.

References:

1. Ogawa-Ohnishi, M., Matsushita, W. and Matsubayashi, Y. Identification of three hydroxyproline O-arabinosyltransferases in Arabidopsis thaliana. Nat. Chem. Biol. 9 (2013) 726-730. [PMID: 24036508]

[EC 2.4.2.58 created 2016]

EC 2.5.1.132

Accepted name: 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate synthase

Reaction: phosphoenolpyruvate + D-mannose 6-phosphate + H2O = 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate + phosphate

Glossary: 3-deoxy-D-glycero-D-galacto-nononate = KDN

Other name(s): 2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic acid synthase; KDN 9-P synthase

Systematic name: phosphoenolpyruvate:D-mannose-6-phosphate 1-(2-carboxy-2-oxoethyl)transferase

Comments: The enzyme participates in the biosynthesis of the sialic acid 3-deoxy-D-glycero-D-galacto-nononate (KDN). The human sialic acid synthase (EC 2.5.1.57) is also able to catalyse the reaction. KDN is abundant in extracellular glycoconjugates of lower vertebrates such as fish and amphibians, but is also found in the capsular polysaccharides of bacteria that belong to the Bacteroides genus.

References:

1. Angata, T., Nakata, D., Matsuda, T., Kitajima, K. and Troy, F.A., 2nd. Biosynthesis of KDN (2-keto-3-deoxy-D-glycero-D-galacto-nononic acid). Identification and characterization of a KDN-9-phosphate synthetase activity from trout testis. J. Biol. Chem. 274 (1999) 22949-22956. [PMID: 10438460]

2. Lawrence, S.M., Huddleston, K.A., Pitts, L.R., Nguyen, N., Lee, Y.C., Vann, W.F., Coleman, T.A. and Betenbaugh, M.J. Cloning and expression of the human N-acetylneuraminic acid phosphate synthase gene with 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid biosynthetic ability. J. Biol. Chem. 275 (2000) 17869-17877. [PMID: 10749855]

3. Wang, L., Lu, Z., Allen, K.N., Mariano, P.S. and Dunaway-Mariano, D. Human symbiont Bacteroides thetaiotaomicron synthesizes 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN). Chem. Biol. 15 (2008) 893-897. [PMID: 18804026]

[EC 2.5.1.132 created 2016]

[EC 2.6.1.68 Deleted entry: ornithine(lysine) transaminase. Now classified as EC 2.6.1.13, ornithine aminotransferase and EC 2.6.1.36, L-lysine 6-transaminase (EC 2.6.1.68 created 1989, deleted 2016)]

EC 2.7.1.209

Accepted name: L-erythrulose 4-kinase

Reaction: ATP + L-erythrulose = ADP + L-erythrulose 4-phosphate

Other name(s): lerK (gene name)

Systematic name: ATP:L-erythrulose 4-phosphotransferase

Comments: The enzyme, characterized from the bacterium Mycobacterium smegmatis, participates in the degradation of L-threitol.

References:

1. Huang, H., Carter, M.S., Vetting, M.W., Al-Obaidi, N., Patskovsky, Y., Almo, S.C. and Gerlt, J.A. A general strategy for the discovery of metabolic pathways: D-threitol, L-threitol, and erythritol utilization in Mycobacterium smegmatis. J. Am. Chem. Soc. 137 (2015) 14570-14573. [PMID: 26560079]

[EC 2.7.1.209 created 2016]

EC 2.7.1.210

Accepted name: D-erythrulose 4-kinase

Reaction: ATP + D-erythrulose = ADP + D-erythrulose 4-phosphate

Other name(s): derK (gene name)

Systematic name: ATP:D-erythrulose 4-phosphotransferase

Comments: The enzyme, characterized from the bacterium Mycobacterium smegmatis, participates in the degradation of erythritol and D-threitol.

References:

1. Huang, H., Carter, M.S., Vetting, M.W., Al-Obaidi, N., Patskovsky, Y., Almo, S.C. and Gerlt, J.A. A general strategy for the discovery of metabolic pathways: D-threitol, L-threitol, and erythritol utilization in Mycobacterium smegmatis. J. Am. Chem. Soc. 137 (2015) 14570-14573. [PMID: 26560079]

[EC 2.7.1.210 created 2016]

EC 2.8.3.24

Accepted name: (R)-2-hydroxy-4-methylpentanoate CoA-transferase

Reaction: 4-methylpentanoyl-CoA + (R)-2-hydroxy-4-methylpentanoate = 4-methylpentanoate + (R)-2-hydroxy-4-methylpentanoyl-CoA

Glossary: (R)-2-hydroxy-4-methylpentanoate = D-leucate
4-methylpentanoate = isocaproate

Other name(s): hadA (gene name)

Systematic name: 4-methylpentanoyl-CoA:(R)-2-hydroxy-4-methylpentanoate CoA-transferase

Comments: The enzyme, characterized from the bacterium Peptoclostridium difficile, participates in an L-leucine fermentation pathway. The reaction proceeds via formation of a covalent anhydride intermediate between a conserved aspartate residue and the acyl group of the CoA thioester substrate.

References:

1. Kim, J., Darley, D., Selmer, T. and Buckel, W. Characterization of (R)-2-hydroxyisocaproate dehydrogenase and a family III coenzyme A transferase involved in reduction of L-leucine to isocaproate by Clostridium difficile. Appl. Environ. Microbiol. 72 (2006) 6062-6069. [PMID: 16957230]

[EC 2.8.3.24 created 2016]

EC 3.1.3.101

Accepted name: validoxylamine A 7'-phosphate phosphatase

Reaction: validoxylamine A 7'-phosphate + H2O = validoxylamine A + phosphate

For diagram of reaction click here.

Glossary: validoxylamine A = (1S,2S,3R,6S)-4-(hydroxymethyl)-6-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}cyclohex-4-ene-1,2,3-triol

Other name(s): vldH (gene name)

Systematic name: validoxylamine-A 7'-phosphate phosphohydrolase

Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus subsp. limoneus, is involved in the biosynthesis of the antifungal agent validamycin A.

References:

1. Asamizu, S., Yang, J., Almabruk, K.H. and Mahmud, T. Pseudoglycosyltransferase catalyzes nonglycosidic C-N coupling in validamycin a biosynthesis. J. Am. Chem. Soc. 133 (2011) 12124-12135. [PMID: 21766819]

[EC 3.1.3.101 created 2016]

EC 3.1.3.102

Accepted name: FMN hydrolase

Reaction: FMN + H2O = riboflavin + phosphate

Other name(s): FMN phosphatase; AtcpFHy1

Systematic name: FMN phosphohydrolase

Comments: Requires Mg2+. The enzyme, found in many isoforms purified from both bacteria and plants, is a member of the haloacid dehalogenase superfamily. Most of the isoforms have a wide substrate specificity [2], but isoforms specific for FMN also exist [3].

References:

1. Sandoval, F.J. and Roje, S. An FMN hydrolase is fused to a riboflavin kinase homolog in plants. J. Biol. Chem. 280 (2005) 38337-38345. [PMID: 16183635]

2. Kuznetsova, E., Proudfoot, M., Gonzalez, C.F., Brown, G., Omelchenko, M.V., Borozan, I., Carmel, L., Wolf, Y.I., Mori, H., Savchenko, A.V., Arrowsmith, C.H., Koonin, E.V., Edwards, A.M. and Yakunin, A.F. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J. Biol. Chem. 281 (2006) 36149-36161. [PMID: 16990279]

3. Rawat, R., Sandoval, F.J., Wei, Z., Winkler, R. and Roje, S. An FMN hydrolase of the haloacid dehalogenase superfamily is active in plant chloroplasts. J. Biol. Chem. 286 (2011) 42091-42098. [PMID: 22002057]

[EC 3.1.3.102 created 2016]

EC 3.3.2.15

Accepted name: trans-2,3-dihydro-3-hydroxyanthranilic acid synthase

Reaction: (2S)-2-amino-4-deoxychorismate + H2O = (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate + pyruvate

Glossary: (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate = trans-2,3-dihydro-3-hydroxyanthranilate

Other name(s): isochorismatase (ambiguous); phzD (gene name)

Systematic name: (2S)-2-amino-4-deoxychorismate pyruvate-hydrolase

Comments: Isolated from the bacterium Pseudomonas aeruginosa. Involved in phenazine biosynthesis.

References:

1. Mavrodi, D.V., Bonsall, R.F., Delaney, S.M., Soule, M.J., Phillips, G. and Thomashow, L.S. Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PAO1. J. Bacteriol. 183 (2001) 6454-6465. [PMID: 11591691]

2. Parsons, J.F., Calabrese, K., Eisenstein, E. and Ladner, J.E. Structure and mechanism of Pseudomonas aeruginosa PhzD, an isochorismatase from the phenazine biosynthetic pathway. Biochemistry 42 (2003) 5684-5693. [PMID: 12741825]

[EC 3.3.2.15 created 2016]

EC 3.5.1.120

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.

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. [PMID: 17259310]

[EC 3.5.1.120 created 2016]

EC 3.5.4.42

Accepted name: N-isopropylammelide isopropylaminohydrolase

Reaction: N-isopropylammelide + H2O = cyanuric acid + isopropylamine

Glossary: N-isopropylammelide = 2,4-dihydroxy-6-(isopropylamino)-1,3,5-triazine
cyanuric acid = 1,3,5-triazine-2,4,6(1H,3H,5H)-trione = 2,4,6-trihydroxy-s-triazine

Other name(s): atzC (gene name)

Systematic name: N-isopropylammelide isopropylaminohydrolase

Comments: Requires Zn2+. This bacterial enzyme is involved indegradation of the herbicide atrazine. It can hydrolyse other N-substituted amino dihydroxy-s-triazine molecules, and prefers substrates with linear N-alkyl groups to those with branched alkyl groups.

References:

1. Sadowsky, M.J., Tong, Z., de Souza, M. and Wackett, L.P. AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes. J. Bacteriol. 180 (1998) 152-158. [PMID: 9422605]

2. Shapir, N., Osborne, J.P., Johnson, G., Sadowsky, M.J. and Wackett, L.P. Purification, substrate range, and metal center of AtzC: the N-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism. J. Bacteriol. 184 (2002) 5376-5384. [PMID: 12218024]

3. Balotra, S., Warden, A.C., Newman, J., Briggs, L.J., Scott, C. and Peat, T.S. X-ray structure and mutagenesis studies of the N-isopropylammelide isopropylaminohydrolase, AtzC. PLoS One 10 (2015) e0137700. [PMID: 26390431]

[EC 3.5.4.42 created 2000 as EC 3.5.99.4, transferred 2016 to EC 3.5.4.42]

[EC 3.5.99.4 Transferred entry: N-isopropylammelide isopropylaminohydrolase, now classified as EC 3.5.4.42, N-isopropylammelide isopropylaminohydrolase (EC 3.5.99.4 created 2000, deleted 2016)]

*EC 3.6.1.9

Accepted name: nucleotide diphosphatase

Reaction: a nucleoside triphosphate + H2O = a nucleotide + diphosphate

Other name(s): ENPP1 (gene name); nucleotide pyrophosphatase; nucleotide-sugar pyrophosphatase; nucleoside-triphosphate diphosphatase

Systematic name: nucleoside-triphosphate diphosphohydrolase

Comments: The enzyme preferentially hydrolyses ATP, but can also hydrolyse other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates. In vitro the enzyme also acts as a nucleotidohydrolase on ADP, NAD+, NADP+, FAD, and CoA.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9032-64-8

References:

1. Chern, C.J., Macdonald, A.B. and Morris, A.J. Purification and properties of a nucleoside triphosphate pyrophosphohydrolase from red cells of the rabbit. J. Biol. Chem. 244 (1969) 5489-5495. [PMID: 4310599]

2. Kelly, S.J., Dardinger, D.E. and Butler, L.G. Hydrolysis of phosphonate esters catalyzed by 5'-nucleotide phosphodiesterase. Biochemistry 14 (1975) 4983-4988. [PMID: 170964]

3. Landt, M. and Butler, L.G. 5'-Nucleotide phosphodiesterase: isolation of covalently bound 5'-adenosine monophosphate, an intermediate in the catalytic mechanism. Biochemistry 17 (1978) 4130-4135. [PMID: 213103]

4. Zhang, J. and Inouye, M. MazG, a nucleoside triphosphate pyrophosphohydrolase, interacts with Era, an essential GTPase in Escherichia coli. J. Bacteriol. 184 (2002) 5323-5329. [PMID: 12218018]

[EC 3.6.1.9 created 1961 (EC 3.6.1.19 created 1972, incorporated 2016), modified 2016]

[EC 3.6.1.19 Transferred entry: nucleoside-triphosphate diphosphatase, now included in EC 3.6.1.9, nucleotide diphosphatase (EC 3.6.1.19 created 1972, deleted 2016)]

*EC 4.2.1.106

Accepted name: bile-acid 7α-dehydratase

Reaction: 7α,12α-dihydroxy-3-oxochol-4-en-24-oyl-CoA = 12α-hydroxy-3-oxochola-4,6-dien-24-oyl-CoA + H2O

For diagram of reaction click here.

Other name(s): baiE (gene name); 7α,12α-dihydroxy-3-oxochol-4-enoate hydro-lyase; 7α,12α-dihydroxy-3-oxochol-4-enoate hydro-lyase (12α-hydroxy-3-oxochola-4,6-dienoate-forming)

Systematic name: 7α,12α-dihydroxy-3-oxochol-4-enoyl-CoA hydro-lyase (12α-hydroxy-3-oxochola-4,6-dienoyl-CoA-forming)

Comments: This enzyme, characterized from the gut bacterium Clostridium scindens (previously known as Eubacterium sp. strain VPI 12708), participates in the 7-dehydroxylation process associated with bile acid degradation.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Mallonee, D.H., White, W.B. and Hylemon, P.B. Cloning and sequencing of a bile acid-inducible operon from Eubacterium sp. strain VPI 12708. J. Bacteriol. 172 (1990) 7011-7019. [PMID: 2254270]

2. Dawson, J.A., Mallonee, D.H., Björkhem, I. and Hylemon, P.B. Expression and characterization of a C24 bile acid 7α-dehydratase from Eubacterium sp. strain VPI 12708 in Escherichia coli. J. Lipid Res. 37 (1996) 1258-1267. [PMID: 8808760]

3. Bhowmik, S., Chiu, H.P., Jones, D.H., Chiu, H.J., Miller, M.D., Xu, Q., Farr, C.L., Ridlon, J.M., Wells, J.E., Elsliger, M.A., Wilson, I.A., Hylemon, P.B. and Lesley, S.A. Structure and functional characterization of a bile acid 7α dehydratase BaiE in secondary bile acid synthesis. Proteins 84 (2016) 316-331. [PMID: 26650892]

[EC 4.2.1.106 created 2005, modified 2016]

EC 4.2.1.164

Accepted name: dTDP-4-dehydro-2,6-dideoxy-D-glucose 3-dehydratase

Reaction: dTDP-4-dehydro-2,6-dideoxy-α-D-threo-hexopyranose + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ = dTDP-4-dehydro-2,3,6-trideoxy-α-D-hexopyranose + H2O + 2 oxidized ferredoxin [iron-sulfur] cluster

For diagram of reaction click here.

Other name(s): SpnQ; TDP-4-keto-2,6-dideoxy-D-glucose 3-dehydrase

Systematic name: dTDP-2,6-dideoxy-α-D-threo-hexopyranose hydro-lyase (dTDP-2,3,6-trideoxy-α-D-hexopyranose-forming)

Comments: A pyridoxal-phosphate protein. The enzyme, isolated from the bacterium Saccharopolyspora spinosa, participates in the biosynthesis of forosamine. Requires ferredoxin/ferredoxin reductase or flavodoxin/flavodoxin reductase [1].

References:

1. Hong, L., Zhao, Z. and Liu, H.W. Characterization of SpnQ from the spinosyn biosynthetic pathway of Saccharopolyspora spinosa: mechanistic and evolutionary implications for C-3 deoxygenation in deoxysugar biosynthesis. J. Am. Chem. Soc. 128 (2006) 14262-14263. [PMID: 17076492]

2. Hong, L., Zhao, Z., Melancon, C.E., 3rd, Zhang, H. and Liu, H.W. In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J. Am. Chem. Soc. 130 (2008) 4954-4967. [PMID: 18345667]

[EC 4.2.1.164 created 2016]

EC 4.2.1.165

Accepted name: chlorophyllide a 31-hydratase

Reaction: (1) 3-devinyl-3-(1-hydroxyethyl)-chlorophyllide a = chlorophyllide a + H2O
(2) 3-deacetyl-3-(1-hydroxyethyl)-bacteriochlorophyllide a = 3-deacetyl-3-vinyl-bacteriochlorophyllide a + H2O

For diagram of reaction click here.

Other name(s): bchF (gene name)

Systematic name: chlorophyllide-a 31-hydro-lyase

Comments: The enzyme, together with EC 1.3.7.15, chlorophyllide-a reductase, and EC 1.1.1.396, bacteriochlorophyllide-a dehydrogenase, is involved in the conversion of chlorophyllide a to bacteriochlorophyllide a. The enzymes can act in multiple orders, resulting in the formation of different intermediates, but the final product of the cumulative action of the three enzymes is always bacteriochlorophyllide a. The enzyme catalyses the hydration of a vinyl group on ring A, converting it to a hydroxyethyl group.

References:

1. Pudek, M.R. and Richards, W.R. A possible alternate pathway of bacteriochlorophyll biosynthesis in a mutant of Rhodopseudomonas sphaeroides. Biochemistry 14 (1975) 3132-3137. [PMID: 1080053]

2. Burke, D.H., Alberti, M. and Hearst, J.E. bchFNBH bacteriochlorophyll synthesis genes of Rhodobacter capsulatus and identification of the third subunit of light-independent protochlorophyllide reductase in bacteria and plants. J. Bacteriol. 175 (1993) 2414-2422. [PMID: 8385667]

3. Lange, C., Kiesel, S., Peters, S., Virus, S., Scheer, H., Jahn, D. and Moser, J. Broadened substrate specificity of 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC) indicates a new route for the biosynthesis of bacteriochlorophyll a. J. Biol. Chem. 290 (2015) 19697-19709. [PMID: 26088139]

4. Harada, J., Teramura, M., Mizoguchi, T., Tsukatani, Y., Yamamoto, K. and Tamiaki, H. Stereochemical conversion of C3-vinyl group to 1-hydroxyethyl group in bacteriochlorophyll c by the hydratases BchF and BchV: adaptation of green sulfur bacteria to limited-light environments. Mol. Microbiol. 98 (2015) 1184-1198. [PMID: 26331578]

[EC 4.2.1.165 created 2016]

EC 4.2.1.166

Accepted name: phosphinomethylmalate isomerase

Reaction: phosphinomethylmalate = phosphinomethylisomalate (overall reaction)
(1a) phosphinomethylmalate = 2-(phosphinatomethylidene)butanedioate + H2O
(1b) 2-(phosphinatomethylidene)butanedioate + H2O = phosphinomethylisomalate

Other name(s): pmi (gene name)

Systematic name: phosphinomethylmalate(phosphinomethylisomalate) hydro-lyase (cis-aconitate-forming)

Comments: The enzyme, characterized from the bacterium Streptomyces viridochromogenes, is involved in bialaphos biosynthesis. The enzyme from the bacterium Kitasatospora phosalacinea participates in the biosynthesis of the related compound phosalacine. Both compounds contain the nonproteinogenic amino acid L-phosphinothricin that acts as a potent inhibitor of EC 6.3.1.2, glutamine synthetase. The similar enzyme EC 4.2.1.3, aconitate hydratase, cannot catalyse this reaction.

References:

1. Heinzelmann, E., Kienzlen, G., Kaspar, S., Recktenwald, J., Wohlleben, W. and Schwartz, D. The phosphinomethylmalate isomerase gene pmi, encoding an aconitase-like enzyme, is involved in the synthesis of phosphinothricin tripeptide in Streptomyces viridochromogenes. Appl. Environ. Microbiol. 67 (2001) 3603-3609. [PMID: 11472937]

[EC 4.2.1.166 created 2016]

EC 4.2.1.167

Accepted name: (R)-2-hydroxyglutaryl-CoA dehydratase

Reaction: (R)-2-hydroxyglutaryl-CoA = (E)-glutaconyl-CoA + H2O

Other name(s): hgdAB (gene names)

Systematic name: (R)-2-hydroxyglutaryl-CoA hydro-lyase ((E)-glutaconyl-CoA-forming)

Comments: The enzymes from the bacteria Acidaminococcus fermentans and Clostridium symbiosum are involved in the fermentation of L-glutamate. The enzyme contains [4F-4S] clusters, FMNH2 and riboflavin. It must be activated by an activator protein. Once activated, it can catalyse many turnovers.

References:

1. Buckel, W. The reversible dehydration of (R)-2-hydroxyglutarate to (E)-glutaconate. Eur. J. Biochem. 106 (1980) 439-447. [PMID: 7398622]

2. Schweiger, G., Dutscho, R. and Buckel, W. Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. An iron-sulfur protein. Eur. J. Biochem. 169 (1987) 441-448. [PMID: 3691501]

3. Muller, U. and Buckel, W. Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Eur. J. Biochem. 230 (1995) 698-704. [PMID: 7607244]

4. Hans, M., Sievers, J., Muller, U., Bill, E., Vorholt, J.A., Linder, D. and Buckel, W. 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum. Eur. J. Biochem. 265 (1999) 404-414. [PMID: 10491198]

5. Locher, K.P., Hans, M., Yeh, A.P., Schmid, B., Buckel, W. and Rees, D.C. Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A. J. Mol. Biol. 307 (2001) 297-308. [PMID: 11243821]

6. Parthasarathy, A., Pierik, A.J., Kahnt, J., Zelder, O. and Buckel, W. Substrate specificity of 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum: toward a bio-based production of adipic acid. Biochemistry 50 (2011) 3540-3550. [PMID: 21434666]

[EC 4.2.1.167 created 2016]

*EC 4.2.3.152

Accepted name: 2-epi-5-epi-valiolone synthase

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

For diagram of reaction click here.

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

Other name(s): AcbC; ValA; CetA; SalQ; C7-cyclitol synthase

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

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

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Stratmann, A., Mahmud, T., Lee, S., Distler, J., Floss, H.G. and Piepersberg, W. The AcbC protein from Actinoplanes species is a C7-cyclitol synthase related to 3-dehydroquinate synthases and is involved in the biosynthesis of the α-glucosidase inhibitor acarbose. J. Biol. Chem. 274 (1999) 10889-10896. [PMID: 10196166]

2. Yu, Y., Bai, L., Minagawa, K., Jian, X., Li, L., Li, J., Chen, S., Cao, E., Mahmud, T., Floss, H.G., Zhou, X. and Deng, Z. Gene cluster responsible for validamycin biosynthesis in Streptomyces hygroscopicus subsp. jinggangensis 5008. Appl. Environ. Microbiol. 71 (2005) 5066-5076. [PMID: 16151088]

3. Wu, X., Flatt, P.M., Schlorke, O., Zeeck, A., Dairi, T. and Mahmud, T. A comparative analysis of the sugar phosphate cyclase superfamily involved in primary and secondary metabolism. Chembiochem 8 (2007) 239-248. [PMID: 17195255]

4. Choi, W.S., Wu, X., Choeng, Y.H., Mahmud, T., Jeong, B.C., Lee, S.H., Chang, Y.K., Kim, C.J. and Hong, S.K. Genetic organization of the putative salbostatin biosynthetic gene cluster including the 2-epi-5-epi-valiolone synthase gene in Streptomyces albus ATCC 21838. Appl. Microbiol. Biotechnol. 80 (2008) 637-645. [PMID: 18648803]

5. Kean, K.M., Codding, S.J., Asamizu, S., Mahmud, T. and Karplus, P.A. Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus. Biochemistry 53 (2014) 4250-4260. [PMID: 24832673]

[EC 4.2.3.152 created 2015, modified 2016]

EC 4.2.3.154

Accepted name: demethyl-4-deoxygadusol synthase

Reaction: D-sedoheptulose 7-phosphate = demethyl-4-deoxygadusol + phosphate + H2O

For diagram of reaction click here.

Glossary: demethyl-4-deoxygadusol = 2,3,5-trihydroxy-5-(hydroxymethyl)cyclohex-2-en-1-one

Other name(s): Nos2 (gene name); Anb2 (gene name)

Systematic name: D-sedoheptulose-7-phosphate phosphate-lyase (cyclizing; demethyl-4-deoxygadusol-forming)

Comments: The enzyme, characterized from the cyanobacterium Nostoc punctiforme PCC 73102, is involved in the biosynthesis of the sunscreen compound shinorine. It requires a divalent metal ion (Zn2+ or Co2+) and an NAD+ cofactor, which is transiently reduced during the reaction. cf. EC 4.2.3.152, 2-epi-5-epi-valiolone synthase and EC 4.2.3.155, 2-epi-valiolone synthase.

References:

1. Balskus, E.P. and Walsh, C.T. The genetic and molecular basis for sunscreen biosynthesis in cyanobacteria. Science 329 (2010) 1653-1656. [PMID: 20813918]

2. Asamizu, S., Xie, P., Brumsted, C.J., Flatt, P.M. and Mahmud, T. Evolutionary divergence of sedoheptulose 7-phosphate cyclases leads to several distinct cyclic products. J. Am. Chem. Soc. 134 (2012) 12219-12229. [PMID: 22741921]

[EC 4.2.3.154 created 2016]

EC 4.2.3.155

Accepted name: 2-epi-valiolone synthase

Reaction: D-sedoheptulose 7-phosphate = 2-epi-valiolone + phosphate

For diagram of reaction click here.

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

Systematic name: D-sedoheptulose-7-phosphate phosphate-lyase (cyclizing; 2-epi-valiolone-forming)

Comments: The enzyme, characterized from the bacteria Actinosynnema mirum and Stigmatella aurantiaca DW4/3-1, produces 2-epi-valiolone, which is believed to function as a precursor in aminocyclitol biosynthesis. It requires a divalent metal ion (Zn2+ or Co2+) and an NAD+ cofactor, which is transiently reduced during the reaction. cf. EC 4.2.3.152, 2-epi-5-epi-valiolone synthase and EC 4.2.3.154, desmethyl-4-deoxygadusol synthase.

References:

1. Asamizu, S., Xie, P., Brumsted, C.J., Flatt, P.M. and Mahmud, T. Evolutionary divergence of sedoheptulose 7-phosphate cyclases leads to several distinct cyclic products. J. Am. Chem. Soc. 134 (2012) 12219-12229. [PMID: 22741921]

[EC 4.2.3.155 created 2016]

EC 4.3.1.31

Accepted name: L-tryptophan ammonia lyase

Reaction: L-tryptophan = 3-indoleacrylate + ammonia

Glossary: 3-indoleacrylate = (2E)-3-(1H-indol-3-yl)prop-2-enoate

Other name(s): WAL

Systematic name: L-tryptophan ammonia-lyase (3-indoleacrylate-forming)

Comments: The enzyme, characterized from the bacterium Rubrivivax benzoatilyticus JA2, requires no cofactors. It acts on L-phenylalanine and L-glutamate with about 60% of the activity with L-tryptophan, and on L-tyrosine, glycine, and L-alanine with about 30% of the activity.

References:

1. Kumavath, R.N., Ramana ChV., Sasikala Ch, Barh, D., Kumar, A.P. and Azevedo, V. Isolation and characterization of L-tryptophan ammonia lyase from Rubrivivax benzoatilyticus strain JA2. Curr Protein Pept Sci 16 (2015) 775-781. [PMID: 25961404]

[EC 4.3.1.31 created 2016]

EC 4.99.1.9

Accepted name: coproporphyrin ferrochelatase

Reaction: Fe-coproporphyrin III + 2 H+ = coproporphyrin III + Fe2+

Glossary: Fe-coproporphyrin III = coproheme III

Other name(s): hemH (gene name)

Systematic name: protoheme ferro-lyase (protoporphyrin-forming)

Comments: The enzyme, present in Gram-positive bacteria, participates in heme biosynthesis. It can also catalyse the reaction of EC 4.99.1.1, protoporphyrin IX ferrochelatase, at a much lower level.

References:

1. Hansson, M. and Hederstedt, L. Purification and characterisation of a water-soluble ferrochelatase from Bacillus subtilis. Eur. J. Biochem. 220 (1994) 201-208. [PMID: 8119288]

2. Al-Karadaghi, S., Hansson, M., Nikonov, S., Jonsson, B. and Hederstedt, L. Crystal structure of ferrochelatase: the terminal enzyme in heme biosynthesis. Structure 5 (1997) 1501-1510. [PMID: 9384565]

3. Hansson, M.D., Karlberg, T., Soderberg, C.A., Rajan, S., Warren, M.J., Al-Karadaghi, S., Rigby, S.E. and Hansson, M. Bacterial ferrochelatase turns human: Tyr13 determines the apparent metal specificity of Bacillus subtilis ferrochelatase. J. Biol. Inorg. Chem. 16 (2011) 235-242. [PMID: 21052751]

4. Dailey, H.A., Gerdes, S., Dailey, T.A., Burch, J.S. and Phillips, J.D. Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin. Proc. Natl. Acad. Sci. USA 112 (2015) 2210-2215. [PMID: 25646457]

[EC 4.99.1.9 created 2016]

*EC 5.1.1.14

Accepted name: nocardicin A epimerase

Reaction: (1) isonocardicin C = nocardicin C
(2) isonocardicin A = nocardicin A

For diagram of reaction click here.

Other name(s): isonocardicin A epimerase; nocJ (gene name)

Systematic name: nocardicin-C epimerase

Comments: Requires pyridoxal 5'-phosphate. The enzyme, characterized from the bacterium Nocardia uniformis, is involved in the biosynthesis of the monolactam antibiotic nocardicin A. It catalyses the epimerization of the amino group at position 9' from (S)- configuration to (R)-. The enzyme can act on both isonocardicin A and isonocardicin C, but the in vivo substrate appears to be the latter [3].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 118246-75-6

References:

1. Wilson, B.A., Bantia, S., Salituro, G.M., Reeve, A.M. and Townsend, C.A. Cell-free biosynthesis of nocardicin A from nocardicin E and S-adenosylmethionine. J. Am. Chem. Soc. 110 (1988) 8238-8239.

2. Kelly, W.L. and Townsend, C.A. Mutational analysis and characterization of nocardicin C-9' epimerase. J. Biol. Chem. 279 (2004) 38220-38227. [PMID: 15252031]

3. Kelly, W.L. and Townsend, C.A. Mutational analysis of nocK and nocL in the nocardicin a producer Nocardia uniformis. J. Bacteriol. 187 (2005) 739-746. [PMID: 15629944]

[EC 5.1.1.14 created 1992, modified 2016]

EC 5.1.3.38

Accepted name: D-erythrulose 1-phosphate 3-epimerase

Reaction: D-erythrulose 1-phosphate = L-erythrulose 1-phosphate

Other name(s): eryC (gene name)

Systematic name: D-erythrulose-1-phosphate 3-epimerase

Comments: The enzyme, characterized from the pathogenic bacterium Brucella abortus, which causes brucellosis in livestock, participates in erythritol catabolism.

References:

1. Barbier, T., Collard, F., Zuniga-Ripa, A., Moriyon, I., Godard, T., Becker, J., Wittmann, C., Van Schaftingen, E. and Letesson, J.J. Erythritol feeds the pentose phosphate pathway via three new isomerases leading to D-erythrose-4-phosphate in Brucella. Proc. Natl. Acad. Sci. USA 111 (2014) 17815-17820. [PMID: 25453104]

[EC 5.1.3.38 created 2016]

EC 5.1.3.39

Accepted name: L-erythrulose 4-phosphate epimerase

Reaction: L-erythrulose 4-phosphate = D-erythrulose 4-phosphate

Other name(s): lerI (gene name)

Systematic name: L-erythrulose-4-phosphate 3-epimerase

Comments: The enzyme, characterized from the bacterium Mycobacterium smegmatis, participates in the degradation of L-threitol.

References:

1. Huang, H., Carter, M.S., Vetting, M.W., Al-Obaidi, N., Patskovsky, Y., Almo, S.C. and Gerlt, J.A. A general strategy for the discovery of metabolic pathways: D-threitol, L-threitol, and erythritol utilization in Mycobacterium smegmatis. J. Am. Chem. Soc. 137 (2015) 14570-14573. [PMID: 26560079]

[EC 5.1.3.39 created 2016]

EC 5.3.1.33

Accepted name: L-erythrulose 1-phosphate isomerase

Reaction: L-erythrulose 1-phosphate = D-erythrulose 4-phosphate

Other name(s): eryH (gene name)

Systematic name: L-erythrulose-1-phosphate isomerase

Comments: The enzyme, characterized from the pathogenic bacterium Brucella abortus, which causes brucellosis in livestock, participates in erythritol catabolism.

References:

1. Barbier, T., Collard, F., Zuniga-Ripa, A., Moriyon, I., Godard, T., Becker, J., Wittmann, C., Van Schaftingen, E. and Letesson, J.J. Erythritol feeds the pentose phosphate pathway via three new isomerases leading to D-erythrose-4-phosphate in Brucella. Proc. Natl. Acad. Sci. USA 111 (2014) 17815-17820. [PMID: 25453104]

[EC 5.3.1.33 created 2016]

EC 5.3.1.34

Accepted name: D-erythrulose 4-phosphate isomerase

Reaction: D-erythrulose 4-phosphate = D-erythrose 4-phosphate

Other name(s): eryI (gene name)

Systematic name: D-erythrulose-4-phosphate ketose-aldose isomerase

Comments: The enzyme, characterized from the pathogenic bacterium Brucella abortus, which causes brucellosis in livestock, participates in erythritol catabolism.

References:

1. Barbier, T., Collard, F., Zuniga-Ripa, A., Moriyon, I., Godard, T., Becker, J., Wittmann, C., Van Schaftingen, E. and Letesson, J.J. Erythritol feeds the pentose phosphate pathway via three new isomerases leading to D-erythrose-4-phosphate in Brucella. Proc. Natl. Acad. Sci. USA 111 (2014) 17815-17820. [PMID: 25453104]

[EC 5.3.1.34 created 2016]

EC 5.3.3.20

Accepted name: 2-hydroxyisobutanoyl-CoA mutase

Reaction: 2-hydroxyisobutanoyl-CoA = (S)-3-hydroxybutanoyl-CoA

Other name(s): hcmAB (gene names)

Systematic name: 2-hydroxyisobutanoyl-CoA mutase

Comments: The enzyme, characterized from the bacterium Aquincola tertiaricarbonis, uses radical chemistry to rearrange the positions of both a methyl group and a hydroxyl group. It consists of two subunits, the smaller one containing a cobalamin cofactor. It plays a central role in the degradation of assorted substrates containing a tert-butyl moiety.

References:

1. Yaneva, N., Schuster, J., Schafer, F., Lede, V., Przybylski, D., Paproth, T., Harms, H., Muller, R.H. and Rohwerder, T. Bacterial acyl-CoA mutase specifically catalyzes coenzyme B12-dependent isomerization of 2-hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA. J. Biol. Chem. 287 (2012) 15502-15511. [PMID: 22433853]

2. Kurteva-Yaneva, N., Zahn, M., Weichler, M.T., Starke, R., Harms, H., Muller, R.H., Strater, N. and Rohwerder, T. Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase. J. Biol. Chem. 290 (2015) 9727-9737. [PMID: 25720495]

[EC 5.3.3.20 created 2016]

*EC 6.3.2.47

Accepted name: dapdiamide synthase

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

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

Other name(s): DdaF; dapdiamide A synthase

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

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

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

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

2. Hollenhorst, M.A., Bumpus, S.B., Matthews, M.L., Bollinger, J.M., Jr., Kelleher, N.L. and Walsh, C.T. The nonribosomal peptide synthetase enzyme DdaD tethers N(β)-fumaramoyl-L-2,3-diaminopropionate for Fe(II)/α-ketoglutarate-dependent epoxidation by DdaC during dapdiamide antibiotic biosynthesis. J. Am. Chem. Soc. 132 (2010) 15773-15781. [PMID: 20945916]

[EC 6.3.2.47 created 2015, modified 2016]


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