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. They were prepared for the NC-IUBMB by Kristian Axelsen, Richard Cammack, Ron Caspi, Minoru Kanehisa, 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 entries were added on the date indicated and fully approved after four weeks.

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


Contents

EC 1.1.1.312 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase (22 May 2011)
EC 1.1.1.313 sulfoacetaldehyde reductase (22 May 2011)
EC 1.1.1.314 germacrene A alcohol dehydrogenase (22 May 2011)
EC 1.2.1.45 transferred now EC 1.1.1.312 (22 May 2011)
EC 1.2.1.81 sulfoacetaldehyde dehydrogenase (acylating) (22 May 2011)
EC 1.2.7.10 oxalate oxidoreductase (22 May 2011)
*EC 1.3.1.14 dihydroorotate dehydrogenase (NAD+) (22 May 2011)
*EC 1.3.1.15 dihydroorotate dehydrogenase (NADP+) (22 May 2011)
EC 1.3.1.87 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate dehydrogenase (22 May 2011)
EC 1.3.3.1 transferred now EC 1.3.98.1 (22 May 2011)
*EC 1.3.5.2 dihydroorotate dehydrogenase (quinone) (22 May 2011)
EC 1.3.5.5 15-cis-phytoene desaturase (22 May 2011)
EC 1.3.7.8 benzoyl-CoA reductase (22 May 2011)
EC 1.3.7.9 4-hydroxybenzoyl-CoA reductase (22 May 2011)
EC 1.3.8 With flavin as acceptor (22 May 2011)
EC 1.3.8.1 butyryl-CoA dehydrogenase (22 May 2011)
EC 1.3.98 With other, known, acceptors (22 May 2011)
EC 1.3.98.1 dihydroorotate dehydrogenase (fumarate) (22 May 2011)
EC 1.3.99.2 transferred now EC 1.3.8.1 (22 May 2011)
EC 1.3.99.15 transferred now EC 1.3.7.8 (22 May 2011)
EC 1.3.99.20 transferred now EC 1.3.7.9 (22 May 2011)
EC 1.4.98 With other, known, acceptors (22 May 2011)
EC 1.4.98.1 methylamine dehydrogenase (amicyanin) (22 May 2011)
EC 1.4.99.3 transferred now EC 1.4.98.1 (22 May 2011)
*EC 1.6.5.3 NADH:ubiquinone reductase (H+-translocating) (22 May 2011)
EC 1.6.5.9 NADH:ubiquinone reductase (non-electrogenic) (22 May 2011)
EC 1.7.1.14 nitric oxide reductase [NAD(P), nitrous oxide-forming] (22 May 2011)
EC 1.7.2.5 nitric oxide reductase (cytochrome c) (22 May 2011)
EC 1.7.5.2 nitric oxide reductase (menaquinol) (22 May 2011)
EC 1.7.99.7 transferred now EC 1.7.2.5 (22 May 2011)
EC 1.8.1.17 dimethylsulfone reductase (22 May 2011)
EC 1.8.2.3 sulfide-cytochrome-c reductase (flavocytochrome c) (22 May 2011)
EC 1.8.2.4 dimethyl sulfide:cytochrome c2 reductase (22 May 2011)
EC 1.8.3.6 farnesylcysteine lyase (22 May 2011)
EC 1.8.5.4 sulfide:quinone reductase (22 May 2011)
*EC 1.10.3.3 L-ascorbate oxidase (22 May 2011)
EC 1.10.3.9 photosystem II (22 May 2011)
EC 1.10.3.10 ubiquinol oxidase (H+-transporting) (22 May 2011)
EC 1.10.3.11 ubiquinol oxidase (22 May 2011)
EC 1.10.3.12 menaquinol oxidase (H+-transporting) (22 May 2011)
*EC 1.11.1.11 L-ascorbate peroxidase (22 May 2011)
*EC 1.11.1.14 lignin peroxidase (22 May 2011)
EC 1.11.1.21 catalase-peroxidase (22 May 2011)
EC 1.12.1.4 hydrogenase (NAD+, ferredoxin) (22 May 2011)
*EC 1.13.11.12 linoleate 13S-lipoxygenase (22 May 2011)
EC 1.13.11.57 gallate dioxygenase (22 May 2011)
EC 1.13.11.58 linoleate 9S-lipoxygenase (22 May 2011)
EC 1.14.11.33 DNA oxidative demethylase (22 May 2011)
*EC 1.14.13.25 methane monooxygenase (soluble) (22 May 2011)
EC 1.14.13.42 deleted covered by EC 1.14.13.68 (22 May 2011)
EC 1.14.13.123 germacrene A hydroxylase (22 May 2011)
EC 1.14.13.124 phenylalanine N-monooxygenase (22 May 2011)
EC 1.14.13.125 tryptophan N-monooxygenase (22 May 2011)
EC 1.14.13.126 vitamin D3 24-hydroxylase (22 May 2011)
EC 1.14.13.127 3-(3-hydroxyphenyl)propanoate hydroxylase (22 May 2011)
EC 1.14.13.128 7-methylxanthine demethylase (22 May 2011)
EC 1.14.13.129 β-carotene 3-hydroxylase (22 May 2011)
EC 1.14.13.130 pyrrole-2-carboxylate monooxygenase (22 May 2011)
EC 1.14.18.3 methane monooxygenase (particulate) (22 May 2011)
EC 1.14.19.7 (S)-2-hydroxypropylphosphonic acid epoxidase (22 May 2011)
EC 1.14.99.42 zeaxanthin 7,8-dioxygenase (22 May 2011)
EC 1.14.99.43 β-amyrin 24-hydroxylase (22 May 2011)
EC 1.14.99.44 diapolycopene oxygenase (22 May 2011)
EC 1.14.99.45 carotene ε-monooxygenase (22 May 2011)
*EC 1.16.3.1 ferroxidase (22 May 2011)
EC 1.16.5 With quinone or similar compound as acceptor
EC 1.16.5.1 ascorbate ferrireductase (transmembrane) (22 May 2011)
EC 1.16.98 With other, known, acceptor
EC 1.16.98.1 iron:rusticyanin reductase (22 May 2011)
*EC 1.18.1.3 ferredoxin—NAD+ reductase (22 May 2011)
*EC 2.1.1.149 myricetin O-methyltransferase (22 May 2011)
EC 2.1.1.207 tRNA (cytidine34-2'-O)-methyltransferase (22 May 2011)
EC 2.3.1.196 benzyl alcohol O-benzoyltransferase (22 May 2011)
EC 2.4.1.262 soyasapogenol glucuronosyltransferase (22 May 2011)
EC 2.4.1.263 abscisate β-glucosyltransferase (22 May 2011)
*EC 2.5.1.29 geranylgeranyl diphosphate synthase (22 May 2011)
EC 2.7.1.170 anhydro-N-acetylmuramic acid kinase (22 May 2011)
*EC 2.8.1.6 biotin synthase (22 May 2011)
EC 3.1.1.85 pimelyl-[acyl-carrier protein] methyl ester esterase (22 May 2011)
EC 3.1.1.86 rhamnogalacturonan acetylesterase (22 May 2011)
EC 3.1.3.84 ADP-ribose 1"-phosphate phosphatase (22 May 2011)
EC 3.2.1.170 mannosylglycerate hydrolase (22 May 2011)
*EC 4.1.1.31 phosphoenolpyruvate carboxylase (22 May 2011)
*EC 4.1.99.5 octadecanal decarbonylase (22 May 2011)
EC 4.2.1.122 tryptophan synthase (indole-salvaging) (22 May 2011)
EC 4.2.1.123 tetrahymanol synthase (22 May 2011)
EC 4.2.1.124 arabidiol synthase (22 May 2011)
EC 4.2.1.125 dammarenediol II synthase (22 May 2011)
EC 4.2.1.126 N-acetylmuramic acid 6-phosphate etherase (22 May 2011)
EC 4.2.3.74 presilphiperfolanol synthase (22 May 2011)
EC 4.2.3.75 (–)-germacrene D synthase (22 May 2011)
EC 4.2.3.76 (+)-δ-selinene synthase (22 May 2011)
EC 4.2.3.77 (+)-germacrene D synthase (22 May 2011)
EC 5.3.3.16 4-oxalomesaconate tautomerase (22 May 2011)
EC 5.4.99.31 thalianol synthase (22 May 2011)
EC 5.4.99.32 protostadienol synthase (22 May 2011)
EC 5.4.99.33 cucurbitadienol synthase (22 May 2011)
EC 5.4.99.34 germanicol synthase (22 May 2011)
EC 5.4.99.35 taraxerol synthase (22 May 2011)
EC 5.4.99.36 isomultiflorenol synthase (22 May 2011)
EC 6.3.2.37 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—D-lysine ligase (22 May 2011)

EC 1.1.1.312

Accepted name: 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase

Reaction: 4-carboxy-2-hydroxymuconate semialdehyde hemiacetal + NADP+ = 2-oxo-2H-pyran-4,6-dicarboxylate + NADPH + H+

For diagram of reaction click here

Other name(s): 2-hydroxy-4-carboxymuconate 6-semialdehyde dehydrogenase; 4-carboxy-2-hydroxy-cis,cis-muconate-6-semialdehyde:NADP+ oxidoreductase; α-hydroxy-γ-carboxymuconic ε-semialdehyde dehydrogenase; 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase; LigC; ProD

Systematic name: 4-carboxy-2-hydroxymuconate semialdehyde hemiacetal:NADP+ 2-oxidoreductase

Comments: The enzyme does not act on unsubstituted aliphatic or aromatic aldehydes or glucose; NAD+ can replace NADP+, but with lower affinity. The enzyme was initially believed to act on 4-carboxy-2-hydroxy-cis,cis-muconate 6-semialdehyde and produce 4-carboxy-2-hydroxy-cis,cis-muconate [1]. However, later studies showed that the substrate is the hemiacetal form [3], and the product is 2-oxo-2H-pyran-4,6-dicarboxylate [2,4].

References:

1. Maruyama, K., Ariga, N., Tsuda, M. and Deguchi, K. Purification and properties of α-hydroxy-γ-carboxymuconic ε-semialdehyde dehydrogenase. J. Biochem. (Tokyo) 83 (1978) 1125-1134. [PMID: 26671]

2. Maruyama, K. Isolation and identification of the reaction product of α-hydroxy-γ-carboxymuconic ε-semialdehyde dehydrogenase. J. Biochem. 86 (1979) 1671-1677. [PMID: 528534]

3. Maruyama, K. Purification and properties of 2-pyrone-4,6-dicarboxylate hydrolase. J. Biochem. (Tokyo) 93 (1983) 557-565. [PMID: 6841353]

4. Masai, E., Momose, K., Hara, H., Nishikawa, S., Katayama, Y. and Fukuda, M. Genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in Sphingomonas paucimobilis SYK-6. J. Bacteriol. 182 (2000) 6651-6658. [PMID: 11073908]

[EC 1.1.1.312 created 1978 as EC 1.2.1.45, transferred 2011 to EC 1.1.1.312]

EC 1.1.1.313

Accepted name: sulfoacetaldehyde reductase

Reaction: isethionate + NADP+ = 2-sulfoacetaldehyde + NADPH + H+

Glossary: isethionate = 2-hydroxyethanesulfonate

Other name(s): isfD (gene name)

Systematic name: isethionate:NADP+ oxidoreductase

Comments: Catalyses the reaction only in the opposite direction. Involved in taurine degradation. The bacterium Chromohalobacter salexigens strain DSM 3043 possesses two enzymes that catalyse this reaction, a constitutive enzyme (encoded by isfD2) and an inducible enzyme (encoded by isfD). The latter is induced by taurine, and is responsible for most of the activity observed in taurine-grown cells.

References:

1. Krejcik, Z., Hollemeyer, K., Smits, T.H. and Cook, A.M. Isethionate formation from taurine in Chromohalobacter salexigens: purification of sulfoacetaldehyde reductase. Microbiology 156 (2010) 1547-1555. [PMID: 20133363]

[EC 1.1.1.313 created 2011]

EC 1.1.1.314

Accepted name: germacrene A alcohol dehydrogenase

Reaction: germacra-1(10),4,11(13)-trien-12-ol + 2 NADP+ + H2O = germacra-1(10),4,11(13)-trien-12-oate + 2 NADPH + 3 H+ (overall reaction)
(1a) germacra-1(10),4,11(13)-trien-12-ol + NADP+ = germacra-1(10),4,11(13)-trien-12-al + NADPH + H+
(1b) germacra-1(10),4,11(13)-trien-12-al + NADP+ + H2O = germacra-1(10),4,11(13)-trien-12-oate + NADPH + 2 H+

For diagram of reaction click here.

Systematic name: germacra-1(10),4,11(13)-trien-12-ol:NADP+ oxidoreductase

Comments: In Lactuca sativa EC 1.1.1.314 is a mutifunctional enzyme with EC 1.14.13.123, germacrene A hydroxylase [2].

References:

1. de Kraker, J.W., Franssen, M.C., Dalm, M.C., de Groot, A. and Bouwmeester, H.J. Biosynthesis of germacrene A carboxylic acid in chicory roots. Demonstration of a cytochrome P450 (+)-germacrene A hydroxylase and NADP+-dependent sesquiterpenoid dehydrogenase(s) involved in sesquiterpene lactone biosynthesis. Plant Physiol. 125 (2001) 1930-1940. [PMID: 11299372]

2. Nguyen, D.T., Gopfert, J.C., Ikezawa, N., Macnevin, G., Kathiresan, M., Conrad, J., Spring, O. and Ro, D.K. Biochemical conservation and evolution of germacrene A oxidase in asteraceae. J. Biol. Chem. 285 (2010) 16588-16598. [PMID: 20351109]

[EC 1.1.1.314 created 2011]

[EC 1.2.1.45 Transferred entry: 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase. Now EC 1.1.1.312, 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase. (EC 1.2.1.45 created 1978, deleted 2011)]

EC 1.2.1.81

Accepted name: sulfoacetaldehyde dehydrogenase (acylating)

Reaction: 2-sulfoacetaldehyde + CoA + NADP+ = sulfoacetyl-CoA + NADPH + H+

Other name(s): SauS

Systematic name: 2-sulfoacetaldehyde:NADP+ oxidoreductase (CoA-acetylating)

Comments: The enzyme is involved in degradation of sulfoacetate. In this pathway the reaction is catalysed in the reverse direction. The enzyme is specific for sulfoacetaldehyde and NADP+.

References:

1. Weinitschke, S., Hollemeyer, K., Kusian, B., Bowien, B., Smits, T.H. and Cook, A.M. Sulfoacetate is degraded via a novel pathway involving sulfoacetyl-CoA and sulfoacetaldehyde in Cupriavidus necator H16. J. Biol. Chem. 285 (2010) 35249-35254. [PMID: 20693281]

[EC 1.2.1.81 created 2011]

EC 1.2.7.10

Accepted name: oxalate oxidoreductase

Reaction: oxalate + ferredoxin = 2 CO2 + reduced ferredoxin

Systematic name: oxalate:ferredoxin oxidoreductase

Comments: Contains thiamine diphosphate and [4Fe-4S] clusters. Acceptors include ferredoxin and the nickel-dependent carbon monoxide dehydrogenase (EC 1.2.7.4)

References:

1. Daniel, S.L., Pilsl, C. and Drake, H.L. Oxalate metabolism by the acetogenic bacterium Moorella thermoacetica. FEMS Microbiol. Lett. 231 (2004) 39-43. [PMID: 14769464]

2. Pierce, E., Becker, D.F. and Ragsdale, S.W. Identification and characterization of oxalate oxidoreductase, a novel thiamine pyrophosphate-dependent 2-oxoacid oxidoreductase that enables anaerobic growth on oxalate. J. Biol. Chem. 285 (2010) 40515-40524. [PMID: 20956531]

[EC 1.2.7.10 created 2011]

*EC 1.3.1.14

Accepted name: dihydroorotate dehydrogenase (NAD+)

Reaction: (S)-dihydroorotate + NAD+ = orotate + NADH + H+

Other name(s): orotate reductase (NADH); orotate reductase (NADH2); DHOdehase (ambiguous); DHOD (ambiguous); DHODase (ambiguous); dihydroorotate oxidase, pyrD (gene name)

Systematic name: (S)-dihydroorotate:NAD+ oxidoreductase

Comments: Binds FMN, FAD and a [2Fe-2S] cluster. The enzyme consists of two subunits, an FMN binding catalytic subunit and a FAD and iron-sulfur binding electron transfer subunit [4]. The reaction, which takes place in the cytosol, is the only redox reaction in the de-novo biosynthesis of pyrimidine nucleotides. Other class 1 dihydroorotate dehydrogenases use either fumarate (EC 1.3.98.1) or NADP+ (EC 1.3.1.15) as electron acceptor. The membrane bound class 2 dihydroorotate dehydrogenase (EC 1.3.5.2) uses quinone as electron acceptor.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 37255-26-8

References:

1. Friedmann, H.C. and Vennesland, B. Purification and properties of dihydroorotic acid dehydrogenase. J. Biol. Chem. 233 (1958) 1398-1406. [PMID: 13610849]

2. Friedmann, H.C. and Vennesland, B. Crystalline dihydroorotic dehydrogenase. J. Biol. Chem. 235 (1960) 1526-1532. [PMID: 13825167]

3. Lieberman, I. and Kornberg, A. Enzymic synthesis and breakdown of a pyrimidine, orotic acid. I. Dihydro-orotic dehydrogenase. Biochim. Biophys. Acta 12 (1953) 223-234. [PMID: 13115431]

4. Nielsen, F.S., Andersen, P.S. and Jensen, K.F. The B form of dihydroorotate dehydrogenase from Lactococcus lactis consists of two different subunits, encoded by the pyrDb and pyrK genes, and contains FMN, FAD, and [FeS] redox centers. J. Biol. Chem. 271 (1996) 29359-29365. [PMID: 8910599]

5. Rowland, P., Nørager, S., Jensen, K.F. and Larsen, S. Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster. Structure 8 (2000) 1227-1238. [PMID: 11188687]

6. Kahler, A.E., Nielsen, F.S. and Switzer, R.L. Biochemical characterization of the heteromeric Bacillus subtilis dihydroorotate dehydrogenase and its isolated subunits. Arch. Biochem. Biophys. 371 (1999) 191-201. [PMID: 10545205]

7. Marcinkeviciene, J., Tinney, L.M., Wang, K.H., Rogers, M.J. and Copeland, R.A. Dihydroorotate dehydrogenase B of Enterococcus faecalis. Characterization and insights into chemical mechanism. Biochemistry 38 (1999) 13129-13137. [PMID: 10529184]

[EC 1.3.1.14 created 1972, modified 2011]

*EC 1.3.1.15

Accepted name: dihydroorotate dehydrogenase (NADP+)

Reaction: (S)-dihydroorotate + NADP+ = orotate + NADPH + H+

Other name(s): orotate reductase; dihydro-orotic dehydrogenase; L-5,6-dihydro-orotate:NAD+ oxidoreductase; orotate reductase (NADPH)

Systematic name: (S)-dihydroorotate:NADP+ oxidoreductase

Comments: Binds FMN and FAD [2]. Other class 1 dihydroorotate dehydrogenases use either fumarate (EC 1.3.98.1) or NAD+ (EC 1.3.1.14) as electron acceptor. The membrane bound class 2 dihydroorotate dehydrogenase (EC 1.3.5.2) uses quinone as electron acceptor .

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 37255-27-9

References:

1. Taylor, W.H., Taylor, M.L. and Eames, D.F. Two functionally different dihydroorotic dehydrogenases in bacteria. J. Bacteriol. 91 (1966) 2251-2256. [PMID: 4380263]

2. Udaka, S. and Vennesland, B. Properties of triphosphopyridine nucleotide-linked dihydroorotic dehydrogenase. J. Biol. Chem. 237 (1962) 2018-2024. [PMID: 13923427]

[EC 1.3.1.15 created 1972, modified 2011]

EC 1.3.1.87

Accepted name: 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate dehydrogenase

Reaction: (1) 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate + NAD+ = 3-(2,3-dihydroxyphenyl)propanoate + NADH + H+
(2) (2E)-3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)prop-2-enoate + NAD+ = (2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate + NADH + H+

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

Other name(s): hcaB (gene name); cis-dihydrodiol dehydrogenase; 2,3-dihydroxy-2,3-dihydro-phenylpropionate dehydrogenase

Systematic name: 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate:NAD+ oxidoreductase

Comments: This enzyme catalyses a step in the pathway of phenylpropanoid compounds degradation.

References:

1. Díaz, E., Ferrández, A. and García, J.L. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180 (1998) 2915-2923. [PMID: 9603882]

[EC 1.3.1.87 created 2011]

[EC 1.3.3.1 Transferred entry: dihydroorotate oxidase. Now EC 1.3.98.1 [dihydroorotate dehydrogenase (fumarate)] (EC 1.3.3.1 created 1961, deleted 2011)]

*EC 1.3.5.2

Accepted name: dihydroorotate dehydrogenase (quinone)

Reaction: (S)-dihydroorotate + a quinone = orotate + a quinol

Other name(s): dihydroorotate:ubiquinone oxidoreductase; (S)-dihydroorotate:(acceptor) oxidoreductase; (S)-dihydroorotate:acceptor oxidoreductase; DHOdehase (ambiguous); DHOD (ambiguous); DHODase (ambiguous); DHODH

Systematic name: (S)-dihydroorotate:quinone oxidoreductase

Comments: This Class 2 dihydroorotate dehydrogenase enzyme contains FMN [4]. The enzyme is found in eukaryotes in the mitochondrial membrane, and in some Gram negative bacteria associated with the cytoplasmic membrane [2,5]. The reaction is the only redox reaction in the de-novo biosynthesis of pyrimidine nucleotides [2,4]. The best quinone electron acceptors for the enzyme from bovine liver are ubiquinone-6 and ubiquinone-7, although simple quinones, such as benzoquinone, can also act as acceptor at lower rates [2]. Methyl-, ethyl-, tert-butyl and benzyl (S)-dihydroorotates are also substrates, but methyl esters of (S)-1-methyl and (S)-3-methyl and (S)-1,3-dimethyldihydroorotates are not [2]. Class 1 dihydroorotate dehydrogenases use either fumarate (EC 1.3.98.1), NAD+ (EC 1.3.1.14) or NADP+ (EC 1.3.1.15) as electron acceptor.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 59088-23-2

References:

1. Forman, H.J. and Kennedy, J. Mammalian dihydroorotate dehydrogenase: physical and catalytic properties of the primary enzyme. Arch. Biochem. Biophys. 191 (1978) 23-31. [PMID: 216313]

2. Hines, V., Keys, L.D., III and Johnston, M. Purification and properties of the bovine liver mitochondrial dihydroorotate dehydrogenase. J. Biol. Chem. 261 (1986) 11386-11392. [PMID: 3733756]

3. Bader, B., Knecht, W., Fries, M. and Löffler, M. Expression, purification, and characterization of histidine-tagged rat and human flavoenzyme dihydroorotate dehydrogenase. Protein Expr. Purif. 13 (1998) 414-422. [PMID: 9693067]

4. Fagan, R.L., Nelson, M.N., Pagano, P.M. and Palfey, B.A. Mechanism of flavin reduction in Class 2 dihydroorotate dehydrogenases. Biochemistry 45 (2006) 14926-14932. [PMID: 17154530]

5. Björnberg, O., Grüner, A.C., Roepstorff, P. and Jensen, K.F. The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. Biochemistry 38 (1999) 2899-2908. [PMID: 10074342]

[EC 1.3.5.2 created 1983 as EC 1.3.99.11, transferred 2009 to EC 1.3.5.2, modified 2011]

EC 1.3.5.5

Accepted name: 15-cis-phytoene desaturase

Reaction: 15-cis-phytoene + 2 plastoquinone = 9,15,9'-tricis-ζ-carotene + 2 plastoquinol (overall reaction)
(1a) 15-cis-phytoene + plastoquinone = 15,9'-dicis-phytofluene + plastoquinol
(1b) 15,9'-dicis-phytofluene + plastoquinone = 9,15,9'-tricis-ζ-carotene + plastoquinol

Other name(s): phytoene desaturase (ambiguous); PDS; plant-type phytoene desaturase

Systematic name: 15-cis-phytoene:plastoquinone oxidoreductase

Comments: This enzyme is involved in carotenoid biosynthesis in plants and cyanobacteria. The enzyme from Synechococcus can also use NAD+ and NADP+ as electron acceptor under anaerobic conditions. The enzyme from Gentiana lutea shows no activity with NAD+ or NADP+ [1].

References:

1. Breitenbach, J., Zhu, C. and Sandmann, G. Bleaching herbicide norflurazon inhibits phytoene desaturase by competition with the cofactors. J. Agric. Food Chem. 49 (2001) 5270-5272. [PMID: 11714315]

2. Schneider, C., Boger, P. and Sandmann, G. Phytoene desaturase: heterologous expression in an active state, purification, and biochemical properties. Protein Expr. Purif. 10 (1997) 175-179. [PMID: 9226712]

3. Fraser, P.D., Linden, H. and Sandmann, G. Purification and reactivation of recombinant Synechococcus phytoene desaturase from an overexpressing strain of Escherichia coli. Biochem. J. 291 (1993) 687-692. [PMID: 8489496]

4. Breitenbach, J. and Sandmann, G. ζ-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta 220 (2005) 785-793. [PMID: 15503129]

[EC 1.3.5.5 created 2011]

EC 1.3.7.8

Accepted name: benzoyl-CoA reductase

Reaction: cyclohexa-1,5-diene-1-carbonyl-CoA + oxidized ferredoxin + 2 ADP + 2 phosphate = benzoyl-CoA + reduced ferredoxin + 2 ATP + 2 H2O

Other name(s): benzoyl-CoA reductase (dearomatizing)

Systematic name: cyclohexa-1,5-diene-1-carbonyl-CoA:ferredoxin oxidoreductase (aromatizing, ATP-forming)

Comments: An iron-sulfur protein. Requires Mg2+ or Mn2+. Inactive towards aromatic acids that are not CoA esters but will also catalyse the reaction: ammonia + acceptor + 2 ADP + 2 phosphate + H2O = hydroxylamine + reduced acceptor + 2 ATP. In the presence of reduced acceptor, but in the absence of oxidizable substrate, the enzyme catalyses the hydrolysis of ATP to ADP plus phosphate.

References:

1. Boll, M. and Fuchs, G. Benzoyl-coenzyme A reductase (dearomatizing), a key enzyme of anaerobic aromatic metabolism. ATP dependence of the reaction, purification and some properties of the enzyme from Thauera aromatica strain K172. Eur. J. Biochem. 234 (1995) 921-933. [PMID: 8575453]

2. Kung, J.W., Baumann, S., von Bergen, M., Muller, M., Hagedoorn, P.L., Hagen, W.R. and Boll, M. Reversible biological Birch reduction at an extremely low redox potential. J. Am. Chem. Soc. 132 (2010) 9850-9856. [PMID: 20578740]

[EC 1.3.7.8 created 1999 as EC 1.3.99.15, transferred 2011 to EC 1.3.7.8]

EC 1.3.7.9

Accepted name: 4-hydroxybenzoyl-CoA reductase

Reaction: benzoyl-CoA + oxidized ferredoxin + H2O = 4-hydroxybenzoyl-CoA + reduced ferredoxin

Other name(s): 4-hydroxybenzoyl-CoA reductase (dehydroxylating); 4-hydroxybenzoyl-CoA:(acceptor) oxidoreductase

Systematic name: benzoyl-CoA:acceptor oxidoreductase

Comments: A molybdenum-flavin-iron-sulfur protein that is involved in the anaerobic pathway of phenol metabolism in bacteria. A ferredoxin with two [4Fe-4S] clusters functions as the natural electron donor [3].

References:

1. Glockler, R., Tschech, A. and Fuchs, G. Reductive dehydroxylation of 4-hydroxybenzoyl-CoA to benzoyl-CoA in a denitrifying, phenol-degrading Pseudomonas species. FEBS Lett. 251 (1989) 237-240. [PMID: 2753161]

2. Heider, J., Boll, M., Breese, K., Breinig, S., Ebenau-Jehle, C., Feil, U., Gad'on, N., Laempe, D., Leuthner, B., Mohamed, M.E.S., Schneider, S., Burchhardt, G. and Fuchs, G. Differential induction of enzymes involved in anaerobic metabolism of aromatic compounds in the denitrifying bacterium Thauera aromatica. Arch. Microbiol. 170 (1998) 120-131. [PMID: 9683649]

3. Breese, K. and Fuchs, G. 4-Hydroxybenzoyl-CoA reductase (dehydroxylating) from the denitrifying bacterium Thauera aromatica - prosthetic groups, electron donor, and genes of a member of the molybdenum-flavin-iron-sulfur proteins. Eur. J. Biochem. 251 (1998) 916-923. [PMID: 9490068]

4. Brackmann, R. and Fuchs, G. Enzymes of anaerobic metabolism of phenolic compounds. 4-Hydroxybenzoyl-CoA reductase (dehydroxylating) from a denitrifying Pseudomonas species. Eur. J. Biochem. 213 (1993) 563-571. [PMID: 8477729]

5. Heider, J. and Fuchs, G. Anaerobic metabolism of aromatic compounds. Eur. J. Biochem. 243 (1997) 577-596. [PMID: 9057820]

[EC 1.3.7.9 created 2000 as EC 1.3.99.20, transferred 2011 to EC 1.3.7.9]

EC 1.3.8 With flavin as acceptor

EC 1.3.8.1

Accepted name: butyryl-CoA dehydrogenase

Reaction: butanoyl-CoA + electron-transfer flavoprotein = but-2-enoyl-CoA + reduced electron-transfer flavoprotein

Other name(s): butyryl dehydrogenase; unsaturated acyl-CoA reductase; ethylene reductase; enoyl-coenzyme A reductase; unsaturated acyl coenzyme A reductase; butyryl coenzyme A dehydrogenase; short-chain acyl CoA dehydrogenase; short-chain acyl-coenzyme A dehydrogenase; 3-hydroxyacyl CoA reductase; butanoyl-CoA:(acceptor) 2,3-oxidoreductase

Systematic name: butanoyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase

Comments: A flavoprotein (FAD). The enzyme catalyses the oxidation of saturated acyl-CoA thioesters to give a 2,3-unsaturated product by removal of the two pro-R-hydrogen atoms.

References:

1. Mahler, H.R. Studies on the fatty acid oxidizing system of animal tissue. IV. The prosthetic group of butyryl coenzyme A dehydrogenase. J. Biol. Chem. 206 (1954) 13-26. [PMID: 13130522]

2. Green, D.E., Mii, S., Mahler, H.R. and Bock, R.M. Studies on the fatty acid oxidizing system of animal tissue. III. Butyryl coenzyme A dehydrogenase. J. Biol. Chem. 206 (1954) 1-12. [PMID: 13130521]

3. Hauge, J.G., Crane, F.L. and Beinert, H. On the mechanism of dehydrogenation of fatty acyl derivatives of coenzyme A. III. Palmityl CoA dehydrogenase. J. Biol. Chem. 219 (1956) 727-733. [PMID: 13319294]

4. Beinert, H. Acyl coenzyme A dehydrogenase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 447-466.

[EC 1.3.8.1 created 1961 as EC 1.3.2.1, transferred 1964 to EC 1.3.99.2, transferred 2011 to EC 1.3.8.1]

EC 1.3.98 With other, known, acceptors

EC 1.3.98.1

Accepted name: dihydroorotate dehydrogenase (fumarate)

Reaction: (S)-dihydroorotate + fumarate = orotate + succinate

Other name(s): DHOdehase (ambiguous); dihydroorotate dehydrogenase (ambiguous); dihydoorotic acid dehydrogenase (ambiguous); DHOD (ambiguous); DHODase (ambiguous); dihydroorotate oxidase, pyr4 (gene name)

Systematic name: (S)-dihydroorotate:fumarate oxidoreductase

Comments: Binds FMN. The reaction, which takes place in the cytosol, is the only redox reaction in the de novo biosynthesis of pyrimidine nucleotides. Molecular oxygen can replace fumarate in vitro. Other class 1 dihydroorotate dehydrogenases use either NAD+ (EC 1.3.1.14) or NADP+ (EC 1.3.1.15) as electron acceptor. The membrane bound class 2 dihydroorotate dehydrogenase (EC 1.3.5.2) uses quinone as electron acceptor.

References:

1. Björnberg, O., Rowland, P., Larsen, S. and Jensen, K.F. Active site of dihydroorotate dehydrogenase A from Lactococcus lactis investigated by chemical modification and mutagenesis. Biochemistry 36 (1997) 16197-16205. [PMID: 9405053]

2. Rowland, P., Björnberg, O., Nielsen, F.S., Jensen, K.F. and Larsen, S. The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function. Protein Sci. 7 (1998) 1269-1279. [PMID: 9655329]

3. Nørager, S., Arent, S., Björnberg, O., Ottosen, M., Lo Leggio, L., Jensen, K.F. and Larsen, S. Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function. J. Biol. Chem. 278 (2003) 28812-28822. [PMID: 12732650]

4. Zameitat, E., Pierik, A.J., Zocher, K. and Löffler, M. Dihydroorotate dehydrogenase from Saccharomyces cerevisiae: spectroscopic investigations with the recombinant enzyme throw light on catalytic properties and metabolism of fumarate analogues. FEMS Yeast Res. 7 (2007) 897-904. [PMID: 17617217]

5. Inaoka, D.K., Sakamoto, K., Shimizu, H., Shiba, T., Kurisu, G., Nara, T., Aoki, T., Kita, K. and Harada, S. Structures of Trypanosoma cruzi dihydroorotate dehydrogenase complexed with substrates and products: atomic resolution insights into mechanisms of dihydroorotate oxidation and fumarate reduction. Biochemistry 47 (2008) 10881-10891. [PMID: 18808149]

6. Cheleski, J., Wiggers, H.J., Citadini, A.P., da Costa Filho, A.J., Nonato, M.C. and Montanari, C.A. Kinetic mechanism and catalysis of Trypanosoma cruzi dihydroorotate dehydrogenase enzyme evaluated by isothermal titration calorimetry. Anal. Biochem. 399 (2010) 13-22. [PMID: 19932077]

[EC 1.3.98.1 created 1961 as EC 1.3.3.1, transferred 2011 to EC 1.3.98.1]

[EC 1.3.99.2 Transferred entry: butyryl-CoA dehydrogenase. Now EC 1.3.8.1, butyryl-CoA dehydrogenase. (EC 1.3.99.2 created 1961 as EC 1.3.2.1, transferred 1964 to EC 1.3.99.2, deleted 2011)]

[EC 1.3.99.15 Transferred entry: benzoyl-CoA reductase. Now EC 1.3.7.8. (EC 1.3.99.15 created 1999, deleted 2011)]

[EC 1.3.99.20 Transferred entry: EC 1.3.99.20, 4-hydroxybenzoyl-CoA reductase. Now EC 1.3.7.9, 4-hydroxybenzoyl-CoA reductase. (EC 1.3.99.20 created 2000, deleted 2011)]

EC 1.4.98 With other, known, acceptors

EC 1.4.98.1

Accepted name: methylamine dehydrogenase (amicyanin)

Reaction: methylamine + H2O + amicyanin = formaldehyde + ammonia + reduced amicyanin

Other name(s): amine dehydrogenase; primary-amine dehydrogenase; amine: (acceptor) oxidoreductase (deaminating); primary-amine:(acceptor) oxidoreductase (deaminating)

Systematic name: methylamine:amicyanin oxidoreductase (deaminating)

Comments: Contains tryptophan tryptophylquinone (TTQ) cofactor. The enzyme oxidizes aliphatic monoamines and diamines, histamine and ethanolamine, but not secondary and tertiary amines, quaternary ammonium salts or aromatic amines.

References:

1. De Beer, R., Duine, J.A., Frank, J., Jr. and Large, P.J. The prosthetic group of methylamine dehydrogenase from Pseudomonas AM1: evidence for a quinone structure. Biochim. Biophys. Acta 622 (1980) 370-374. [PMID: 6246962]

2. Eady, R.R. and Large, P.J. Purification and properties of an amine dehydrogenase from Pseudomonas AM1 and its role in growth on methylamine. Biochem. J. 106 (1968) 245-255. [PMID: 4388687]

3. Eady, R.R. and Large, P.J. Microbial oxidation of amines. Spectral and kinetic properties of the primary amine dehydrogenase of Pseudomonas AM1. Biochem. J. 123 (1971) 757-771. [PMID: 5124384]

4. Cavalieri, C., Biermann, N., Vlasie, M.D., Einsle, O., Merli, A., Ferrari, D., Rossi, G.L. and Ubbink, M. Structural comparison of crystal and solution states of the 138 kDa complex of methylamine dehydrogenase and amicyanin from Paracoccus versutus. Biochemistry 47 (2008) 6560-6570. [PMID: 18512962]

5. Meschi, F., Wiertz, F., Klauss, L., Cavalieri, C., Blok, A., Ludwig, B., Heering, H.A., Merli, A., Rossi, G.L. and Ubbink, M. Amicyanin transfers electrons from methylamine dehydrogenase to cytochrome c-551i via a ping-pong mechanism, not a ternary complex. J. Am. Chem. Soc. 132 (2010) 14537-14545. [PMID: 20873742]

[EC 1.4.98.1 created 1978 as EC 1.4.99.3, modified 1986, transferred 2011 to EC 1.4.98.1]

[EC 1.4.99.3 Transferred entry: amine dehydrogenase. Now EC 1.4.98.1, methylamine dehydrogenase (amicyanin) (EC 1.4.99.3 created 1978, modified 1986, deleted 2011)]

*EC 1.6.5.3

Accepted name: NADH:ubiquinone reductase (H+-translocating)

Reaction: NADH + ubiquinone + 5 H+in = NAD+ + ubiquinol + 4 H+out

Other name(s): ubiquinone reductase; type 1 dehydrogenase; complex 1 dehydrogenase; coenzyme Q reductase; complex I (electron transport chain); complex I (mitochondrial electron transport); complex I (NADH:Q1 oxidoreductase); dihydronicotinamide adenine dinucleotide-coenzyme Q reductase; DPNH-coenzyme Q reductase; DPNH-ubiquinone reductase; mitochondrial electron transport complex 1; mitochondrial electron transport complex I; NADH coenzyme Q1 reductase; NADH-coenzyme Q oxidoreductase; NADH-coenzyme Q reductase; NADH-CoQ oxidoreductase; NADH-CoQ reductase; NADH-ubiquinone reductase; NADH-ubiquinone oxidoreductase; NADH-ubiquinone-1 reductase; reduced nicotinamide adenine dinucleotide-coenzyme Q reductase; NADH:ubiquinone oxidoreductase complex; NADH-Q6 oxidoreductase; electron transfer complex I; NADH2 dehydrogenase (ubiquinone)

Systematic name: NADH:ubiquinone oxidoreductase

Comments: A flavoprotein (FMN) containing iron-sulfur clusters. The complex is present in mitochondria and aerobic bacteria. Breakdown of the complex can release EC 1.6.99.3, NADH dehydrogenase. In photosynthetic bacteria, reversed electron transport through this enzyme can reduce NAD+ to NADH.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9028-04-0

References:

1. Hatefi, Y., Ragan, C.I. and Galante, Y.M. The enzymes and the enzyme complexes of the mitochondrial oxidative phosphorylation system. In: Martonosi, A. (Ed.), The Enzymes of Biological Membranes, 2nd edn, vol. 4, Plenum Press, New York, 1985, pp. 1-70.

2. Herter, S.M., Kortluke, C.M. and Drews, G. Complex I of Rhodobacter capsulatus and its role in reverted electron transport. Arch. Microbiol. 169 (1998) 98-105. [PMID: 9446680]

3. Hunte, C., Zickermann, V. and Brandt, U. Functional modules and structural basis of conformational coupling in mitochondrial complex I. Science 329 (2010) 448-451. [PMID: 20595580]

4. Efremov, R.G., Baradaran, R. and Sazanov, L.A. The architecture of respiratory complex I. Nature 465 (2010) 441-445. [PMID: 20505720]

[EC 1.6.5.3 created 1961, deleted 1965, reinstated 1983, modified 2011]

EC 1.6.5.9

Accepted name: NADH:ubiquinone reductase (non-electrogenic)

Reaction: NADH + H+ + ubiquinone = NAD+ + ubiquinol

Other name(s): ubiquinone reductase; coenzyme Q reductase; dihydronicotinamide adenine dinucleotide-coenzyme Q reductase; DPNH-coenzyme Q reductase; DPNH-ubiquinone reductase; NADH-coenzyme Q oxidoreductase; NADH-coenzyme Q reductase; NADH-CoQ oxidoreductase; NADH-CoQ reductase; NADH-ubiquinone reductase; NADH-ubiquinone oxidoreductase; reduced nicotinamide adenine dinucleotide-coenzyme Q reductase; NADH-Q6 oxidoreductase; electron transfer complex I; NADH2 dehydrogenase (ubiquinone)

Systematic name: NADH:ubiquinone oxidoreductase

Comments: A flavoprotein (FAD). Occurs in mitochondria of yeast and plants, and in aerobic bacteria. Has low activity with NADPH.

References:

1. Moller, I.M, and Palmer, J.M. Direct evidence for the presence of a rotenone-resistant NADH dehydrogenase on the inner surface of plant mitochondria. Physiologia Plantarum 54 (1982) 267-274.

2. de Vries, S. and Grivell, L.A. Purification and characterization of a rotenone-insensitive NADH:Q6 oxidoreductase from mitochondria of Saccharomyces cerevisiae. Eur. J. Biochem. 176 (1988) 377-384. [PMID: 3138118]

3. Kerscher, S.J., Okun, J.G. and Brandt, U. A single external enzyme confers alternative NADH:ubiquinone oxidoreductase activity in Yarrowia lipolytica. J. Cell Sci. 112 ( Pt 14) (1999) 2347-2354. [PMID: 10381390]

4. Rasmusson, A.G., Soole, K.L. and Elthon, T.E. Alternative NAD(P)H dehydrogenases of plant mitochondria. Annu. Rev. Plant Biol. 55 (2004) 23-39. [PMID: 15725055]

[EC 1.6.5.9 created 2011]

EC 1.7.1.14

Accepted name: nitric oxide reductase [NAD(P), nitrous oxide-forming]

Reaction: N2O + NAD(P)+ + H2O = 2 NO + NAD(P)H + H+

Other name(s): fungal nitric oxide reductase; cytochrome P450nor; NOR (ambiguous)

Systematic name: nitrous oxide:NAD(P) oxidoreductase

Comments: A heme-thiolate protein (P450). The enzyme from Fusarium oxysporum utilizes only NADH, but the isozyme from Trichosporon cutaneum utilizes both NADH and NADPH. The electron transfer from NAD(P)H to heme occurs directly, not requiring flavin or other redox cofactors.

References:

1. Shoun, H. and Tanimoto, T. Denitrification by the fungus Fusarium oxysporum and involvement of cytochrome P-450 in the respiratory nitrite reduction. J. Biol. Chem. 266 (1991) 11078-11082. [PMID: 2040619]

2. Shiro, Y., Fujii, M., Iizuka, T., Adachi, S., Tsukamoto, K., Nakahara, K. and Shoun, H. Spectroscopic and kinetic studies on reaction of cytochrome P450nor with nitric oxide. Implication for its nitric oxide reduction mechanism. J. Biol. Chem. 270 (1995) 1617-1623. [PMID: 7829493]

3. Zhang, L., Kudo, T., Takaya, N. and Shoun, H. The B' helix determines cytochrome P450nor specificity for the electron donors NADH and NADPH. J. Biol. Chem. 277 (2002) 33842-33847. [PMID: 12105197]

4. Oshima, R., Fushinobu, S., Su, F., Zhang, L., Takaya, N. and Shoun, H. Structural evidence for direct hydride transfer from NADH to cytochrome P450nor. J. Mol. Biol. 342 (2004) 207-217. [PMID: 15313618]

[EC 1.7.1.14 created 2011]

EC 1.7.2.5

Accepted name: nitric oxide reductase (cytochrome c)

Reaction: nitrous oxide + 2 ferricytochrome c + H2O = 2 nitric oxide + 2 ferrocytochrome c + 2 H+

Systematic name: nitrous oxide:ferricytochrome-c oxidoreductase

Comments: The enzyme from Pseudomonas aeruginosa contains a dinuclear centre comprising a non-heme iron centre and heme b3, plus heme c, heme b and calcium; the acceptor is cytochrome c551

References:

1. Hendriks, J., Warne, A., Gohlke, U., Haltia, T., Ludovici, C., Lubben, M. and Saraste, M. The active site of the bacterial nitric oxide reductase is a dinuclear iron center. Biochemistry 37 (1998) 13102-13109. [PMID: 9748316]

2. Hendriks, J., Gohlke, U. and Saraste, M. From NO to OO: nitric oxide and dioxygen in bacterial respiration. J. Bioenerg. Biomembr. 30 (1998) 15-24. [PMID: 9623801]

3. Heiss, B., Frunzke, K. and Zumpft, W.G. Formation of the N-N bond from nitric oxide by a membrane-bound cytochrome bc complex of nitrate-respiring (denitrifying) Pseudomonas stutzeri. J. Bacteriol. 171 (1989) 3288-3297. [PMID: 2542222]

4. Cheesman, M.R., Zumft, W.G. and Thomson, A.J. The MCD and EPR of the heme centers of nitric oxide reductase from Pseudomonas stutzeri: evidence that the enzyme is structurally related to the heme-copper oxidases. Biochemistry 37 (1998) 3994-4000. [PMID: 9521721]

5. Kumita, H., Matsuura, K., Hino, T., Takahashi, S., Hori, H., Fukumori, Y., Morishima, I. and Shiro, Y. NO reduction by nitric-oxide reductase from denitrifying bacterium Pseudomonas aeruginosa: characterization of reaction intermediates that appear in the single turnover cycle. J. Biol. Chem. 279 (2004) 55247-55254. [PMID: 15504726]

6. Hino, T., Matsumoto, Y., Nagano, S., Sugimoto, H., Fukumori, Y., Murata, T., Iwata, S. and Shiro, Y. Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330 (2010) 1666-1670. [PMID: 21109633]

[EC 1.7.2.5 created 1992 as EC 1.7.99.7, transferred 2011 to EC 1.7.2.5]

EC 1.7.5.2

Accepted name: nitric oxide reductase (menaquinol)

Reaction: 2 nitric oxide + menaquinol = nitrous oxide + menaquinone + H2O

Comments: Contains copper.

References:

1. Cramm, R., Pohlmann, A. and Friedrich, B. Purification and characterization of the single-component nitric oxide reductase from Ralstonia eutropha H16. FEBS Lett. 460 (1999) 6-10. [PMID: 10571051]

2. Suharti, Strampraad, M.J., Schroder, I. and de Vries, S. A novel copper A containing menaquinol NO reductase from Bacillus azotoformans. Biochemistry 40 (2001) 2632-2639. [PMID: 11327887]

3. Suharti, Heering, H.A. and de Vries, S. NO reductase from Bacillus azotoformans is a bifunctional enzyme accepting electrons from menaquinol and a specific endogenous membrane-bound cytochrome c551. Biochemistry 43 (2004) 13487-13495. [PMID: 15491156]

[EC 1.7.5.2 created 2011]

[EC 1.7.99.6 Transferred entry: EC 1.7.99.6, nitrous-oxide reductase. Now EC 1.7.2.4. (EC 1.7.99.6 created 1989, modified 1999, deleted 2011)]

[EC 1.7.99.7 Transferred entry: nitric-oxide reductase. Now EC 1.7.2.5 nitric oxide reductase (cytochrome c) (EC 1.7.99.7 created 1992, modified 1999, deleted 2011)]

EC 1.8.1.17

Accepted name: dimethylsulfone reductase

Reaction: dimethyl sulfoxide + H2O + NAD+ = dimethyl sulfone + NADH + H+

Comments: A molybdoprotein.

References:

1. Borodina, E., Kelly, D.P., Rainey, F.A., Ward-Rainey, N.L. and Wood, A.P. Dimethylsulfone as a growth substrate for novel methylotrophic species of Hyphomicrobium and Arthrobacter. Arch. Microbiol. 173 (2000) 425-437. [PMID: 10896224]

2. Borodina, E., Kelly, D.P., Schumann, P., Rainey, F.A., Ward-Rainey, N.L. and Wood, A.P. Enzymes of dimethylsulfone metabolism and the phylogenetic characterization of the facultative methylotrophs Arthrobacter sulfonivorans sp. nov., Arthrobacter methylotrophus sp. nov., and Hyphomicrobium sulfonivorans sp. nov. Arch. Microbiol. 177 (2002) 173-183. [PMID: 11807567]

[EC 1.8.1.17 created 2011]

EC 1.8.2.3

Accepted name: sulfide-cytochrome-c reductase (flavocytochrome c)

Reaction: hydrogen sulfide + 2 ferricytochrome c = sulfur + 2 ferrocytochrome c + 2 H+

Systematic name: hydrogen-sulfide:flavocytochrome c oxidoreductase

Comments: The enzyme from Allochromatium vinosum contains covalently bound FAD and covalently-bound c-type hemes.

References:

1. Kusai, K. and Yamanaka, T. The oxidation mechanisms of thiosulphate and sulphide in Chlorobium thiosulphatophilum: roles of cytochrome c-551 and cytochrome c-553. Biochim. Biophys. Acta 325 (1973) 304-314. [PMID: 4357558]

2. Fukumori, Y. and Yamanaka, T. Flavocytochrome c of Chromatium vinosum. Some enzymatic properties and subunit structure. J. Biochem. 85 (1979) 1405-1414. [PMID: 222744]

3. Gray, G.O., Gaul, D.F. and Knaff, D.B. Partial purification and characterization of two soluble c-type cytochromes from Chromatium vinosum. Arch. Biochem. Biophys. 222 (1983) 78-86. [PMID: 6301383]

4. Chen, Z.W., Koh, M., Van Driessche, G., Van Beeumen, J.J., Bartsch, R.G., Meyer, T.E., Cusanovich, M.A. and Mathews, F.S. The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium. Science 266 (1994) 430-432. [PMID: 7939681]

5. Sorokin, D.Yu, de Jong, G.A., Robertson, L.A. and Kuenen, G.J. Purification and characterization of sulfide dehydrogenase from alkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria. FEBS Lett. 427 (1998) 11-14. [PMID: 9613590]

6. Kostanjevecki, V., Brige, A., Meyer, T.E., Cusanovich, M.A., Guisez, Y. and van Beeumen, J. A membrane-bound flavocytochrome c-sulfide dehydrogenase from the purple phototrophic sulfur bacterium Ectothiorhodospira vacuolata. J. Bacteriol. 182 (2000) 3097-3103. [PMID: 10809687]

[EC 1.8.2.3 created 2011]

EC 1.8.2.4

Accepted name: dimethyl sulfide:cytochrome c2 reductase

Reaction: dimethyl sulfide + 2 ferricytochrome c2 = dimethyl sulfoxide + 2 ferrocytochrome c2

Other name(s): Ddh (gene name)

Systematic name: dimethyl sulfide:ferricytochrome-c2 oxidoreductase

Comments: The enzyme from Rhodovulum sulfidophilum binds molybdopterin guanine dinucleotide, heme b and [4Fe-4S] clusters.

References:

1. Hanlon, S.P., Toh, T.H., Solomon, P.S., Holt, R.A. and McEwan, A.G. Dimethylsulfide:acceptor oxidoreductase from Rhodobacter sulfidophilus. The purified enzyme contains b-type haem and a pterin molybdenum cofactor. Eur. J. Biochem. 239 (1996) 391-396. [PMID: 8706745]

2. McDevitt, C.A., Hugenholtz, P., Hanson, G.R. and McEwan, A.G. Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes. Mol. Microbiol. 44 (2002) 1575-1587. [PMID: 12067345]

[EC 1.8.2.4 created 2011]

EC 1.8.3.6

Accepted name: farnesylcysteine lyase

Reaction: S-(2E,6E)-farnesyl-L-cysteine + O2 + H2O = (2E,6E)-farnesal + L-cysteine + H2O2

Other name(s): FC lyase; FCLY

Systematic name: S-(2E,6E)-farnesyl-L-cysteine oxidase

Comments: A flavoprotein (FAD). In contrast to mammalian EC 1.8.3.5 (prenylcysteine oxidase) the farnesylcysteine lyase from Arabidopsis is specific for S-farnesyl-L-cysteine and shows no activity with S-geranylgeranyl-L-cysteine.

References:

1. Huizinga, D.H., Denton, R., Koehler, K.G., Tomasello, A., Wood, L., Sen, S.E. and Crowell, D.N. Farnesylcysteine lyase is involved in negative regulation of abscisic acid signaling in Arabidopsis. Mol Plant 3 (2010) 143-155. [PMID: 19969520]

2. Crowell, D.N., Huizinga, D.H., Deem, A.K., Trobaugh, C., Denton, R. and Sen, S.E. Arabidopsis thaliana plants possess a specific farnesylcysteine lyase that is involved in detoxification and recycling of farnesylcysteine. Plant J. 50 (2007) 839-847. [PMID: 17425716]

[EC 1.8.3.6 created 2011]

EC 1.8.5.4

Accepted name: sulfide:quinone reductase

Reaction: n HS- + n quinone = polysulfide + n quinol

Systematic name: sulfide:quinone oxidoreductase

Comments: Contains FAD. Ubiquinone, plastoquinone or menaquinone can act as acceptor in different species. This enzyme catalyses the formation of sulfur globules. It is also an important step in anoxygenic bacterial photosynthesis.

References:

1. Arieli, B., Shahak, Y., Taglicht, D., Hauska, G. and Padan, E. Purification and characterization of sulfide-quinone reductase, a novel enzyme driving anoxygenic photosynthesis in Oscillatoria limnetica. J. Biol. Chem. 269 (1994) 5705-5711. [PMID: 8119908]

2. Reinartz, M., Tschape, J., Bruser, T., Truper, H.G. and Dahl, C. Sulfide oxidation in the phototrophic sulfur bacterium Chromatium vinosum. Arch. Microbiol. 170 (1998) 59-68. [PMID: 9639604]

3. Nubel, T., Klughammer, C., Huber, R., Hauska, G. and Schutz, M. Sulfide:quinone oxidoreductase in membranes of the hyperthermophilic bacterium Aquifex aeolicus (VF5). Arch. Microbiol. 173 (2000) 233-244. [PMID: 10816041]

4. Brito, J.A., Sousa, F.L., Stelter, M., Bandeiras, T.M., Vonrhein, C., Teixeira, M., Pereira, M.M. and Archer, M. Structural and functional insights into sulfide:quinone oxidoreductase. Biochemistry 48 (2009) 5613-5622. [PMID: 19438211]

5. Cherney, M.M., Zhang, Y., Solomonson, M., Weiner, J.H. and James, M.N. Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification. J. Mol. Biol. 398 (2010) 292-305. [PMID: 20303979]

6. Marcia, M., Langer, J.D., Parcej, D., Vogel, V., Peng, G. and Michel, H. Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase. Biochim. Biophys. Acta 1798 (2010) 2114-2123. [PMID: 20691146]

[EC 1.8.5.4 created 2011]

*EC 1.10.3.3

Accepted name: L-ascorbate oxidase

Reaction: 4 L-ascorbate + O2 = 4 monodehydroascorbate + 2 H2O

Other name(s): ascorbase; ascorbic acid oxidase; ascorbate oxidase; ascorbic oxidase; ascorbate dehydrogenase; L-ascorbic acid oxidase; AAO; L-ascorbate:O2 oxidoreductase; AA oxidase

Systematic name: L-ascorbate:oxygen oxidoreductase

Comments: A multicopper protein.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9029-44-1

References:

1. Yamazaki, I. and Piette, L.H. Mechanism of free radical formation and disappearance during the ascorbic acid oxidase and peroxidase reactions. Biochim. Biophys. Acta 50 (1961) 62-69. [PMID: 13787201]

2. Stark, G.R. and Dawson, C.R. Ascorbic acid oxidase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 8, Academic Press, New York, 1963, pp. 297-311.

3. Messerschmidt, A., Ladenstein, R., Huber, R., Bolognesi, M., Avigliano, L., Petruzzelli, R., Rossi, A. and Finazzi-Agro, A. Refined crystal structure of ascorbate oxidase at 1.9 Å resolution. J. Mol. Biol. 224 (1992) 179-205. [PMID: 1548698]

[EC 1.10.3.3 created 1961, modified 2011]

EC 1.10.3.9

Accepted name: photosystem II

Reaction: 2 H2O + 2 plastoquinone + 4 = O2 + 2 plastoquinol

Systematic name: H2O:plastoquinone reductase (light-dependent)

Comments: Contains chlorophyll a, β-carotene, pheophytin, plastoquinone, a Mn4Ca cluster, heme and non-heme iron. Four successive photoreactions, resulting in a storage of four positive charges, are required to oxidize two water molecules to one oxygen molecule.

References:

1. Knaff, D.B., Malkin, R., Myron, J.C. and Stoller, M. The role of plastoquinone and β-carotene in the primary reaction of plant photosystem II. Biochim. Biophys. Acta 459 (1977) 402-411. [PMID: 849432]

2. Guskov, A., Kern, J., Gabdulkhakov, A., Broser, M., Zouni, A. and Saenger, W. Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride. Nat. Struct. Mol. Biol. 16 (2009) 334-342. [PMID: 19219048]

[EC 1.10.3.9 created 2011]

EC 1.10.3.10

Accepted name: ubiquinol oxidase (H+-transporting)

Reaction: 2 ubiquinol + O2 + n H+in = 2 ubiquinone + 2 H2O + n H+out

Other name(s): cytochrome bb3 oxidase; cytochrome bo oxidase; cytochrome bd-I oxidase

Systematic name: ubiquinol:O2 oxidoreductase (H+-transporting)

Comments: Contains a dinuclear centre comprising two hemes, or heme and copper. Reduction of O2 on the periplasmic side of the membrane leads to release of protons in the periplasm, generating a transmembrane proton gradient. In addition, the bb3 and bo oxidases, but not the bd oxidase, contribute to the proton gradient by actively pumping protons across the membrane.

References:

1. Abramson, J., Riistama, S., Larsson, G., Jasaitis, A., Svensson-Ek, M., Laakkonen, L., Puustinen, A., Iwata, S. and Wikstrom, M. The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site. Nat. Struct. Biol. 7 (2000) 910-917. [PMID: 11017202]

2. Belevich, I., Borisov, V.B., Zhang, J., Yang, K., Konstantinov, A.A., Gennis, R.B. and Verkhovsky, M.I. Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site. Proc. Natl. Acad. Sci. USA 102 (2005) 3657-3662. [PMID: 15728392]

3. Yap, L.L., Lin, M.T., Ouyang, H., Samoilova, R.I., Dikanov, S.A. and Gennis, R.B. The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli. Biochim. Biophys. Acta 1797 (2010) 1924-1932. [PMID: 20416270]

4. Shepherd, M., Sanguinetti, G., Cook, G.M. and Poole, R.K. Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism. J. Biol. Chem. 285 (2010) 18464-18472. [PMID: 20392690]

[EC 1.10.3.10 created 2011]

EC 1.10.3.11

Accepted name: ubiquinol oxidase

Reaction: 2 ubiquinol + O2 = 2 ubiquinone + 2 H2O

Other name(s): plant alternative oxidase; cyanide-insensitive oxidase; cytochrome bd-II oxidase

Systematic name: ubiquinol:O2 oxidoreductase (non-electrogenic)

Comments: The enzyme in mitochondria from thermogenic tissues of plants and from certain protists contains a dinuclear iron complex. Cytochrome bd-II from Escherichia coli contains a diheme active site.

References:

1. Bendall, D.S. and Bonner, W.D. Cyanide-insensitive respiration in plant mitochondria. Plant Physiol. 47 (1971) 236-245. [PMID: 16657603]

2. Siedow, J.N., Umbach, A.L. and Moore, A.L. The active site of the cyanide-resistant oxidase from plant mitochondria contains a binuclear iron center. FEBS Lett. 362 (1995) 10-14. [PMID: 7698344]

3. Williams, B.A., Elliot, C., Burri, L., Kido, Y., Kita, K., Moore, A.L. and Keeling, P.J. A broad distribution of the alternative oxidase in microsporidian parasites. PLoS Pathog. 6 (2010) e1000761. [PMID: 20169184]

4. Shepherd, M., Sanguinetti, G., Cook, G.M. and Poole, R.K. Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism. J. Biol. Chem. 285 (2010) 18464-18472. [PMID: 20392690]

[EC 1.10.3.11 created 2011]

EC 1.10.3.12

Accepted name: menaquinol oxidase (H+-transporting)

Reaction: 2 menaquinol + O2 = 2 menaquinone + 2 H2O

Other name(s): cytochrome aa3-600 oxidase; cytochrome bd oxidase

Systematic name: menaquinol:O2 oxidoreductase (H+-transporting)

Comments: Cytochrome aa3-600, one of the principal respiratory oxidases from Bacillus subtilis, is a member of the heme-copper superfamily of oxygen reductases, and is a close homologue of the cytochrome bo3 ubiquinol oxidase from Escherichia coli, but uses menaquinol instead of ubiquinol as a substrate. The enzyme also pumps protons across the membrane bilayer, generating a proton motive force.

References:

1. Lauraeus, M. and Wikstrom, M. The terminal quinol oxidases of Bacillus subtilis have different energy conservation properties. J. Biol. Chem. 268 (1993) 11470-11473. [PMID: 8388393]

2. Lemma, E., Simon, J., Schagger, H. and Kroger, A. Properties of the menaquinol oxidase (Qox) and of qox deletion mutants of Bacillus subtilis. Arch. Microbiol. 163 (1995) 432-438. [PMID: 7575098]

3. Yi, S.M., Narasimhulu, K.V., Samoilova, R.I., Gennis, R.B. and Dikanov, S.A. Characterization of the semiquinone radical stabilized by the cytochrome aa3-600 menaquinol oxidase of Bacillus subtilis. J. Biol. Chem. 285 (2010) 18241-18251. [PMID: 20351111]

[EC 1.10.3.12 created 2011]

*EC 1.11.1.11

Accepted name: L-ascorbate peroxidase

Reaction: (1a) 2 L-ascorbate + H2O2 + 2 H+ = 2 monodehydroascorbate + 2 H2O
(1b) 2 monodehydroascorbate = L-ascorbate + L-dehydroascorbate (spontaneous)

Other name(s): L-ascorbic acid peroxidase; L-ascorbic acid-specific peroxidase; ascorbate peroxidase; ascorbic acid peroxidase

Systematic name: L-ascorbate:hydrogen-peroxide oxidoreductase

Comments: A heme protein. Oxidizes ascorbate and low molecular weight aromatic substrates. The monodehydroascorbate radical produced is either directly reduced back to ascorbate by EC 1.6.5.4 [monodehydroascorbate reductase (NADH)] or undergoes non-enzymatic disproportionation to ascorbate and dehydroascorbate.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 72906-87-7

References:

1. Shigeoka, S., Nakano, Y. and Kitaoka, S. Purification and some properties of L-ascorbic-acid-specific peroxidase in Euglena gracilis. Z. Arch. Biochem. Biophys. 201 (1980) 121-127. [PMID: 6772104]

2. Shigeoka, S., Nakano, Y. and Kitaoka, S. Metabolism of hydrogen peroxide in Euglena gracilis Z by L-ascorbic acid peroxidase. Biochem. J. 186 (1980) 377-380. [PMID: 6768357]

3. Nakano, Y and Asada, K. Purification of ascorbate peroxidase in spinach chloroplasts; its inactivation in ascorbate-depleted medium and reactivation by monodehydroascorbate radical. Plant Cell Physiol. 28 (1987) 131-140.

4. Patterson, W.R. and Poulos, T.L. Crystal structure of recombinant pea cytosolic ascorbate peroxidase. Biochemistry 34 (1995) 4331-4341. [PMID: 7703247]

6. Sharp, K.H., Moody, P.C., Brown, K.A. and Raven, E.L. Crystal structure of the ascorbate peroxidase-salicylhydroxamic acid complex. Biochemistry 43 (2004) 8644-8651. [PMID: 15236572]

7. Macdonald, I.K., Badyal, S.K., Ghamsari, L., Moody, P.C. and Raven, E.L. Interaction of ascorbate peroxidase with substrates: a mechanistic and structural analysis. Biochemistry 45 (2006) 7808-7817. [PMID: 16784232]

[EC 1.11.1.11 created 1983, modified 2010, modified 2011]

*EC 1.11.1.14

Accepted name: lignin peroxidase

Reaction: (3,4-dimethoxyphenyl)methanol + H2O2 = 3,4-dimethoxybenzaldehyde + 2 H2O

Glossary: veratryl alcohol = 3,4-dimethoxyphenyl)methanol

Other name(s): diarylpropane oxygenase; ligninase I; diarylpropane peroxidase; LiP; diarylpropane:oxygen,hydrogen-peroxide oxidoreductase (C-C-bond-cleaving)

Systematic name: 1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol:hydrogen-peroxide oxidoreductase

Comments: A hemoprotein, involved in the oxidative breakdown of lignin by white-rot basidiomycete fungi. The enzyme from Phanerochaete chrysosporium oxidizes typical peroxidase dye substrates at the heme iron, a reaction involving the formation of Compound II (FeIV=O); it also oxidizes (3,4-dimethoxyphenyl)methanol (veratryl alcohol) to the radical cation. The bound veratryl alcohol radical is proposed to bring about the oxidative cleavage of C-C and ether (C-O-C) bonds in lignin model compounds of the diarylpropane and arylpropane-aryl ether type.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, UM-BBD, CAS registry number: 93792-13-3

References:

1. Kersten, P.J., Tien, M., Kalyanaraman, B. and Kirk, T.K. The ligninase of Phanerochaete chrysosporium generates cation radicals from methoxybenzenes. J. Biol. Chem. 260 (1985) 2609-2612. [PMID: 2982828]

2. Paszczynski, A., Huynh, V.-B. and Crawford, R. Comparison of ligninase-I and peroxidase-M2 from the white-rot fungus Phanerochaete chrysosporium. Arch. Biochem. Biophys. 244 (1986) 750-765. [PMID: 3080953]

3. Harvey, P.J., Schoemaker, H.E. and Palmer, J.M. Veratryl alcohol as a mediator and the role of radical cations in lignin biodegradation by Phanerochaete chrysosporium. FEBS Lett. 195 (1986) 242-246.

4. Doyle, W.A., Blodig, W., Veitch, N.C., Piontek, K. and Smith, A.T. Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis. Biochemistry 37 (1998) 15097-15105. [PMID: 9790672]

5. Wariishi, H., Marquez, L., Dunford, H.B. and Gold, M.H. Lignin peroxidase compounds II and III. Spectral and kinetic characterization of reactions with peroxides. J. Biol. Chem. 265 (1990) 11137-11142. [PMID: 2162833]

6. Cai, D.Y. and Tien, M. Characterization of the oxycomplex of lignin peroxidases from Phanerochaete chrysosporium: equilibrium and kinetics studies. Biochemistry 29 (1990) 2085-2091. [PMID: 2328240]

7. Khindaria, A., Yamazaki, I. and Aust, S.D. Veratryl alcohol oxidation by lignin peroxidase. Biochemistry 34 (1995) 16860-16869. [PMID: 8527462]

8. Khindaria, A., Yamazaki, I. and Aust, S.D. Stabilization of the veratryl alcohol cation radical by lignin peroxidase. Biochemistry 35 (1996) 6418-6424. [PMID: 8639588]

9. Khindaria, A., Nie, G. and Aust, S.D. Detection and characterization of the lignin peroxidase compound II-veratryl alcohol cation radical complex. Biochemistry 36 (1997) 14181-14185. [PMID: 9369491]

[EC 1.11.1.14 created 1992, modified 2006, modified 2011]

EC 1.11.1.21

Accepted name: catalase-peroxidase

Reaction: (1) donor + H2O2 = oxidized donor + 2 H2O
(2) 2 H2O2 = O2 + 2 H2O

Other name(s): katG (gene name)

Systematic name: donor:hydrogen-peroxide oxidoreductase

Comments: Differs from EC 1.11.1.7, peroxidase in having a relatively high catalase (EC 1.11.1.6) activity with H2O2 as donor, releasing O2; both activities use the same heme active site. In Mycobacterium tuberculosis it is responsible for activation of the commonly used antitubercular drug, isoniazid.

References:

1. Loewen, P.C., Triggs, B.L., George, C.S. and Hrabarchuk, B.E. Genetic mapping of katG, a locus that affects synthesis of the bifunctional catalase-peroxidase hydroperoxidase I in Escherichia coli. J. Bacteriol. 162 (1985) 661-667. [PMID: 3886630]

2. Hochman, A. and Goldberg, I. Purification and characterization of a catalase-peroxidase and a typical catalase from the bacterium Klebsiella pneumoniae. Biochim. Biophys. Acta 1077 (1991) 299-307. [PMID: 2029529]

3. Fraaije, M.W., Roubroeks, H.P., van Berkel, W.H.J. Purification and characterization of an intracellular catalase-peroxidase from Penicillium simplicissimum. Eur. J. Biochem. 235 (1996) 192-198. [PMID: 8631329]

4. Bertrand, T., Eady, N.A., Jones, J.N., Jesmin, Nagy, J.M., Jamart-Gregoire, B., Raven, E.L. and Brown, K.A. Crystal structure of Mycobacterium tuberculosis catalase-peroxidase. J. Biol. Chem. 279 (2004) 38991-38999. [PMID: 15231843]

5. Vlasits, J., Jakopitsch, C., Bernroitner, M., Zamocky, M., Furtmuller, P.G. and Obinger, C. Mechanisms of catalase activity of heme peroxidases. Arch. Biochem. Biophys. 500 (2010) 74-81. [PMID: 20434429]

[EC 1.11.1.21 created 2011]

EC 1.12.1.4

Accepted name: hydrogenase (NAD+, ferredoxin)

Reaction: 2 H2 + NAD+ + 2 oxidized ferredoxin = 5 H+ + NADH + 2 reduced ferredoxin

Other name(s): bifurcating [FeFe] hydrogenase

Systematic name: hydrogen:NAD+, ferredoxin oxidoreductase

Comments: The enzyme from Thermotoga maritima contains a [FeFe] cluster (H-cluster) and iron-sulfur clusters. It works in the direction evolving hydrogen as a means of eliminating excess reducing equivalents.

References:

1. Verhagen, M.F., O'Rourke, T. and Adams, M.W. The hyperthermophilic bacterium, Thermotoga maritima, contains an unusually complex iron-hydrogenase: amino acid sequence analyses versus biochemical characterization. Biochim. Biophys. Acta 1412 (1999) 212-229. [PMID: 10482784]

2. Schut, G.J. and Adams, M.W. The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production. J. Bacteriol. 191 (2009) 4451-4457. [PMID: 19411328]

[EC 1.12.1.4 created 2011]

*EC 1.13.11.12

Accepted name: linoleate 13S-lipoxygenase

Reaction: linoleate + O2 = (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate

Other name(s): 13-lipoxidase; carotene oxidase; 13-lipoperoxidase; fat oxidase; 13-lipoxydase; lionoleate:O2 13-oxidoreductase

Systematic name: linoleate:oxygen 13-oxidoreductase

Comments: Contains nonheme iron. A common plant lipoxygenase that oxidizes linoleate and α-linolenate, the two most common polyunsaturated fatty acids in plants, by inserting molecular oxygen at the C13 position with (S)-configuration. This enzyme produces precursors for several important compounds, including the plant hormone jasmonic acid. EC 1.13.11.58, linoleate 9S-lipoxygenase, catalyses a similar reaction at the second available position of these fatty acids.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9029-60-1

References:

1. Christopher, J., Pistorius, E. and Axelrod, B. Isolation of an enzyme of soybean lipoxidase. Biochim. Biophys. Acta 198 (1970) 12-19. [PMID: 5461103]

2. Theorell, H., Holman, R.T. and Åkesson, Å. Crystalline lipoxidase. Acta Chem. Scand. 1 (1947) 571-576. [PMID: 18907700]

3. Zimmerman, D.C. Specificity of flaxseed lipoxidase. Lipids 5 (1970) 392-397. [PMID: 5447012]

4. Royo, J., Vancanneyt, G., Perez, A.G., Sanz, C., Stormann, K., Rosahl, S. and Sanchez-Serrano, J.J. Characterization of three potato lipoxygenases with distinct enzymatic activities and different organ-specific and wound-regulated expression patterns. J. Biol. Chem. 271 (1996) 21012-21019. [PMID: 8702864]

5. Bachmann, A., Hause, B., Maucher, H., Garbe, E., Voros, K., Weichert, H., Wasternack, C. and Feussner, I. Jasmonate-induced lipid peroxidation in barley leaves initiated by distinct 13-LOX forms of chloroplasts. Biol. Chem. 383 (2002) 1645-1657. [PMID: 12452441]

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

EC 1.13.11.57

Accepted name: gallate dioxygenase

Reaction: gallate + O2 = (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate

Other name(s): GalA

Systematic name: gallate:oxygen oxidoreductase

Comments: Contains non-heme Fe2+. The enzyme is a ring-cleavage dioxygenase that acts specifically on gallate to produce the keto-tautomer of 4-oxalomesaconate [1,2].

References:

1. Nogales, J., Canales, A., Jiménez-Barbero, J., García, J.L. and Díaz, E. Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440. The prototype of a new subgroup of extradiol dioxygenases. J. Biol. Chem. 280 (2005) 35382-35390. [PMID: 16030014]

2. Nogales, J., Canales, A., Jimenez-Barbero, J., Serra, B., Pingarron, J.M., Garcia, J.L. and Diaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359-374. [PMID: 21219457]

[EC 1.13.11.57 created 2011]

EC 1.13.11.58

Accepted name: linoleate 9S-lipoxygenase

Reaction: linoleate + O2 = (9S,10E,12Z)-9-hydroperoxy-10,12-octadecadienoate

Glossary: linoleate = (9Z,12Z)-octadeca-9,12-dienoate

Other name(s): 9-lipoxygenase; 9S-lipoxygenase; linoleate 9-lipoxygenase; LOX1 (gene name); 9S-LOX

Systematic name: linoleate:oxygen 9S-oxidoreductase

Comments: Contains nonheme iron. A common plant lipoxygenase that oxidizes linoleate and α-linolenate, the two most common polyunsaturated fatty acids in plants, by inserting molecular oxygen at the C9 position with (S)-configuration. The enzyme plays a physiological role during the early stages of seedling growth. The enzyme from Arabidopsis thaliana shows comparable activity towards linoleate and linolenate [4]. EC 1.13.11.12 (linoleate 13S-lipoxygenase) catalyses a similar reaction at another position of these fatty acids.

References:

1. Vellosillo, T., Martinez, M., Lopez, M.A., Vicente, J., Cascon, T., Dolan, L., Hamberg, M. and Castresana, C. Oxylipins produced by the 9-lipoxygenase pathway in Arabidopsis regulate lateral root development and defense responses through a specific signaling cascade. Plant Cell 19 (2007) 831-846. [PMID: 17369372]

2. Boeglin, W.E., Itoh, A., Zheng, Y., Coffa, G., Howe, G.A. and Brash, A.R. Investigation of substrate binding and product stereochemistry issues in two linoleate 9-lipoxygenases. Lipids 43 (2008) 979-987. [PMID: 18795358]

3. Andreou, A.Z., Hornung, E., Kunze, S., Rosahl, S. and Feussner, I. On the substrate binding of linoleate 9-lipoxygenases. Lipids 44 (2009) 207-215. [PMID: 19037675]

4. Bannenberg, G., Martinez, M., Hamberg, M. and Castresana, C. Diversity of the enzymatic activity in the lipoxygenase gene family of Arabidopsis thaliana. Lipids 44 (2009) 85-95. [PMID: 18949503]

[EC 1.13.11.58 created 2011]

EC 1.14.11.33

Accepted name: DNA oxidative demethylase

Reaction: DNA-base-CH3 + 2-oxoglutarate + O2 = DNA-base + formaldehyde + succinate + CO2

Other name(s): alkylated DNA repair protein; α-ketoglutarate-dependent dioxygenase ABH1; alkB (gene name)

Systematic name: Methyl DNA-base, 2-oxoglutarate:oxygen oxidoreductase (formaldehyde-forming)

Comments: Contains iron; activity is slightly stimulated by ascorbate. Catalyses oxidative demethylation of the DNA base lesions N1-methyladenine, N3-methylcytosine, N1-methylguanine, and N3-methylthymine. It works better on single-stranded DNA (ssDNA) and is capable of repairing damaged bases in RNA.

References:

1. Falnes, P.O., Johansen, R.F. and Seeberg, E. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419 (2002) 178-182. [PMID: 12226668]

2. Yi, C., Yang, C.G. and He, C. A non-heme iron-mediated chemical demethylation in DNA and RNA. Acc. Chem. Res. 42 (2009) 519-529. [PMID: 19852088]

3. Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.G., Cui, Q. and He, C. Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature 468 (2010) 330-333. [PMID: 21068844]

[EC 1.14.11.33 created 2011]

*EC 1.14.13.25

Accepted name: methane monooxygenase (soluble)

Reaction: methane + NAD(P)H + H+ + O2 = methanol + NAD(P)+ + H2O

Other name(s): methane hydroxylase

Systematic name: methane,NAD(P)H:oxygen oxidoreductase (hydroxylating)

Comments: The enzyme is soluble, in contrast to the particulate enzyme, EC 1.14.18.3. Broad specificity; many alkanes can be hydroxylated, and alkenes are converted into the corresponding epoxides; CO is oxidized to CO2, ammonia is oxidized to hydroxylamine, and some aromatic compounds and cyclic alkanes can also be hydroxylated, but more slowly.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, UM-BBD, CAS registry number: 51961-97-8

References:

1. Colby, J. Stirling, D.I. and Dalton, H. The soluble methane mono-oxygenase of Methylococcus capsulatus (Bath). Its ability to oxygenate n-alkanes, n-alkenes, ethers, and alicyclic, aromatic and heterocyclic compounds. Biochem. J. 165 (1977) 395-402. [PMID: 411486]

2. Hyman, M.R. and Wood, P.M. Methane oxidation by Nitrosomonas europaea. Biochem. J. 212 (1983) 31-37. [PMID: 6870854]

3. Stirling, D.I. and Dalton, H. Properties of the methane mono-oxygenase from extracts of Methylosinus trichosporium OB3b and evidence for its similarity to the enzyme from Methylococcus capsulatus (Bath). Eur. J. Biochem. 96 (1979) 205-212. [PMID: 572296]

4. Tonge, G.M., Harrison, D.E.F. and Higgins, I.J. Purification and properties of the methane mono-oxygenase enzyme system from Methylosinus trichosporium OB3b. Biochem. J. 161 (1977) 333-344. [PMID: 15544]

[EC 1.14.13.25 created 1984, modified 2011]

[EC 1.14.13.42 Deleted entry: hydroxyphenylacetonitrile 2-monooxygenase. The activity is covered by EC 1.14.13.68, 4-hydroxyphenylacetaldehyde oxime monooxygenase, that performs the two consecutive reactions in the conversion of (Z)-4-hydroxyphenylacetaldehyde oxime to (S)-4-hydroxymandelonitrile (EC 1.14.13.42 created 1992, deleted 2011)]

EC 1.14.13.123

Accepted name: germacrene A hydroxylase

Reaction: (+)-germacrene A + NADPH + H+ + O2 = germacra-1(10),4,11(13)-trien-12-ol + NADP+ + H2O

For diagram of reaction click here.

Systematic name: (+)-germacrene-A,NADPH:oxygen oxidoreductase (12-hydroxylating)

Comments: A heme-thiolate protein (P-450). This is probably part of the biosynthesis of many sesquiterpenoid lactones. In Lactuca sativa EC 1.14.13.213 is a mutifunctional enzyme with EC 1.1.1.314, germacrene A alcohol dehydrogenase [2].

References:

1. de Kraker, J.W., Franssen, M.C., Dalm, M.C., de Groot, A. and Bouwmeester, H.J. Biosynthesis of germacrene A carboxylic acid in chicory roots. Demonstration of a cytochrome P450 (+)-germacrene A hydroxylase and NADP+-dependent sesquiterpenoid dehydrogenase(s) involved in sesquiterpene lactone biosynthesis. Plant Physiol. 125 (2001) 1930-1940. [PMID: 11299372]

2. Nguyen, D.T., Gopfert, J.C., Ikezawa, N., Macnevin, G., Kathiresan, M., Conrad, J., Spring, O. and Ro, D.K. Biochemical conservation and evolution of germacrene A oxidase in asteraceae. J. Biol. Chem. 285 (2010) 16588-16598. [PMID: 20351109]

[EC 1.14.13.123 created 2011]

EC 1.14.13.124

Accepted name: phenylalanine N-monooxygenase

Reaction: L-phenylalanine + 2 O2 + 2 NADPH + 2 H+ = (E)-phenylacetaldoxime + 2 NADP+ + CO2 + 3 H2O (overall reaction)
(1a) L-phenylalanine + O2 + NADPH + H+ = N-hydroxy-L-phenylalanine + NADP+ + H2O
(1b) N-hydroxy-L-phenylalanine + O2 + NADPH + H+ = N,N-dihydroxy-L-phenylalanine + NADP+ + H2O
(1c) N,N-dihydroxy-L-phenylalanine = (E)-phenylacetaldoxime + CO2 + H2O

Other name(s): phenylalanine N-hydroxylase; CYP79A2

Systematic name: L-phenylalanine,NADPH:oxygen oxidoreductase (N-hydroxylating)

Comments: A heme-thiolate protein (P-450). This enzyme catalyses two successive N-hydroxylations of L-phenylalanine, the first committed steps in the biosynthesis of benzylglucosinolate. The product of the two hydroxylations, N,N-dihydroxy-L-phenylalanine, is extremely labile and dehydrates spontaneously.The dehydrated product is then subject to a decarboxylation that produces the oxime. It is still not known whether the decarboxylation is spontaneous or catalysed by the enzyme. The product, (E)-phenylacetaldoxime, undergoes a spontaneous isomerization to the (Z) form.

References:

1. Wittstock, U. and Halkier, B.A. Cytochrome P450 CYP79A2 from Arabidopsis thaliana L. Catalyzes the conversion of L-phenylalanine to phenylacetaldoxime in the biosynthesis of benzylglucosinolate. J. Biol. Chem. 275 (2000) 14659-14666. [PMID: 10799553]

[EC 1.14.13.124 created 2011]

EC 1.14.13.125

Accepted name: tryptophan N-monooxygenase

Reaction: L-tryptophan + 2 O2 + 2 NADPH + 2 H+ = (E)-indol-3-ylacetaldoxime + 2 NADP+ + CO2 + 3 H2O (overall reaction)
(1a) L-tryptophan + O2 + NADPH + H+ = N-hydroxy-L-tryptophan + NADP+ + H2O
(1b) N-hydroxy-L-tryptophan + O2 + NADPH + H+ = N,N-dihydroxy-L-tryptophan + NADP+ + H2O
(1c) N,N-dihydroxy-L-tryptophan = (E)-indol-3-ylacetaldoxime + CO2 + H2O

Other name(s): tryptophan N-hydroxylase; CYP79B1; CYP79B2; CYP79B3

Systematic name: L-tryptophan,NADPH:oxygen oxidoreductase (N-hydroxylating)

Comments: A heme-thiolate protein (P-450). This enzyme catalyses two successive N-hydroxylations of L-tryptophan, the first steps in the biosynthesis of the both auxin and the indole alkaloid phytoalexin camalexin. The product of the two hydroxylations, N,N-dihydroxy-L-tryptophan, is extremely labile and dehydrates spontaneously.The dehydrated product is then subject to a decarboxylation that produces the oxime. It is still not known whether the decarboxylation is spontaneous or catalysed by the enzyme. The product, (E)-indol-3-ylacetaldoxime, undergoes a spontaneous isomerization to the (Z) form.

References:

1. Mikkelsen, M.D., Hansen, C.H., Wittstock, U. and Halkier, B.A. Cytochrome P450 CYP79B2 from Arabidopsis catalyzes the conversion of tryptophan to indole-3-acetaldoxime, a precursor of indole glucosinolates and indole-3-acetic acid. J. Biol. Chem. 275 (2000) 33712-33717. [PMID: 10922360]

2. Hull, A.K., Vij, R. and Celenza, J.L. Arabidopsis cytochrome P450s that catalyze the first step of tryptophan-dependent indole-3-acetic acid biosynthesis. Proc. Natl. Acad. Sci. USA 97 (2000) 2379-2384. [PMID: 10681464]

3. Zhao, Y., Hull, A.K., Gupta, N.R., Goss, K.A., Alonso, J., Ecker, J.R., Normanly, J., Chory, J. and Celenza, J.L. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes Dev. 16 (2002) 3100-3112. [PMID: 12464638]

4. Naur, P., Hansen, C.H., Bak, S., Hansen, B.G., Jensen, N.B., Nielsen, H.L. and Halkier, B.A. CYP79B1 from Sinapis alba converts tryptophan to indole-3-acetaldoxime. Arch. Biochem. Biophys. 409 (2003) 235-241. [PMID: 12464264]

[EC 1.14.13.125 created 2011]

EC 1.14.13.126

Accepted name: vitamin D3 24-hydroxylase

Reaction: (1) calcitriol + NADPH + H+ + O2 = calcitetrol + NADP+ + H2O
(2) calcidiol + NADPH + H+ + O2 = secalciferol + NADP+ + H2O

Glossary: calcidiol = 25-hydroxyvitamin D3
calcitriol = 1α,25-dihydroxyvitamin D3
calcitetrol = 1α,24R,25-trihydroxyvitamin D3
secalciferol = (24R)-24,25-dihydroxycalciol = 24R,25-dihydroxyvitamin D3

Other name(s): CYP24A1

Systematic name: calcitriol,NADPH:oxygen oxidoreductase (24-hydroxylating)

Comments: A heme-thiolate enzyme (P-450). The second donor, NADPH, donates electrons through EC 1.18.1.2, ferredoxin—NADP+ reductase and a [2Fe-2S] ferredoxin. The enzyme can perform up to 6 rounds of hydroxylation of the substrate calcitriol leading to calcitroic acid. The human enzyme also shows 23-hydroxylating activity leading to 1,25 dihydroxyvitamin D3-26,23-lactone as end product while the mouse and rat enzymes do not.

References:

1. Masuda, S., Strugnell, S.A., Knutson, J.C., St-Arnaud, R. and Jones, G. Evidence for the activation of 1α-hydroxyvitamin D2 by 25-hydroxyvitamin D-24-hydroxylase: delineation of pathways involving 1α,24-dihydroxyvitamin D2 and 1α,25-dihydroxyvitamin D2. Biochim. Biophys. Acta 1761 (2006) 221-234. [PMID: 16516540]

2. Hamamoto, H., Kusudo, T., Urushino, N., Masuno, H., Yamamoto, K., Yamada, S., Kamakura, M., Ohta, M., Inouye, K. and Sakaki, T. Structure-function analysis of vitamin D 24-hydroxylase (CYP24A1) by site-directed mutagenesis: amino acid residues responsible for species-based difference of CYP24A1 between humans and rats. Mol. Pharmacol. 70 (2006) 120-128. [PMID: 16617161]

3. Sakaki, T., Kagawa, N., Yamamoto, K. and Inouye, K. Metabolism of vitamin D3 by cytochromes P450. Front. Biosci. 10 (2005) 119-134. [PMID: 15574355]

4. Prosser, D.E., Kaufmann, M., O'Leary, B., Byford, V. and Jones, G. Single A326G mutation converts human CYP24A1 from 25-OH-D3-24-hydroxylase into -23-hydroxylase, generating 1α,25-(OH)2D3-26,23-lactone. Proc. Natl. Acad. Sci. USA 104 (2007) 12673-12678. [PMID: 17646648]

5. Kusudo, T., Sakaki, T., Abe, D., Fujishima, T., Kittaka, A., Takayama, H., Hatakeyama, S., Ohta, M. and Inouye, K. Metabolism of A-ring diastereomers of 1α,25-dihydroxyvitamin D3 by CYP24A1. Biochem. Biophys. Res. Commun. 321 (2004) 774-782. [PMID: 15358094]

6. Sawada, N., Kusudo, T., Sakaki, T., Hatakeyama, S., Hanada, M., Abe, D., Kamao, M., Okano, T., Ohta, M. and Inouye, K. Novel metabolism of 1 α,25-dihydroxyvitamin D3 with C24-C25 bond cleavage catalyzed by human CYP24A1. Biochemistry 43 (2004) 4530-4537. [PMID: 15078099]

7. Prosser, D.E. and Jones, G. Enzymes involved in the activation and inactivation of vitamin D. Trends Biochem. Sci. 29 (2004) 664-673. [PMID: 15544953]

[EC 1.14.13.126 created 2011]

EC 1.14.13.127

Accepted name: 3-(3-hydroxyphenyl)propanoate hydroxylase

Reaction: (1) 3-(3-hydroxyphenyl)propanoate + NADH + H+ + O2 = 3-(2,3-dihydroxyphenyl)propanoate + H2O + NAD+
(2) (2E)-3-(3-hydroxyphenyl)prop-2-enoate + NADH + H+ + O2 = (2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate + H2O + NAD+

Glossary: 3-hydroxycinnamate = 3-coumarate = 3-(3-hydroxyphenyl)prop-2-enoate

Other name(s): mhpA (gene name)

Systematic name: 3-(3-hydroxyphenyl)propanoate,NADH:oxygen oxidoreductase (2-hydroxylating)

Comments: A flavoprotein (FAD). This enzyme participates in a meta-cleavage pathway employed by the bacterium Escherichia coli for the degradation of various phenylpropanoid compounds.

References:

1. Burlingame, R. and Chapman, P.J. Catabolism of phenylpropionic acid and its 3-hydroxy derivative by Escherichia coli. J. Bacteriol. 155 (1983) 113-121. [PMID: 6345502]

2. Burlingame, R.P., Wyman, L. and Chapman, P.J. Isolation and characterization of Escherichia coli mutants defective for phenylpropionate degradation. J. Bacteriol. 168 (1986) 55-64. [PMID: 3531186]

3. Ferrández, A., García, J.L. and Díaz, E. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12. J. Bacteriol. 179 (1997) 2573-2581. [PMID: 9098055]

4. Díaz, E., Ferrández, A. and García, J.L. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180 (1998) 2915-2923. [PMID: 9603882]

[EC 1.14.13.127 created 2011]

EC 1.14.13.128

Accepted name: 7-methylxanthine demethylase

Reaction: 7-methylxanthine + O2 + NAD(P)H + H+ = xanthine + NAD(P)+ + H2O + formaldehyde

Systematic name: 7-methylxanthine:oxygen oxidoreductase (demethylating)

Comments: A non-heme iron oxygenase. NADH is the preferred cofactor. Part of the caffeine degradation pathway in Pseudomonas putida. Also demethylates 1,7-dimethylxanthine (paraxanthine), theobromine, 3-methylxanthine, and caffeine with lower efficiency.

References:

1. Summers, R.M., Louie, T.M., Yu, C.L. and Subramanian, M. Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source. Microbiology 157 (2011) 583-592. [PMID: 20966097]

[EC 1.14.13.128 created 2011]

EC 1.14.13.129

Accepted name: β-carotene 3-hydroxylase

Reaction: β-carotene + 2 NADH + 2 H+ + 2 O2 = zeaxanthin + 2 NAD+ + 2 H2O (overall reaction)
(1a) β-carotene + NADH + H+ + O2 = β-cryptoxanthin + NAD+ + H2O
(1b) β-cryptoxanthin + NADH + H+ + O2 = zeaxanthin + NAD+ + H2O

For diagram of reaction click here and another example.

Other name(s): β-carotene 3,3'-monooxygenase; CrtZ

Systematic name: β-carotene,NADH:oxygen 3-oxidoreductase

Comments: Requires ferredoxin and Fe(II). Also acts on other carotenoids with a β-end group. In some species canthaxanthin is the preferred substrate.

References:

1. Sun, Z., Gantt, E. and Cunningham, F.X., Jr. Cloning and functional analysis of the β-carotene hydroxylase of Arabidopsis thaliana. J. Biol. Chem. 271 (1996) 24349-24352. [PMID: 8798688]

2. Fraser, P.D., Miura, Y. and Misawa, N. In vitro characterization of astaxanthin biosynthetic enzymes. J. Biol. Chem. 272 (1997) 6128-6135. [PMID: 9045623]

3. Fraser, P.D., Shimada, H. and Misawa, N. Enzymic confirmation of reactions involved in routes to astaxanthin formation, elucidated using a direct substrate in vitro assay. Eur. J. Biochem. 252 (1998) 229-236. [PMID: 9523693]

4. Bouvier, F., Keller, Y., d'Harlingue, A. and Camara, B. Xanthophyll biosynthesis: molecular and functional characterization of carotenoid hydroxylases from pepper fruits (Capsicum annuum L.). Biochim. Biophys. Acta 1391 (1998) 320-328. [PMID: 9555077]

5. Linden, H. Carotenoid hydroxylase from Haematococcus pluvialis: cDNA sequence, regulation and functional complementation. Biochim. Biophys. Acta 1446 (1999) 203-212. [PMID: 10524195]

6. Zhu, C., Yamamura, S., Nishihara, M., Koiwa, H. and Sandmann, G. cDNAs for the synthesis of cyclic carotenoids in petals of Gentiana lutea and their regulation during flower development. Biochim. Biophys. Acta 1625 (2003) 305-308. [PMID: 12591618]

7. Choi, S.K., Matsuda, S., Hoshino, T., Peng, X. and Misawa, N. Characterization of bacterial β-carotene 3,3'-hydroxylases, CrtZ, and P450 in astaxanthin biosynthetic pathway and adonirubin production by gene combination in Escherichia coli. Appl. Microbiol. Biotechnol. 72 (2006) 1238-1246. [PMID: 16614859]

[EC 1.14.13.129 created 2011]

EC 1.14.13.130

Accepted name: pyrrole-2-carboxylate monooxygenase

Reaction: pyrrole-2-carboxylate + NADH + H+ + O2 = 5-hydroxypyrrole-2-carboxylate + NAD+ + H2O

Other name(s): pyrrole-2-carboxylate oxygenase

Systematic name: pyrrole-2-carboxylate,NADH:oxygen oxidoreductase (5-hydroxylating)

Comments: A flavoprotein (FAD). The enzyme initiates the degradation of pyrrole-2-carboxylate.

References:

1. Hormann, K. and Andreesen, J.R. Purification and characterization of a pyrrole-2-carboxylate oxygenase from Arthrobacter strain Py1. Biol. Chem. Hoppe-Seyler 375 (1994) 211-218. [PMID: 8011178]

2. Becker, D., Schrader, T. and Andreesen, J.R. Two-component flavin-dependent pyrrole-2-carboxylate monooxygenase from Rhodococcus sp. Eur. J. Biochem. 249 (1997) 739-747. [PMID: 9395321]

[EC 1.14.13.130 created 2011]

EC 1.14.18.3

Accepted name: methane monooxygenase (particulate)

Reaction: methane + quinol + O2 = methanol + quinone + H2O

Systematic name: methane,quinol:oxygen oxidoreductase

Comments: Contains copper. It is membrane-bound, in contrast to the soluble methane monooxygenase (EC 1.14.13.25).

References:

1. Shiemke, A.K., Cook, S.A., Miley, T. and Singleton, P. Detergent solubilization of membrane-bound methane monooxygenase requires plastoquinol analogs as electron donors. Arch. Biochem. Biophys. 321 (1995) 421-428. [PMID: 7646068]

2. Basu, P., Katterle, B., Andersson, K.K. and Dalton, H. The membrane-associated form of methane mono-oxygenase from Methylococcus capsulatus (Bath) is a copper/iron protein. Biochem. J. 369 (2003) 417-427. [PMID: 12379148]

3. Kitmitto, A., Myronova, N., Basu, P. and Dalton, H. Characterization and structural analysis of an active particulate methane monooxygenase trimer from Methylococcus capsulatus (Bath). Biochemistry 44 (2005) 10954-10965. [PMID: 16101279]

4. Balasubramanian, R. and Rosenzweig, A.C. Structural and mechanistic insights into methane oxidation by particulate methane monooxygenase. Acc. Chem. Res. 40 (2007) 573-580. [PMID: 17444606]

[EC 1.14.18.3 created 2011]

EC 1.14.19.7

Accepted name: (S)-2-hydroxypropylphosphonic acid epoxidase

Reaction: (S)-2-hydroxypropylphosphonate + 2 NADH + O2 = (1R,2S)-epoxypropylphosphonate + 2 H2O + 2 NAD+

Glossary: (1R,2S)-epoxypropylphosphonate = fosfomycin

Other name(s): HPP epoxidase; HppE; 2-hydroxypropylphosphonic acid epoxidase; Fom4; (S)-2-hydroxypropylphosphonate epoxidase

Systematic name: (S)-2-hydroxypropylphosphonate,NADH:oxygen epoxidase

Comments: Contains one non-heme iron centre per monomer [1,5]. FMN is required to mediate the transfer of reducing equivalents from NADH to the active site iron [1]. This is the last enzyme in the biosynthetic pathway of fosfomycin, a broad-spectrum antibiotic produced by certain Streptomyces species.

References:

1. Munos, J.W., Moon, S.J., Mansoorabadi, S.O., Chang, W., Hong, L., Yan, F., Liu, A. and Liu, H.W. Purification and characterization of the epoxidase catalyzing the formation of fosfomycin from Pseudomonas syringae. Biochemistry 47 (2008) 8726-8735. [PMID: 18656958]

2. Yan, F., Moon, S.J., Liu, P., Zhao, Z., Lipscomb, J.D., Liu, A. and Liu, H.W. Determination of the substrate binding mode to the active site iron of (S)-2-hydroxypropylphosphonic acid epoxidase using 17O-enriched substrates and substrate analogues. Biochemistry 46 (2007) 12628-12638. [PMID: 17927218]

3. Hidaka, T., Goda, M., Kuzuyama, T., Takei, N., Hidaka, M. and Seto, H. Cloning and nucleotide sequence of fosfomycin biosynthetic genes of Streptomyces wedmorensis. Mol. Gen. Genet. 249 (1995) 274-280. [PMID: 7500951]

4. Liu, P., Mehn, M.P., Yan, F., Zhao, Z., Que, L., Jr. and Liu, H.W. Oxygenase activity in the self-hydroxylation of (S)-2-hydroxypropylphosphonic acid epoxidase involved in fosfomycin biosynthesis. J. Am. Chem. Soc. 126 (2004) 10306-10312. [PMID: 15315444]

5. Higgins, L.J., Yan, F., Liu, P., Liu, H.W. and Drennan, C.L. Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme. Nature 437 (2005) 838-844. [PMID: 16015285]

[EC 1.14.19.7 created 2011]

EC 1.14.99.42

Accepted name: zeaxanthin 7,8-dioxygenase

Reaction: zeaxanthin + 2 O2 = crocetin dialdehyde + 2 (3S)-3-hydroxycyclocitral

Other name(s): zeaxanthin 7,8(7',8')-cleavage dioxygenase; CsZCD

Systematic name: zeaxanthin:oxygen oxidoreductase (7,8-cleaving)

Comments: Presumably the enzyme acts twice on zeaxanthin cleaving 3-hydroxycyclocitral off each 3-hydroxy end group.

References:

1. Bouvier, F., Suire, C., Mutterer, J. and Camara, B. Oxidative remodeling of chromoplast carotenoids: identification of the carotenoid dioxygenase CsCCD and CsZCD genes involved in Crocus secondary metabolite biogenesis. Plant Cell 15 (2003) 47-62. [PMID: 12509521]

[EC 1.14.99.42 created 2011]

EC 1.14.99.43

Accepted name: β-amyrin 24-hydroxylase

Reaction: (1) β-amyrin + AH2 + O2 = 24-hydroxy-β-amyrin + A + H2O
(2) sophoradiol + AH2 + O2 = 24-hydroxysophoradiol + A + H2O

Glossary: 24-hydroxy-β-amyrin = olean-12-ene-3β,24-diol
24-hydroxysophoradiol = soyasapogenol B

Other name(s): sophoradiol 24-hydroxylase; CYP93E1

Systematic name: β-amyrin,AH2:oxygen oxidoreductase (24-hydroxylating)

Comments: A heme-thiolate protein (P-450).

References:

1. Shibuya, M., Hoshino, M., Katsube, Y., Hayashi, H., Kushiro, T. and Ebizuka, Y. Identification of β-amyrin and sophoradiol 24-hydroxylase by expressed sequence tag mining and functional expression assay. FEBS J. 273 (2006) 948-959. [PMID: 16478469]

[EC 1.14.99.43 created 2011]

EC 1.14.99.44

Accepted name: diapolycopene oxygenase

Reaction: 4,4'-diapolycopene + 4 AH2 + 4 O2 = 4,4'-diapolycopenedial + 4 A + 6 H2O

Other name(s): crtP (ambiguous)

Systematic name: 4,4'-diapolycopene,AH2:oxygen oxidoreductase (4,4'-hydroxylating)

Comments: Little activity with neurosporene or lycopene. Involved in the biosynthesis of C30 carotenoids such as staphyloxanthin. The enzyme oxidizes each methyl group to the hydroxymethyl and then a dihydroxymethyl group, followed by the spontaneous loss of water to give an aldehyde group.

References:

1. Mijts, B.N., Lee, P.C. and Schmidt-Dannert, C. Identification of a carotenoid oxygenase synthesizing acyclic xanthophylls: combinatorial biosynthesis and directed evolution. Chem. Biol. 12 (2005) 453-460. [PMID: 15850982]

2. Tao, L., Schenzle, A., Odom, J.M. and Cheng, Q. Novel carotenoid oxidase involved in biosynthesis of 4,4'-diapolycopene dialdehyde. Appl. Environ. Microbiol. 71 (2005) 3294-3301. [PMID: 15933032]

[EC 1.14.99.44 created 2011]

EC 1.14.99.45

Accepted name: carotene ε-monooxygenase

Reaction: α-carotene + O2 + AH2 = α-cryptoxanthin + A + H2O

For diagram of reaction click here.

Other name(s): CYP97C1; LUT1

Systematic name: α-carotene:oxygen oxidoreductase (3-hydroxylating)

Comments: A heme-thiolate protein (P450). Also acts on zeinoxanthin to give lutein.

References:

1. Pogson, B., McDonald, K.A., Truong, M., Britton, G. and DellaPenna, D. Arabidopsis carotenoid mutants demonstrate that lutein is not essential for photosynthesis in higher plants. Plant Cell 8 (1996) 1627-1639. [PMID: 8837513]

2. Tian, L., Musetti, V., Kim, J., Magallanes-Lundback, M. and DellaPenna, D. The Arabidopsis LUT1 locus encodes a member of the cytochrome P450 family that is required for carotenoid ε-ring hydroxylation activity. Proc. Natl. Acad. Sci. USA 101 (2004) 402-407. [PMID: 14709673]

[EC 1.14.99.45 created 2011]

*EC 1.16.3.1

Accepted name: ferroxidase

Reaction: 4 Fe(II) + 4 H+ + O2 = 4 Fe(III) + 2 H2O

Other name(s): ceruloplasmin; caeruloplasmin; ferroxidase I; iron oxidase, iron(II):oxygen oxidoreductase; ferro:O2 oxidoreductase; iron II:oxygen oxidoreductase; hephaestin; HEPH

Systematic name: Fe(II):oxygen oxidoreductase

Comments: The enzyme in blood plasma (ceruloplasmin) belongs to the family of multicopper oxidases. In humans it accounts for 95% of plasma copper. It oxidizes Fe(II) to Fe(III), which allows the subsequent incorporation of the latter into proteins such as apotransferrin and lactoferrin. An enzyme from iron oxidizing bacterium strain TI-1 contains heme a.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9031-37-2, 104404-69-5

References:

1. Osaki, S. Kinetic studies of ferrous ion oxidation with crystalline human ferroxidase (ceruloplasmin). J. Biol. Chem. 241 (1966) 5053-5059. [PMID: 5925868]

2. Osaki, S. and Walaas, O. Kinetic studies of ferrous ion oxidation with crystalline human ferroxidase. II. Rate constants at various steps and formation of a possible enzyme-substrate complex. J. Biol. Chem. 242 (1967) 2653-2657. [PMID: 6027241]

3. Lindley, P.F. Card, G. Zaitseva, I. Zaitsev, V. Reinhammar, B. SelinLindgren, E. and Yoshida, K. An X-ray structural study of human ceruloplasmin in relation to ferroxidase activity. J. Biol. Inorg. Chem. 2 (1997) 454-463.

4. Takai, M., Kamimura, K. and Sugio, T. A new iron oxidase from a moderately thermophilic iron oxidizing bacterium strain TI-1. Eur. J. Biochem. 268 (2001) 1653-1658. [PMID: 11248684]

5. Chen, H., Attieh, Z.K., Su, T., Syed, B.A., Gao, H., Alaeddine, R.M., Fox, T.C., Usta, J., Naylor, C.E., Evans, R.W., McKie, A.T., Anderson, G.J. and Vulpe, C.D. Hephaestin is a ferroxidase that maintains partial activity in sex-linked anemia mice. Blood 103 (2004) 3933-3939. [PMID: 14751926]

[EC 1.16.3.1 created 1972, modified 2011]

EC 1.16.5 With quinone or similar compound as acceptor
EC 1.16.5.1

Accepted name: ascorbate ferrireductase (transmembrane)

Reaction: ascorbate[side 1] + Fe(III)[side 2] = monodehydroascorbate[side 1] + Fe(II)[side 2]

Other name(s): cytochrome b561 (ambiguous)

Systematic name: Fe(III):ascorbate oxidorectuctase (electron-translocating)

Comments: A diheme cytochrome that transfers electrons across a single membrane, such as the outer membrane of the enterocyte, or the tonoplast membrane of the plant cell vacuole. Acts on hexacyanoferrate(III) and other ferric chelates.

References:

1. Flatmark, T. and Terland, O. Cytochrome b561 of the bovine adrenal chromaffin granules. A high potential b-type cytochrome. Biochim. Biophys. Acta 253 (1971) 487-491. [PMID: 4332308]

2. McKie, A.T., Barrow, D., Latunde-Dada, G.O., Rolfs, A., Sager, G., Mudaly, E., Mudaly, M., Richardson, C., Barlow, D., Bomford, A., Peters, T.J., Raja, K.B., Shirali, S., Hediger, M.A., Farzaneh, F. and Simpson, R.J. An iron-regulated ferric reductase associated with the absorption of dietary iron. Science 291 (2001) 1755-1759. [PMID: 11230685]

3. Su, D. and Asard, H. Three mammalian cytochromes b561 are ascorbate-dependent ferrireductases. FEBS J. 273 (2006) 3722-3734. [PMID: 16911521]

4. Berczi, A., Su, D. and Asard, H. An Arabidopsis cytochrome b561 with trans-membrane ferrireductase capability. FEBS Lett. 581 (2007) 1505-1508. [PMID: 17376442]

5. Wyman, S., Simpson, R.J., McKie, A.T. and Sharp, P.A. Dcytb (Cybrd1) functions as both a ferric and a cupric reductase in vitro. FEBS Lett. 582 (2008) 1901-1906. [PMID: 18498772]

6. Glanfield, A., McManus, D.P., Smyth, D.J., Lovas, E.M., Loukas, A., Gobert, G.N. and Jones, M.K. A cytochrome b561 with ferric reductase activity from the parasitic blood fluke, Schistosoma japonicum. PLoS Negl. Trop. Dis. 4 (2010) e884. [PMID: 21103361]

[EC 1.16.5.1 created 2011]

EC 1.16.98.1

Accepted name: iron:rusticyanin reductase

Reaction: Fe(II) + rusticyanin = Fe(III) + reduced rusticyanin

Other name(s): Cyc2

Systematic name: Fe(II):rusticyanin oxidoreductase

Comments: Contains c-type heme, The enzyme in Acidithiobacillus ferrooxidans is a component of an electron transfer chain from Fe(II), comprising this enzyme, the copper protein rusticyanin, cytochrome c4, and cytochrome c oxidase (EC 1.9.3.1)

References:

1. Blake, R.C., 2nd and Shute, E.A. Respiratory enzymes of Thiobacillus ferrooxidans. Kinetic properties of an acid-stable iron:rusticyanin oxidoreductase. Biochemistry 33 (1994) 9220-9228. [PMID: 8049223]

2. Appia-Ayme, C., Bengrine, A., Cavazza, C., Giudici-Orticoni, M.T., Bruschi, M., Chippaux, M. and Bonnefoy, V. Characterization and expression of the co-transcribed cyc1 and cyc2 genes encoding the cytochrome c4 (c552) and a high-molecular-mass cytochrome c from Thiobacillus ferrooxidans ATCC 33020. FEMS Microbiol. Lett. 167 (1998) 171-177. [PMID: 9809418]

3. Yarzabal, A., Brasseur, G., Ratouchniak, J., Lund, K., Lemesle-Meunier, D., DeMoss, J.A. and Bonnefoy, V. The high-molecular-weight cytochrome c Cyc2 of Acidithiobacillus ferrooxidans is an outer membrane protein. J. Bacteriol. 184 (2002) 313-317. [PMID: 11741873]

4. Yarzabal, A., Appia-Ayme, C., Ratouchniak, J. and Bonnefoy, V. Regulation of the expression of the Acidithiobacillus ferrooxidans rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin. Microbiology 150 (2004) 2113-2123. [PMID: 15256554]

5. Taha, T.M., Kanao, T., Takeuchi, F. and Sugio, T. Reconstitution of iron oxidase from sulfur-grown Acidithiobacillus ferrooxidans. Appl. Environ. Microbiol. 74 (2008) 6808-6810. [PMID: 18791023]

6. Castelle, C., Guiral, M., Malarte, G., Ledgham, F., Leroy, G., Brugna, M. and Giudici-Orticoni, M.T. A new iron-oxidizing/O2-reducing supercomplex spanning both inner and outer membranes, isolated from the extreme acidophile Acidithiobacillus ferrooxidans. J. Biol. Chem. 283 (2008) 25803-25811. [PMID: 18632666]

7. Quatrini, R., Appia-Ayme, C., Denis, Y., Jedlicki, E., Holmes, D.S. and Bonnefoy, V. Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. BMC Genomics 10 (2009) 394. [PMID: 19703284]

[EC 1.16.98.1 created 2011]

*EC 1.18.1.3

Accepted name: ferredoxin—NAD+ reductase

Reaction: (1) 2 reduced [2Fe-2S] ferredoxin + NAD+ + H+ = 2 oxidized [2Fe-2S] ferredoxin + NADH
(2) reduced 2[4Fe-4S] ferredoxin + NAD+ + H+ = oxidized 2[4Fe-4S] ferredoxin + NADH

Glossary: ferredoxin

Other name(s): ferredoxin-nicotinamide adenine dinucleotide reductase; ferredoxin reductase; NAD+-ferredoxin reductase; NADH-ferredoxin oxidoreductase; reductase, reduced nicotinamide adenine dinucleotide-ferredoxin; ferredoxin-NAD+ reductase; NADH-ferredoxin reductase; NADH2-ferredoxin oxidoreductase; NADH flavodoxin oxidoreductase; NADH-ferredoxinNAP reductase (component of naphthalene dioxygenase multicomponent enzyme system); ferredoxin-linked NAD+ reductase; NADH-ferredoxinTOL reductase (component of toluene dioxygenase); ferredoxin—NAD reductase

Systematic name: ferredoxin:NAD+ oxidoreductase

Comments: Contains FAD. Reaction (1) is written for a [2Fe-2S] ferredoxin, which is characteristic of some mono- and dioxygenase systems. The alternative reaction (2) is written for a 2[4Fe-4S] ferredoxin, which transfers two electrons, and occurs in metabolism of anaerobic bacteria.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 39369-37-4

References:

1. Jungerman, K., Thauer, R.F., Leimenstoll, G. and Decker, K. Function of reduced pyridine nucleotide-ferredoxin oxidoreductases in saccharolytic Clostridia. Biochim. Biophys. Acta 305 (1973) 268-280. [PMID: 4147457]

2. Haigler, B.E. and Gibson, D.T. Purification and properties of NADH-ferredoxinNAP reductase, a component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816. J. Bacteriol. 172 (1990) 457-464. [PMID: 2294092]

3. Ramachandra, M., Seetharam, R., Emptage, M.H. and Sariaslani, F.S. Purification and characterization of a soybean flour-inducible ferredoxin reductase of Streptomyces griseus. J. Bacteriol. 173 (1991) 7106-7112. [PMID: 1938912]

4. Shaw, J.P. and Harayama, S. Purification and characterisation of the NADH:acceptor reductase component of xylene monooxygenase encoded by the TOL plasmid pWW0 of Pseudomonas putida mt-2. Eur. J. Biochem. 209 (1992) 51-61. [PMID: 1327782]

[EC 1.18.1.3 created 1976 as EC 1.6.7.3, transferred 1978 to EC 1.18.1.3, modified 2011]

EC 1.97.7.1

Accepted name: photosystem I

Reaction: reduced plastocyanin + ferredoxin + = oxidized plastocyanin + reduced ferredoxin

Systematic name: plastocyanin:ferredoxin oxidoreductase (light-dependent)

Comments: Contains chlorophyll, phylloquinones, carotenoids and [4Fe-4S] clusters. Cytochrome c6 can act as an alternative electron donor, and flavodoxin as an alternative acceptor in some species.

References:

1. Takabe, T., Iwasaki, Y., Hibino, T. and Ando, T. Subunit composition of Photosystem I complex that catalyzes light-dependent transfer of electrons from plastocyanin to ferredoxin. J. Biochem. 110 (1991) 622-627. [PMID: 1778985]

2. van Thor, J.J., Geerlings, T.H., Matthijs, H.C. and Hellingwerf, K.J. Kinetic evidence for the PsaE-dependent transient ternary complex photosystem I/Ferredoxin/Ferredoxin:NADP+ reductase in a cyanobacterium. Biochemistry 38 (1999) 12735-12746. [PMID: 10504244]

3. Chitnis, P.R. Photosystem I: function and physiology. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52 (2001) 593-626. [PMID: 11337410]

4. Amunts, A., Toporik, H., Borovikova, A. and Nelson, N. Structure determination and improved model of plant photosystem I. J. Biol. Chem. 285 (2010) 3478-3486. [PMID: 19923216]

[EC 1.97.7.1 created 2011]

*EC 2.1.1.149

Accepted name: myricetin O-methyltransferase

Reaction: 2 S-adenosyl-L-methionine + myricetin = 2 S-adenosyl-L-homocysteine + syringetin (overall reaction)
(1a) S-adenosyl-L-methionine + myricetin = S-adenosyl-L-homocysteine + laricitrin
(1b) S-adenosyl-L-methionine + laricitrin = S-adenosyl-L-homocysteine + syringetin

For diagram of reaction click here

Glossary: myricetin = 3',4',5,5',7-pentahydroxyflavan-4-one
laricitrin = 3',4',5,7-tetrahydroxy-5'-methoxyflavan-4-one
syringetin = 4',5,7-trihydroxy-3',5'-dimethoxyflavan-4-one

Systematic name: S-adenosyl-L-methionine:myricetin O-methyltransferase

Comments: The enzyme from Catharanthus roseus (Madagascar periwinkle) is unusual as it carries out two methylations of the same substrate. Also catalyses the methylation of dihydromyricetin.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 188132-36-7

References:

1. Cacace, S., Schröder, G., Wehinger, E., Strack, D., Schmidt, J. and Schröder, J. A flavonol O-methyltransferase from Catharanthus roseus performing two sequential methylations. Phytochemistry 62 (2003) 127-137. [PMID: 12482447]

[EC 2.1.1.149 created 2003, modified 2011]

EC 2.1.1.207

Accepted name: tRNA (cytidine34-2'-O)-methyltransferase

Reaction: (1) S-adenosyl-L-methionine + cytidine34 in tRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNA
(2) S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine34 in tRNALeu = S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNALeu

Other name(s): yibK (gene name); methyltransferase yibK; TrmL; tRNA methyltransferase L; tRNA (cytidine34/5-carboxymethylaminomethyluridine34-2'-O)-methyltransferase

Systematic name: S-adenosyl-L-methionine:tRNA (cytidine34/5-carboxymethylaminomethyluridine34-2'-O)-methyltransferase

Comments: The enzyme from Escherichia coli catalyses the 2'-O-methylation of cytidine or 5-carboxymethylaminomethyluridine at the wobble position at nucleotide 34 in tRNALeuCmAA and tRNALeucmnm5UmAA. The enzyme is selective for the two tRNALeu isoacceptors and only methylates these when they present the correct anticodon loop sequence and modification pattern. Specifically, YibK requires a pyrimidine nucleoside at position 34, it has a clear preference for an adenosine at position 35, and it fails to methylate without prior addition of the N6-(isopentenyl)-2-methylthioadenosine modification at position 37.

References:

1. Benitez-Paez, A., Villarroya, M., Douthwaite, S., Gabaldon, T. and Armengod, M.E. YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA 16 (2010) 2131-2143. [PMID: 20855540]

[EC 2.1.1.207 created 2011]

EC 2.3.1.196

Accepted name: benzyl alcohol O-benzoyltransferase

Reaction: benzoyl-CoA + benzyl alcohol = benzyl benzoate + CoA

Glossary: benzyl benzoate = benzoic acid benzyl ester

Other name(s): benzoyl-CoA:benzyl alcohol benzoyltransferase; benzoyl-CoA:benzyl alcohol/phenylethanol benzoyltransferase; benzoyl-coenzyme A:benzyl alcohol benzoyltransferase; benzoyl-coenzyme A:phenylethanol benzoyltransferase

Systematic name: benzoyl-CoA:benzyl alcohol O-benzoyltransferase

Comments: The enzyme is involved in volatile benzenoid and benzoic acid biosynthesis. The enzyme from Petunia hybrida also catalyses the formation of 2-phenylethyl benzoate from benzoyl-CoA and 2-phenylethanol. The apparent catalytic efficiency of the enzyme from Petunia hybrida with benzoyl-CoA is almost 6-fold higher than with acetyl-CoA [1].

References:

1. Boatright, J., Negre, F., Chen, X., Kish, C.M., Wood, B., Peel, G., Orlova, I., Gang, D., Rhodes, D. and Dudareva, N. Understanding in vivo benzenoid metabolism in Petunia petal tissue. Plant Physiol. 135 (2004) 1993-2011. [PMID: 15286288]

2. D'Auria, J.C., Chen, F. and Pichersky, E. Characterization of an acyltransferase capable of synthesizing benzylbenzoate and other volatile esters in flowers and damaged leaves of Clarkia breweri. Plant Physiol. 130 (2002) 466-476. [PMID: 12226525]

[EC 2.3.1.196 created 2011]

EC 2.4.1.262

Accepted name: soyasapogenol glucuronosyltransferase

Reaction: UDP-glucuronate + soyasapogenol B = UDP + soyasapogenol B 3-O-D-glucuronide

Other name(s): UGASGT

Systematic name: UDP-D-glucuronate:soyasapogenol 3-O-D-glucuronosyltransferase

Comments: Requires a divalent ion, Mg2+ better than Mn2+, better than Ca2+. Also acts on soysapogenol A and E.

References:

1. Kurosawa, Y., Takahara, H. and Shiraiwa, M. UDP-glucuronic acid:soyasapogenol glucuronosyltransferase involved in saponin biosynthesis in germinating soybean seeds. Planta 215 (2002) 620-629. [PMID: 12172845]

[EC 2.4.1.262 created 2011]

EC 2.4.1.263

Accepted name: abscisate β-glucosyltransferase

Reaction: UDP-D-glucose + abscisate = UDP + β-D-glucopyranosyl abscisate

Other name(s): ABA-glucosyltransferase; ABA-GTase; AOG

Systematic name: UDP-D-glucose:abscisate β-D-glucosyltransferase

Comments: The enzyme acts better on (S)-2-trans-abscisate than the natural (S)-2-cis isomer, abscisate, or its enantiomer, the (R)-2-cis isomer.

References:

1. Xu, Z.J., Nakajima, M., Suzuki, Y. and Yamaguchi, I. Cloning and characterization of the abscisic acid-specific glucosyltransferase gene from adzuki bean seedlings. Plant Physiol. 129 (2002) 1285-1295. [PMID: 12114582]

[EC 2.4.1.263 created 2011]

*EC 2.5.1.29

Accepted name: geranylgeranyl diphosphate synthase

Reaction: (2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate

For diagram of reaction click here

Other name(s): geranylgeranyl-diphosphate synthase; geranylgeranyl pyrophosphate synthetase; geranylgeranyl-PP synthetase; farnesyltransferase; geranylgeranyl pyrophosphate synthase; farnesyltranstransferase (obsolete)

Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase

Comments: Some forms of this enzyme will also use geranyl diphosphate and dimethylallyl diphosphate as donors; it will not use larger prenyl diphosphates as efficient donors.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9032-58-0

References:

1. Sagami, H., Ishi, K. and Ogura, K. Occurrence and unusual properties of geranylgeranyl pyrophosphate synthetase of pig liver. Biochem. Int. 3 (1981) 669-675.

[EC 2.5.1.29 created 1984, modified 2011]

EC 2.7.1.170

Accepted name: anhydro-N-acetylmuramic acid kinase

Reaction: ATP + 1,6-anhydro-N-acetyl-β-muramate + H2O = ADP + N-acetyl-β-muramate 6-phosphate + H+

Other name(s): anhMurNAc kinase; AnmK

Systematic name: ATP:1,6-anhydro-N-acetylmuramate 6-phosphotransferase

Comments: This enzyme, along with EC 4.2.1.126, N-acetylmuramic acid 6-phosphate etherase, is required for the utilization of anhydro-N-acetylmuramic acid in proteobacteria. The substrate is either imported from the medium or derived from the bacterium's own cell wall murein during cell wall recycling.

References:

1. Uehara, T., Suefuji, K., Valbuena, N., Meehan, B., Donegan, M. and Park, J.T. Recycling of the anhydro-N-acetylmuramic acid derived from cell wall murein involves a two-step conversion to N-acetylglucosamine-phosphate. J. Bacteriol. 187 (2005) 3643-3649. [PMID: 15901686]

2. Uehara, T., Suefuji, K., Jaeger, T., Mayer, C. and Park, J.T. MurQ etherase is required by Escherichia coli in order to metabolize anhydro-N-acetylmuramic acid obtained either from the environment or from its own cell wall. J. Bacteriol. 188 (2006) 1660-1662. [PMID: 16452451]

[EC 2.7.1.170 created 2011]

*EC 2.8.1.6

Accepted name: biotin synthase

Reaction: dethiobiotin + [S] + 2 S-adenosyl-L-methionine = biotin + 2 L-methionine + 2 5'-deoxyadenosine

Systematic name: dethiobiotin:sulfur sulfurtransferase

Comments: The enzyme binds a [4Fe-4S] and a [2Fe-2S] cluster. In every reaction cycle, the enzyme consumes two molecules of AdoMet, each producing 5'-deoxyadenosine and a putative dethiobiotinyl carbon radical. Reaction with another equivalent of AdoMet results in abstraction of the C6 methylene pro-S hydrogen atom from 9-mercaptodethiobiotin, and the resulting carbon radical is quenched via formation of an intramolecular C-S bond, thus closing the biotin thiophane ring. The sulfur donor [S] is believed to be the [2Fe-2S] cluster, which is sacrificed in the process, so that in vitro the reaction is a single turnover. In vivo, the [2Fe-2S] cluster can be reassembled by the Isc or Suf iron-sulfur cluster assembly systems, to allow further catalysis.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 80146-93-6

References:

1. Trainor, D.A., Parry, R.J. and Gitterman, A. Biotin biosynthesis. 2. Stereochemistry of sulfur introduction at C-4 of dethiobiotin. J. Am. Chem. Soc. 102 (1980) 1467-1468.

2. Shiuan, D. and Campbell, A. Transcriptional regulation and gene arrangement of Escherichia coli, Citrobacter freundii and Salmonella typhimurium biotin operons. Gene 67 (1988) 203-211. [PMID: 2971595]

3. Zhang, S., Sanyal, I., Bulboaca, G.H., Rich, A. and Flint, D.H. The gene for biotin synthase from Saccharomyces cerevisiae: cloning, sequencing, and complementation of Escherichia coli strains lacking biotin synthase. Arch. Biochem. Biophys. 309 (1994) 29-35. [PMID: 8117110]

4. Ugulava, N.B., Gibney, B.R. and Jarrett, J.T. Biotin synthase contains two distinct iron-sulfur cluster binding sites: chemical and spectroelectrochemical analysis of iron-sulfur cluster interconversions. Biochemistry 40 (2001) 8343-8351. [PMID: 11444981]

5. Berkovitch, F., Nicolet, Y., Wan, J.T., Jarrett, J.T. and Drennan, C.L. Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science 303 (2004) 76-79. [PMID: 14704425]

6. Lotierzo, M., Tse Sum Bui, B., Florentin, D., Escalettes, F. and Marquet, A. Biotin synthase mechanism: an overview. Biochem. Soc. Trans. 33 (2005) 820-823. [PMID: 16042606]

7. Taylor, A.M., Farrar, C.E. and Jarrett, J.T. 9-Mercaptodethiobiotin is formed as a competent catalytic intermediate by Escherichia coli biotin synthase. Biochemistry 47 (2008) 9309-9317. [PMID: 18690713]

8. Reyda, M.R., Fugate, C.J. and Jarrett, J.T. A complex between biotin synthase and the iron-sulfur cluster assembly chaperone HscA that enhances in vivo cluster assembly. Biochemistry 48 (2009) 10782-10792. [PMID: 19821612]

[EC 2.8.1.6 created 1999, modified 2006, modified 2011]

EC 3.1.1.85

Accepted name: pimelyl-[acyl-carrier protein] methyl ester esterase

Reaction: pimelyl-[acyl-carrier protein] methyl ester + H2O = pimelyl-[acyl-carrier protein] + methanol

Other name(s): BioH

Systematic name: pimelyl-[acyl-carrier protein] methyl ester hydrolase

Comments: Involved in biotin biosynthesis in Gram-negative bacteria. The enzyme exhibits carboxylesterase activity, particularly toward substrates with short acyl chains [1,2]. Even though the enzyme can interact with coenzyme A thioesters [3], the in vivo role of the enzyme is to hydrolyse the methyl ester of pimelyl-[acyl carrier protein], terminating the part of the biotin biosynthesis pathway that is catalysed by the fatty acid elongation enzymes [4].

References:

1. Sanishvili, R., Yakunin, A.F., Laskowski, R.A., Skarina, T., Evdokimova, E., Doherty-Kirby, A., Lajoie, G.A., Thornton, J.M., Arrowsmith, C.H., Savchenko, A., Joachimiak, A. and Edwards, A.M. Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J. Biol. Chem. 278 (2003) 26039-26045. [PMID: 12732651]

2. Lemoine, Y., Wach, A. and Jeltsch, J.M. To be free or not: the fate of pimelate in Bacillus sphaericus and in Escherichia coli. Mol. Microbiol. 19 (1996) 645-647. [PMID: 8830257]

3. Tomczyk, N.H., Nettleship, J.E., Baxter, R.L., Crichton, H.J., Webster, S.P. and Campopiano, D.J. Purification and characterisation of the BIOH protein from the biotin biosynthetic pathway. FEBS Lett. 513 (2002) 299-304. [PMID: 11904168]

4. Lin, S., Hanson, R.E. and Cronan, J.E. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat. Chem. Biol. (2010) . [PMID: 20693992]

[EC 3.1.1.85 created 2011]

EC 3.1.1.86

Accepted name: rhamnogalacturonan acetylesterase

Reaction: Hydrolytic cleavage of 2-O-acetyl- or 3-O-acetyl groups of α-D-galacturonic acid in rhamnogalacturonan I.

Other name(s): RGAE

Systematic name: rhamnogalacturonan 2/3-O-acetyl-α-D-galacturonate O-acetylhydrolase

Comments: The degradation of rhamnogalacturonan by rhamnogalacturonases depends on the removal of the acetyl esters from the substrate [1].

References:

1. Kauppinen, S., Christgau, S., Kofod, L.V., Halkier, T., Dorreich, K. and Dalboge, H. Molecular cloning and characterization of a rhamnogalacturonan acetylesterase from Aspergillus aculeatus. Synergism between rhamnogalacturonan degrading enzymes. J. Biol. Chem. 270 (1995) 27172-27178. [PMID: 7592973]

2. Molgaard, A., Kauppinen, S. and Larsen, S. Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Structure 8 (2000) 373-383. [PMID: 10801485]

[EC 3.1.1.86 created 2011]

EC 3.1.3.84

Accepted name: ADP-ribose 1"-phosphate phosphatase

Reaction: ADP-ribose 1"-phosphate + H2O = ADP-ribose + phosphate

Other name(s): POA1; Appr1p phosphatase; Poa1p

Systematic name: ADP-ribose 1"-phosphate phosphohydrolase

Comments: The enzyme is highly specific for ADP-ribose 1"-phosphate. Involved together with EC 3.1.4.37, 2',3'-cyclic-nucleotide 3'-phosphodiesterase, in the breakdown of adenosine diphosphate ribose 1",2"-cyclic phosphate (Appr>p), a by-product of tRNA splicing.

References:

1. Shull, N.P., Spinelli, S.L. and Phizicky, E.M. A highly specific phosphatase that acts on ADP-ribose 1"-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae. Nucleic Acids Res. 33 (2005) 650-660. [PMID: 15684411]

[EC 3.1.3.84 created 2011]

EC 3.2.1.170

Accepted name: mannosylglycerate hydrolase

Reaction: 2-O-(6-phospho-α-D-mannosyl)-D-glycerate + H2O = D-mannose 6-phosphate + D-glycerate

Other name(s): 2-O-(6-phospho-mannosyl)-D-glycerate hydrolase; α-mannosidase (ambiguous); mngB (gene name)

Systematic name: 2-O-(6-phospho-α-D-mannosyl)-D-glycerate acylhydrolase

Comments: The enzyme participates in the mannosylglycerate degradation pathway of some bacteria. Mannosylglycerate is phosphorylated during transport into the cell, and the phosphorylated form is hydrolysed by this enzyme.

References:

1. Sampaio, M.M., Chevance, F., Dippel, R., Eppler, T., Schlegel, A., Boos, W., Lu, Y.J. and Rock, C.O. Phosphotransferase-mediated transport of the osmolyte 2-O-α-mannosyl-D-glycerate in Escherichia coli occurs by the product of the mngA (hrsA) gene and is regulated by the mngR (farR) gene product acting as repressor. J. Biol. Chem. 279 (2004) 5537-5548. [PMID: 14645248]

[EC 3.2.1.170 created 2011]

*EC 4.1.1.31

Accepted name: phosphoenolpyruvate carboxylase

Reaction: phosphate + oxaloacetate = phosphoenolpyruvate + HCO3-

Other name(s): phosphopyruvate (phosphate) carboxylase; PEP carboxylase; phosphoenolpyruvic carboxylase; PEPC; PEPCase; phosphate:oxaloacetate carboxy-lyase (phosphorylating)

Systematic name: phosphate:oxaloacetate carboxy-lyase (adding phosphate, phosphoenolpyruvate-forming)

Comments: This enzyme replenishes oxaloacetate in the tricarboxylic acid cycle when operating in the reverse direction. The reaction proceeds in two steps: formation of carboxyphosphate and the enolate form of pyruvate, followed by carboxylation of the enolate and release of phosphate.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9067-77-0

References:

1. Chen, J.H. and Jones, R.F. Multiple forms of phosphoenolpyruvate carboxylase from Chlamydomonas reeinhardtii. Biochim. Biophys. Acta 214 (1970) 318-325. [PMID: 5501374]

2. Mazelis, M. and Vennesland, B. Carbon dioxide fixation into oxalacetate in higher plants. Plant Physiol. 32 (1957) 591-600. [PMID: 16655053]

3. Tovar-Mendez, A., Mujica-Jimenez, C. and Munoz-Clares, R.A. Physiological implications of the kinetics of maize leaf phosphoenolpyruvate carboxylase. Plant Physiol. 123 (2000) 149-160. [PMID: 10806233]

[EC 4.1.1.31 created 1961, modified 2011]

*EC 4.1.99.5

Accepted name: octadecanal decarbonylase

Reaction: octadecanal + O2 + 2 NADPH + 2 H+ = heptadecane + formate + H2O + 2 NADP+

Other name(s): decarbonylase; aldehyde decarbonylase

Systematic name: octadecanal alkane-lyase

Comments: Contains a diiron center. Involved in the biosynthesis of alkanes. The enzyme from the cyanobacterium Nostoc punctiforme PCC 73102 is only active in vitro in the presence of ferredoxin, ferredoxin reductase and NADPH, and produces mostly C15 to C17 alkanes [2,3]. The enzyme from pea (Pisum sativum) produces alkanes of chain length C18 to C32 and is inhibited by metal-chelating agents [1]. The substrate for this enzyme is formed by EC 1.2.1.80, acyl-[acyl-carrier protein] reductase.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 94185-90-7

References:

1. Cheesbrough, T.M. and, K olattukudy, P.E. Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum. Proc. Natl. Acad. Sci. USA 81 (1984) 6613-6617. [PMID: 6593720]

2. Schirmer, A., Rude, M.A., Li, X., Popova, E. and del Cardayre, S.B. Microbial biosynthesis of alkanes. Science 329 (2010) 559-562. [PMID: 20671186]

3. Warui, D.M., Li, N., Norgaard, H., Krebs, C., Bollinger, J.M. and Booker, S.J. Detection of formate, rather than carbon monoxide, as the stoichiometric coproduct in conversion of fatty aldehydes to alkanes by a cyanobacterial aldehyde decarbonylase. J. Am. Chem. Soc. 133 (2011) 3316-3319. [PMID: 21341652]

[EC 4.1.99.5 created 1989, modified 2011]

EC 4.2.1.122

Accepted name: tryptophan synthase (indole-salvaging)

Reaction: L-serine + indole = L-tryptophan + H2O

Other name(s): tryptophan synthase β2

Systematic name: L-serine hydro-lyase [adding indole, L-tryptophan-forming]

Comments: Most mesophilic bacteria have a multimeric tryptophan synthase complex (EC 4.2.1.20) that forms L-tryptophan from L-serine and 1-C-(indol-3-yl)glycerol 3-phosphate via an indole intermediate. This intermediate, which is formed by the α subunits, is transferred in an internal tunnel to the β units, which convert it to tryptophan. In thermophilic organisms the high temperature enhances diffusion and causes the loss of indole. This enzyme, which does not combine with the α unit to form a complex, salvages the lost indole back to L-tryptophan. It has a much lower Km for indole than the β subunit of EC 4.2.1.20.

References:

1. Hettwer, S. and Sterner, R. A novel tryptophan synthase β-subunit from the hyperthermophile Thermotoga maritima. Quaternary structure, steady-state kinetics, and putative physiological role. J. Biol. Chem. 277 (2002) 8194-8201. [PMID: 11756459]

[EC 4.2.1.122 created 2011]

EC 4.2.1.123

Accepted name: tetrahymanol synthase

Reaction: tetrahymanol = squalene + H2O

Glossary: tetrahymanol = gammaceran-3β-ol

Other name(s): squalene—tetrahymanol cyclase

Systematic name: squalene hydro-lyase (tetrahymanol forming)

Comments: The reaction occurs in the reverse direction.

References:

1. Saar, J., Kader, J.C., Poralla, K. and Ourisson, G. Purification and some properties of the squalene-tetrahymanol cyclase from Tetrahymena thermophila. Biochim. Biophys. Acta 1075 (1991) 93-101. [PMID: 1892870]

2. Giner, J.L., Rocchetti, S., Neunlist, S., Rohmer, M. and Arigoni, D. Detection of 1,2-hydride shifts in the formation of euph-7-ene by the squalene-tetrahymanol cyclase of Tetrahymena pyriformis. Chem. Commun. (Camb.) (2005) 3089-3091. [PMID: 15959594]

[EC 4.2.1.123 created 2011]

EC 4.2.1.124

Accepted name: arabidiol synthase

Reaction: arabidiol = (S)-squalene-2,3-epoxide + H2O

Glossary: arabidiol = (13R)-malabarica-17,21-diene-3β,14-diol

Other name(s): PEN1 (gene name)

Systematic name: (S)-squalene-2,3-epoxide hydro-lyase (arabidiol forming)

Comments: The reaction occurs in the reverse direction.

References:

1. Xiang, T., Shibuya, M., Katsube, Y., Tsutsumi, T., Otsuka, M., Zhang, H., Masuda, K. and Ebizuka, Y. A new triterpene synthase from Arabidopsis thaliana produces a tricyclic triterpene with two hydroxyl groups. Org Lett 8 (2006) 2835-2838. [PMID: 16774269]

[EC 4.2.1.124 created 2011]

EC 4.2.1.125

Accepted name: dammarenediol II synthase

Reaction: dammarenediol II = (S)-squalene-2,3-epoxide + H2O

Other name(s): dammarenediol synthase; 2,3-oxidosqualene (20S)-dammarenediol cyclase; DDS

Systematic name: (S)-squalene-2,3-epoxide hydro-lyase (dammarenediol-II forming)

Comments: The reaction occurs in the reverse direction.

References:

1. Tansakul, P., Shibuya, M., Kushiro, T. and Ebizuka, Y. Dammarenediol-II synthase, the first dedicated enzyme for ginsenoside biosynthesis, in Panax ginseng. FEBS Lett. 580 (2006) 5143-5149. [PMID: 16962103]

2. Han, J.Y., Kwon, Y.S., Yang, D.C., Jung, Y.R. and Choi, Y.E. Expression and RNA interference-induced silencing of the dammarenediol synthase gene in Panax ginseng. Plant Cell Physiol. 47 (2006) 1653-1662. [PMID: 17088293]

[EC 4.2.1.125 created 2011]

EC 4.2.1.126

Accepted name: N-acetylmuramic acid 6-phosphate etherase

Reaction: N-acetylmuramate 6-phosphate + H2O = (R)-lactate + N-acetyl-D-glucosamine 6-phosphate

Other name(s): MurNAc-6-P etherase; MurQ

Systematic name: N-acetylmuramic acid 6-phosphate hydro-lyase (N-acetyl-D-glucosamine 6-phosphate forming)

Comments: This enzyme, along with EC 2.7.1.170, anhydro-N-acetylmuramic acid kinase, is required for the utilization of anhydro-N-acetylmuramic acid in proteobacteria. The substrate is either imported from the medium or derived from the bacterium's own cell wall murein during cell wall recycling.

References:

1. Jaeger, T., Arsic, M. and Mayer, C. Scission of the lactyl ether bond of N-acetylmuramic acid by Escherichia coli "etherase". J. Biol. Chem. 280 (2005) 30100-30106. [PMID: 15983044]

2. Uehara, T., Suefuji, K., Valbuena, N., Meehan, B., Donegan, M. and Park, J.T. Recycling of the anhydro-N-acetylmuramic acid derived from cell wall murein involves a two-step conversion to N-acetylglucosamine-phosphate. J. Bacteriol. 187 (2005) 3643-3649. [PMID: 15901686]

3. Uehara, T., Suefuji, K., Jaeger, T., Mayer, C. and Park, J.T. MurQ etherase is required by Escherichia coli in order to metabolize anhydro-N-acetylmuramic acid obtained either from the environment or from its own cell wall. J. Bacteriol. 188 (2006) 1660-1662. [PMID: 16452451]

4. Hadi, T., Dahl, U., Mayer, C. and Tanner, M.E. Mechanistic studies on N-acetylmuramic acid 6-phosphate hydrolase (MurQ): an etherase involved in peptidoglycan recycling. Biochemistry 47 (2008) 11547-11558. [PMID: 18837509]

5. Jaeger, T. and Mayer, C. N-acetylmuramic acid 6-phosphate lyases (MurNAc etherases): role in cell wall metabolism, distribution, structure, and mechanism. Cell. Mol. Life Sci. 65 (2008) 928-939. [PMID: 18049859]

[EC 4.2.1.126 created 2011]

EC 4.2.3.74

Accepted name: presilphiperfolanol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H2O = presilphiperfolan-8β-ol + diphosphate

For diagram of reaction click here and mechanism click here.

Other name(s): BcBOT2, CND15

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphohydrolase (presilphiperfolan-8β-ol-forming)

Comments: Requires Mg2+. Presilphiperfolan-8β-ol is the precursor of botrydial, a phytotoxic sesquiterpene metabolite secreted by the fungus Botryotinia fuckeliana (Botrytis cinerea), the causal agent of gray mold disease in plants.

References:

1. Pinedo, C., Wang, C.M., Pradier, J.M., Dalmais, B., Choquer, M., Le Pecheur, P., Morgant, G., Collado, I.G., Cane, D.E. and Viaud, M. Sesquiterpene synthase from the botrydial biosynthetic gene cluster of the phytopathogen Botrytis cinerea. ACS Chem Biol 3 (2008) 791-801. [PMID: 19035644]

2. Wang, C.M., Hopson, R., Lin, X. and Cane, D.E. Biosynthesis of the sesquiterpene botrydial in Botrytis cinerea. Mechanism and stereochemistry of the enzymatic formation of presilphiperfolan-8β-ol. J. Am. Chem. Soc. 131 (2009) 8360-8361. [PMID: 19476353]

[EC 4.2.3.74 created 2011]

EC 4.2.3.75

Accepted name: (–)-germacrene D synthase

Reaction: (2E,6E)-farnesyl diphosphate = (–)-germacrene D + diphosphate

For diagram of reaction click here.

Glossary: (–)-germacrene D = (1E,6E,8S)-1-methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(–)-germacrene-D-forming]

Comments: In Solidago canadensis the biosynthesis results in the pro-R hydrogen at C-1 of the farnesy diphosphate ending up at C-11 of the (–)-germacrene D [1]. With Streptomyces coelicolor the pro-S hydrogen at C-1 ends up at C-11 of the (–)-germacrene D [2].

References:

1. Schmidt, C.O., Bouwmeester, H.J., Franke, S. and König, W.A. Mechanisms of the biosynthesis of sesquiterpene enantiomers (+)- and (–)-germacrene D in Solidago canadensis. Chirality 11 (1999) 353-362.

2. He, X. and Cane, D.E. Mechanism and stereochemistry of the germacradienol/germacrene D synthase of Streptomyces coelicolor A3(2). J. Am. Chem. Soc. 126 (2004) 2678-2679. [PMID: 14995166]

3. Lucker, J., Bowen, P. and Bohlmann, J. Vitis vinifera terpenoid cyclases: functional identification of two sesquiterpene synthase cDNAs encoding (+)-valencene synthase and (–)-germacrene D synthase and expression of mono- and sesquiterpene synthases in grapevine flowers and berries. Phytochemistry 65 (2004) 2649-2659. [PMID: 15464152]

4. Prosser, I., Altug, I.G., Phillips, A.L., Konig, W.A., Bouwmeester, H.J. and Beale, M.H. Enantiospecific (+)- and (–)-germacrene D synthases, cloned from goldenrod, reveal a functionally active variant of the universal isoprenoid-biosynthesis aspartate-rich motif. Arch. Biochem. Biophys. 432 (2004) 136-144. [PMID: 15542052]

[EC 4.2.3.75 created 2011]

EC 4.2.3.76

Accepted name: (+)-δ-selinene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (+)-δ-selinene + diphosphate

For diagram of reaction click here.

Glossary: (+)-δ-selinene = (4aR)-1,4a-dimethyl-7-(propan-2-yl)-2,3,4,4a,5,6-hexahydronaphthalene

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-δ-selinene-forming]

Comments: Initial cyclization gives germacrene C in an enzyme bound form which is not released to the medium.

References:

1. Steele, C.L., Crock, J., Bohlmann, J. and Croteau, R. Sesquiterpene synthases from grand fir (Abies grandis). Comparison of constitutive and wound-induced activities, and cDNA isolation, characterization, and bacterial expression of δ-selinene synthase and γ-humulene synthase. J. Biol. Chem. 273 (1998) 2078-2089. [PMID: 9442047]

2. Little, D.B. and Croteau, R.B. Alteration of product formation by directed mutagenesis and truncation of the multiple-product sesquiterpene synthases δ-selinene synthase and γ-humulene synthase. Arch. Biochem. Biophys. 402 (2002) 120-135. [PMID: 12051690]

[EC 4.2.3.76 created 2011]

EC 4.2.3.77

Accepted name: (+)-germacrene D synthase

Reaction: (2E,6E)-farnesyl diphosphate = (+)-germacrene D + diphosphate

For diagram of reaction click here.

Glossary: (+)-germacrene D = (1E,6E,8R)-1-methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-D-forming]

Comments: Requires Mg2+, Mn2+, Ni2+ or Co2+. The formation of (+)-germacrene D involves a 1,2-hydride shift whereas for (–)-germacrene D there is a 1,3-hydride shift (see EC 4.2.3.75).

References:

1. Picaud, S., Olsson, M.E., Brodelius, M. and Brodelius, P.E. Cloning, expression, purification and characterization of recombinant (+)-germacrene D synthase from Zingiber officinale. Arch. Biochem. Biophys. 452 (2006) 17-28. [PMID: 16839518]

[EC 4.2.3.77 created 2011]

EC 5.3.3.16

Accepted name: 4-oxalomesaconate tautomerase

Reaction: (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate = 2-hydroxy-4-carboxyhexa-2,4-dienedioate

Glossary: (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate = keto tautomer of 4-oxalomesaconate, 2-hydroxy-4-carboxyhexa-2,4-dienedioate = enol tautomer of 4-oxalomesaconate

Other name(s): GalD

Systematic name: 4-oxalomesaconate keto-enol-isomerase

Comments: This enzyme has been characterized from the bacterium Pseudomonas putida KT2440 and is involved in the degradation pathway of syringate and gallate. It catalyses the interconversion of two of the tautomers of 4-oxalomesaconate, a reaction that can also occur spontaneously.

References:

1. Nogales, J., Canales, A., Jimenez-Barbero, J., Serra, B., Pingarron, J.M., Garcia, J.L. and Diaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359-374. [PMID: 21219457]

[EC 5.3.3.16 created 2011]

EC 5.4.99.31

Accepted name: thalianol synthase

Reaction: (S)-squalene-2,3-epoxide = thalianol

Systematic name: (S)-2,3-epoxysqualene mutase (cyclizing, thalianol-forming)

References:

1. Fazio, G.C., Xu, R. and Matsuda, S.P.T. Genome mining to identify new plant triterpenoids. J. Am. Chem. Soc. 126 (2004) 5678-5679. [PMID: 15125655]

[EC 5.4.99.31 created 2011]

EC 5.4.99.32

Accepted name: protostadienol synthase

Reaction: (S)-squalene-2,3-epoxide = (17Z)-protosta-17(20),24-dien-3β-ol

Other name(s): PdsA

Systematic name: (S)-2,3-epoxysqualene mutase [cyclizing, (17Z)-protosta-17(20),24-dien-3β-ol-forming]

Comments: (17Z)-Protosta-17(20),24-dien-3β-ol is a precursor of the steroidal antibiotic helvolic acid.

References:

1. Lodeiro, S., Xiong, Q., Wilson, W.K., Ivanova, Y., Smith, M.L., May, G.S. and Matsuda, S.P. Protostadienol biosynthesis and metabolism in the pathogenic fungus Aspergillus fumigatus. Org Lett 11 (2009) 1241-1244. [PMID: 19216560]

[EC 5.4.99.32 created 2011]

EC 5.4.99.33

Accepted name: cucurbitadienol synthase

Reaction: (S)-squalene-2,3-epoxide = cucurbitadienol

Other name(s): CPQ (gene name)

Systematic name: (S)-2,3-epoxysqualene mutase (cyclizing, cucurbitadienol-forming)

References:

1. Shibuya, M., Adachi, S., and Ebizuka, Y. Cucurbitadienol synthase, the first committed enzyme for cucurbitacin biosynthesis, is a distinct enzyme from cycloartenol synthase for phytosterol biosynthesis. Tetrahedron 60 (2004) 6995-7003.

[EC 5.4.99.33 created 2011]

EC 5.4.99.34

Accepted name: germanicol synthase

Reaction: (S)-squalene-2,3-epoxide = germanicol

Other name(s): RsM1

Systematic name: (S)-2,3-epoxysqualene mutase (cyclizing, germanicol-forming)

Comments: The enzyme produces germanicol, β-amyrin and lupeol in the ratio 63:33:4.

References:

1. Basyuni, M., Oku, H., Tsujimoto, E., Kinjo, K., Baba, S. and Takara, K. Triterpene synthases from the Okinawan mangrove tribe, Rhizophoraceae. FEBS J. 274 (2007) 5028-5042. [PMID: 17803686]

[EC 5.4.99.34 created 2011]

EC 5.4.99.35

Accepted name: taraxerol synthase

Reaction: (S)-squalene-2,3-epoxide = taraxerol

Other name(s): RsM2

Systematic name: (S)-2,3-epoxysqualene mutase (cyclizing, taraxerol-forming)

Comments: The enzyme gives taraxerol, β-amyrin and lupeol in the ratio 70:17:13.

References:

1. Basyuni, M., Oku, H., Tsujimoto, E., Kinjo, K., Baba, S. and Takara, K. Triterpene synthases from the Okinawan mangrove tribe, Rhizophoraceae. FEBS J. 274 (2007) 5028-5042. [PMID: 17803686]

[EC 5.4.99.35 created 2011]

EC 5.4.99.36

Accepted name: isomultiflorenol synthase

Reaction: (S)-squalene-2,3-epoxide = isomultiflorenol

Other name(s): LcIMS1

Systematic name: (S)-2,3-epoxysqualene mutase (cyclizing, isomultiflorenol-forming)

References:

1. Hayashi, H., Huang, P., Inoue, K., Hiraoka, N., Ikeshiro, Y., Yazaki, K., Tanaka, S., Kushiro, T., Shibuya, M. and Ebizuka, Y. Molecular cloning and characterization of isomultiflorenol synthase, a new triterpene synthase from Luffa cylindrica, involved in biosynthesis of bryonolic acid. Eur. J. Biochem. 268 (2001) 6311-6317. [PMID: 11733028]

[EC 5.4.99.36 created 2011]

EC 6.3.2.37

Accepted name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—D-lysine ligase

Reaction: ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + D-lysine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-D-lysine

Other name(s): UDP-MurNAc-L-Ala-D-Glu:D-Lys ligase; D-lysine-adding enzyme

Systematic name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:L-lysine α-ligase (ADP-forming)

Comments: The enzyme from Thermotoga maritima also performs the reaction of EC 6.3.2.7, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate–L-lysine ligase. Involved in the synthesis of cell-wall peptidoglycan.

References:

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

[EC 6.3.2.37 created 2011]


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