The Enzyme Database

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, Masaaki Kotera, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

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


Contents

EC 1.1.1.312 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase
EC 1.1.1.313 sulfoacetaldehyde reductase
EC 1.1.1.314 germacrene A alcohol dehydrogenase
EC 1.2.1.45 transferred
EC 1.2.1.81 sulfoacetaldehyde dehydrogenase (acylating)
EC 1.2.7.10 oxalate oxidoreductase
*EC 1.3.1.14 dihydroorotate dehydrogenase (NAD+)
*EC 1.3.1.15 dihydroorotate dehydrogenase (NADP+)
EC 1.3.1.87 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate dehydrogenase
EC 1.3.3.1 transferred
*EC 1.3.5.2 dihydroorotate dehydrogenase (quinone)
EC 1.3.5.5 15-cis-phytoene desaturase
EC 1.3.7.8 benzoyl-CoA reductase
EC 1.3.7.9 4-hydroxybenzoyl-CoA reductase
EC 1.3.8 With a flavin as acceptor
EC 1.3.8.1 short-chain acyl-CoA dehydrogenase
EC 1.3.98 With other, known, acceptors
EC 1.3.98.1 dihydroorotate dehydrogenase (fumarate)
EC 1.3.99.2 transferred
EC 1.3.99.15 transferred
EC 1.3.99.20 transferred
EC 1.4.98.1 methylamine dehydrogenase (amicyanin)
EC 1.4.99.3 transferred
*EC 1.6.5.3 NADH:ubiquinone reductase (H+-translocating)
EC 1.6.5.9 NADH:ubiquinone reductase (non-electrogenic)
EC 1.7.1.14 nitric oxide reductase [NAD(P)+, nitrous oxide-forming]
EC 1.7.2.4 nitrous-oxide reductase
EC 1.7.2.5 nitric oxide reductase (cytochrome c)
EC 1.7.5.2 nitric oxide reductase (menaquinol)
EC 1.7.99.6 transferred
EC 1.7.99.7 transferred
EC 1.8.1.17 dimethylsulfone reductase
EC 1.8.2.3 sulfide-cytochrome-c reductase (flavocytochrome c)
EC 1.8.2.4 dimethyl sulfide:cytochrome c2 reductase
EC 1.8.3.6 farnesylcysteine lyase
EC 1.8.5.3 dimethylsulfoxide reductase
EC 1.8.5.4 sulfide:quinone reductase
*EC 1.10.3.3 L-ascorbate oxidase
EC 1.10.3.9 photosystem II
EC 1.10.3.10 ubiquinol oxidase (H+-transporting)
EC 1.10.3.11 ubiquinol oxidase (non-electrogenic)
EC 1.10.3.12 menaquinol oxidase (H+-transporting)
*EC 1.11.1.11 L-ascorbate peroxidase
*EC 1.11.1.14 lignin peroxidase
EC 1.11.1.21 catalase-peroxidase
EC 1.12.1.4 hydrogenase (NAD+, ferredoxin)
*EC 1.13.11.12 linoleate 13S-lipoxygenase
EC 1.13.11.57 gallate dioxygenase
EC 1.13.11.58 linoleate 9S-lipoxygenase
EC 1.13.12.14 transferred
EC 1.14.11.33 DNA oxidative demethylase
*EC 1.14.13.25 methane monooxygenase (soluble)
EC 1.14.13.42 deleted
EC 1.14.13.122 chlorophyllide-a oxygenase
EC 1.14.13.123 germacrene A hydroxylase
EC 1.14.13.124 phenylalanine N-monooxygenase
EC 1.14.13.125 tryptophan N-monooxygenase
EC 1.14.13.126 vitamin D3 24-hydroxylase
EC 1.14.13.127 3-(3-hydroxyphenyl)propanoate hydroxylase
EC 1.14.13.128 7-methylxanthine demethylase
EC 1.14.13.129 β-carotene 3-hydroxylase
EC 1.14.13.130 pyrrole-2-carboxylate monooxygenase
EC 1.14.18.3 methane monooxygenase (particulate)
EC 1.14.19.7 (S)-2-hydroxypropylphosphonic acid epoxidase
EC 1.14.19.7 (S)-2-hydroxypropylphosphonic acid epoxidase
EC 1.14.99.42 zeaxanthin 7,8-dioxygenase
EC 1.14.99.43 β-amyrin 24-hydroxylase
EC 1.14.99.44 diapolycopene oxygenase
EC 1.14.99.45 carotene ε-monooxygenase
*EC 1.16.3.1 ferroxidase
EC 1.16.5 With a quinone or similar compound as acceptor
EC 1.16.5.1 ascorbate ferrireductase (transmembrane)
EC 1.16.98 With other, known, acceptors
EC 1.16.98.1 iron:rusticyanin reductase
*EC 1.18.1.3 ferredoxin—NAD+ reductase
EC 1.97.7.1 photosystem I
*EC 2.1.1.149 myricetin O-methyltransferase
EC 2.1.1.207 tRNA (cytidine34-2′-O)-methyltransferase
*EC 2.3.1.93 13-hydroxylupanine O-tigloyltransferase
EC 2.3.1.196 benzyl alcohol O-benzoyltransferase
EC 2.4.1.130 transferred
*EC 2.4.1.131 GDP-Man:Man3GlcNAc2-PP-dolichol α-1,2-mannosyltransferase
*EC 2.4.1.132 GDP-Man:Man1GlcNAc2-PP-dolichol α-1,3-mannosyltransferase
*EC 2.4.1.191 luteolin-7-O-diglucuronide 4′-O-glucuronosyltransferase
EC 2.4.1.256 dolichyl-P-Glc:Glc2Man9GlcNAc2-PP-dolichol α-1,2-glucosyltransferase
EC 2.4.1.257 GDP-Man:Man2GlcNAc2-PP-dolichol α-1,6-mannosyltransferase
EC 2.4.1.258 dolichyl-P-Man:Man5GlcNAc2-PP-dolichol α-1,3-mannosyltransferase
EC 2.4.1.259 dolichyl-P-Man:Man6GlcNAc2-PP-dolichol α-1,2-mannosyltransferase
EC 2.4.1.260 dolichyl-P-Man:Man7GlcNAc2-PP-dolichol α-1,6-mannosyltransferase
EC 2.4.1.261 dolichyl-P-Man:Man8GlcNAc2-PP-dolichol α-1,2-mannosyltransferase
EC 2.4.1.262 soyasapogenol glucuronosyltransferase
EC 2.4.1.263 abscisate β-glucosyltransferase
*EC 2.5.1.29 geranylgeranyl diphosphate synthase
*EC 2.5.1.31 ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
*EC 2.5.1.89 tritrans,polycis-undecaprenyl-diphosphate synthase [geranylgeranyl-diphosphate specific]
*EC 2.5.1.92 (2Z,6Z)-farnesyl diphosphate synthase
EC 2.7.1.170 anhydro-N-acetylmuramic acid kinase
*EC 2.7.8.30 undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
EC 2.7.8.33 UDP-N-acetylglucosamine—undecaprenyl-phosphate N-acetylglucosaminephosphotransferase
*EC 2.8.1.6 biotin synthase
EC 3.1.1.85 pimelyl-[acyl-carrier protein] methyl ester esterase
EC 3.1.1.86 rhamnogalacturonan acetylesterase
EC 3.1.2.29 fluoroacetyl-CoA thioesterase
*EC 3.1.3.73 adenosylcobalamin/α-ribazole phosphatase
EC 3.1.3.84 ADP-ribose 1′′-phosphate phosphatase
EC 3.2.1.170 mannosylglycerate hydrolase
*EC 3.2.2.1 purine nucleosidase
*EC 3.4.13.19 membrane dipeptidase
*EC 3.4.15.1 peptidyl-dipeptidase A
*EC 3.4.16.6 carboxypeptidase D
*EC 3.5.1.4 amidase
*EC 4.1.1.31 phosphoenolpyruvate carboxylase
*EC 4.1.1.52 6-methylsalicylate decarboxylase
*EC 4.1.1.77 2-oxo-3-hexenedioate decarboxylase
*EC 4.1.3.39 4-hydroxy-2-oxovalerate aldolase
*EC 4.1.99.5 aldehyde oxygenase (deformylating)
EC 4.1.99.16 geosmin synthase
EC 4.2.1.122 tryptophan synthase (indole-salvaging)
EC 4.2.1.123 tetrahymanol synthase
EC 4.2.1.124 arabidiol synthase
EC 4.2.1.125 dammarenediol II synthase
EC 4.2.1.126 N-acetylmuramic acid 6-phosphate etherase
*EC 4.2.3.22 germacradienol synthase
EC 4.2.3.61 5-epiaristolochene synthase
EC 4.2.3.62 (-)-γ-cadinene synthase [(2Z,6E)-farnesyl diphosphate cyclizing]
EC 4.2.3.63 (+)-cubenene synthase
EC 4.2.3.64 (+)-epicubenol synthase
EC 4.2.3.65 zingiberene synthase
EC 4.2.3.66 β-selinene cyclase
EC 4.2.3.67 cis-muuroladiene synthase
EC 4.2.3.68 β-eudesmol synthase
EC 4.2.3.69 (+)-α-barbatene synthase
EC 4.2.3.70 patchoulol synthase
EC 4.2.3.71 (E,E)-germacrene B synthase
EC 4.2.3.72 α-gurjunene synthase
EC 4.2.3.73 valencene synthase
EC 4.2.3.74 presilphiperfolanol synthase
EC 4.2.3.76 (+)-δ-selinene synthase
EC 4.2.3.77 (+)-germacrene D synthase
*EC 4.3.1.20 erythro-3-hydroxy-L-aspartate ammonia-lyase
EC 5.3.3.16 4-oxalomesaconate tautomerase
EC 5.4.99.31 thalianol synthase
EC 5.4.99.32 protostadienol synthase
EC 5.4.99.33 cucurbitadienol synthase
EC 5.4.99.34 germanicol synthase
EC 5.4.99.35 taraxerol synthase
EC 5.4.99.36 isomultiflorenol synthase
EC 6.3.2.31 coenzyme F420-0:L-glutamate ligase
EC 6.3.2.31 coenzyme F420-0:L-glutamate ligase
EC 6.3.2.37 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—D-lysine ligase
EC 6.4.1.8 acetophenone carboxylase


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 the protocatechuate 3,4-cleavage pathway, 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].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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
2-sulfoacetaldehyde = 2-oxoethanesulfonate
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 costunolide biosynthesis, 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].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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+
Glossary: 2-sulfoacetaldehyde = 2-oxoethanesulfonate
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+.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 + oxidized 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)
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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, IUBMB, 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, IUBMB, 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+
For diagram of 3-phenylpropanoate catabolism, click here and for diagram of cinnamate catabolism, click here
Glossary: (2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate = trans-2,3-dihydroxycinnamate
Other name(s): 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD
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, in cyanobacteria, and in some Gram-negative and Gram-positive bacteria associated with the cytoplasmic membrane [2,5,6]. 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, IUBMB, 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]
6.  Nara, T., Hshimoto, T. and Aoki, T. Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes. Gene 257 (2000) 209–222. [PMID: 11080587]
[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
For diagram of plant and cyanobacteria carotenoid biosynthesis, click here
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].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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
For diagram of Benzoyl-CoA catabolism, click here
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 = hydroxylamine + reduced acceptor + 2 ATP + H2O. In the presence of reduced acceptor, but in the absence of oxidizable substrate, the enzyme catalyses the hydrolysis of ATP to ADP plus phosphate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD, CAS registry number: 176591-18-7
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, modified 2011]
 
 
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].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, UM-BBD, CAS registry number: 133758-58-4
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 a flavin as acceptor
 
EC 1.3.8.1
Accepted name: short-chain acyl-CoA dehydrogenase
Reaction: a short-chain acyl-CoA + electron-transfer flavoprotein = a short-chain trans-2,3-dehydroacyl-CoA + reduced electron-transfer flavoprotein
Glossary: a short-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains less than 6 carbon atoms.
Other name(s): butyryl-CoA dehydrogenase; butanoyl-CoA dehydrogenase; 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; ACADS (gene name).
Systematic name: short-chain acyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase
Comments: Contains FAD as prosthetic group. One of several enzymes that catalyse the first step in fatty acids β-oxidation. The enzyme catalyses the oxidation of saturated short-chain acyl-CoA thioesters to give a trans 2,3-unsaturated product by removal of the two pro-R-hydrogen atoms. The enzyme from beef liver accepts substrates with acyl chain lengths of 3 to 8 carbon atoms. The highest activity was reported with either butanoyl-CoA [2] or pentanoyl-CoA [4]. The enzyme from rat has only 10% activity with hexanoyl-CoA (compared to butanoyl-CoA) and no activity with octanoyl-CoA [6]. cf. EC 1.3.8.7, medium-chain acyl-CoA dehydrogenase, EC 1.3.8.8, long-chain acyl-CoA dehydrogenase, and EC 1.3.8.9, very-long-chain acyl-CoA dehydrogenase.
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, UM-BBD, CAS registry number: 9027-88-7
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.  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.
4.  Shaw, L. and Engel, P.C. The purification and properties of ox liver short-chain acyl-CoA dehydrogenase. Biochem. J. 218 (1984) 511–520. [PMID: 6712627]
5.  Thorpe, C. and Kim, J.J. Structure and mechanism of action of the acyl-CoA dehydrogenases. FASEB J. 9 (1995) 718–725. [PMID: 7601336]
6.  Ikeda, Y., Ikeda, K.O. and Tanaka, K. Purification and characterization of short-chain, medium-chain, and long-chain acyl-CoA dehydrogenases from rat liver mitochondria. Isolation of the holo- and apoenzymes and conversion of the apoenzyme to the holoenzyme. J. Biol. Chem. 260 (1985) 1311–1325. [PMID: 3968063]
7.  McMahon, B., Gallagher, M.E. and Mayhew, S.G. The protein coded by the PP2216 gene of Pseudomonas putida KT2440 is an acyl-CoA dehydrogenase that oxidises only short-chain aliphatic substrates. FEMS Microbiol. Lett. 250 (2005) 121–127. [PMID: 16024185]
[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, modified 2012]
 
 
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 9029-03-2
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 1.4.98.1
Transferred entry: amine dehydrogenase. Now EC 1.4.9.1, methylamine dehydrogenase (amicyanin)
[EC 1.4.98.1 created 1978 as EC 1.4.99.3, modified 1986, transferred 2011 to EC 1.4.98.1, deleted 2011]
 
 
EC 1.4.99.3
Transferred entry: amine dehydrogenase. Now EC 1.4.9.1, 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 + 6 H+[side 1] = NAD+ + ubiquinol + 7 H+[side 2]
Other name(s): ubiquinone reductase (ambiguous); type 1 dehydrogenase; complex 1 dehydrogenase; coenzyme Q reductase (ambiguous); complex I (electron transport chain); complex I (mitochondrial electron transport); complex I (NADH:Q1 oxidoreductase); dihydronicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); DPNH-coenzyme Q reductase (ambiguous); DPNH-ubiquinone reductase (ambiguous); mitochondrial electron transport complex 1; mitochondrial electron transport complex I; NADH coenzyme Q1 reductase; NADH-coenzyme Q oxidoreductase (ambiguous); NADH-coenzyme Q reductase (ambiguous); NADH-CoQ oxidoreductase (ambiguous); NADH-CoQ reductase (ambiguous); NADH-ubiquinone reductase (ambiguous); NADH-ubiquinone oxidoreductase (ambiguous); NADH-ubiquinone-1 reductase; reduced nicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); NADH:ubiquinone oxidoreductase complex; NADH-Q6 oxidoreductase (ambiguous); 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, IUBMB, 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]
5.  Wikstrom, M. and Hummer, G. Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications. Proc. Natl. Acad. Sci. USA 109 (2012) 4431–4436. [PMID: 22392981]
[EC 1.6.5.3 created 1961, deleted 1965, reinstated 1983, modified 2011, modified 2013]
 
 
EC 1.6.5.9
Accepted name: NADH:ubiquinone reductase (non-electrogenic)
Reaction: NADH + H+ + ubiquinone = NAD+ + ubiquinol
Other name(s): ubiquinone reductase (ambiguous); coenzyme Q reductase (ambiguous); dihydronicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); DPNH-coenzyme Q reductase (ambiguous); DPNH-ubiquinone reductase (ambiguous); NADH-coenzyme Q oxidoreductase (ambiguous); NADH-coenzyme Q reductase (ambiguous); NADH-CoQ oxidoreductase (ambiguous); NADH-CoQ reductase (ambiguous); NADH-ubiquinone reductase (ambiguous); NADH-ubiquinone oxidoreductase (ambiguous); reduced nicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); NADH-Q6 oxidoreductase (ambiguous); NADH2 dehydrogenase (ubiquinone) (ambiguous)
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 9028-04-0
References:
1.  Møller, I.M, and Palmer, J.M. Direct evidence for the presence of a rotenone-resistant NADH dehydrogenase on the inner surface of plant mitochondria. Physiol. Plant. 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 (P-450). 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 1.7.2.4
Accepted name: nitrous-oxide reductase
Reaction: nitrogen + H2O + 2 ferricytochrome c = nitrous oxide + 2 ferrocytochrome c + 2 H+
Other name(s): nitrous oxide reductase; N2O reductase; nitrogen:(acceptor) oxidoreductase (N2O-forming)
Systematic name: nitrogen:cytochrome c oxidoreductase (N2O-forming)
Comments: The reaction is observed only in the direction of nitrous oxide reduction. Contains the mixed-valent dinuclear CuA species at the electron entry site of the enzyme, and the tetranuclear Cu-Z centre in the active site. In Paracoccus pantotrophus, the electron donor is cytochrome c552.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, UM-BBD, CAS registry number: 55576-44-8
References:
1.  Coyle, C.L., Zumft, W.G., Kroneck, P.M.H., Körner, H. and Jakob, W. Nitrous oxide reductase from denitrifying Pseudomonas perfectomarina. Purification and properties of a novel multicopper enzyme. Eur. J. Biochem. 153 (1985) 459–467. [PMID: 3000778]
2.  Zumft, W.G. and Kroneck, P.M. Respiratory transformation of nitrous oxide (N2O) to dinitrogen by bacteria and archaea. Adv. Microb. Physiol. 52 (2007) 107–227. [PMID: 17027372]
3.  Dell'Acqua, S., Pauleta, S.R., Paes de Sousa, P.M., Monzani, E., Casella, L., Moura, J.J. and Moura, I. A new CuZ active form in the catalytic reduction of N2O by nitrous oxide reductase from Pseudomonas nautica. J. Biol. Inorg. Chem. 15 (2010) 967–976. [PMID: 20422435]
[EC 1.7.2.4 created 1989 as EC 1.7.99.6, modified 1999, transferred 2011 to EC 1.7.2.4]
 
 
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
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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+
For diagram of dimethyl sulfide catabolism, click here
Comments: A molybdoprotein.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 + H2O = dimethyl sulfoxide + 2 ferrocytochrome c2 + 2 H+
For diagram of dimethyl sulfide catabolism, click here
Other name(s): Ddh (gene name)
Systematic name: dimethyl sulfide:cytochrome-c2 oxidoreductase
Comments: The enzyme from the bacterium Rhodovulum sulfidophilum binds molybdopterin guanine dinucleotide, heme b and [4Fe-4S] clusters.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 1.8.5.3
Accepted name: dimethylsulfoxide reductase
Reaction: dimethylsulfide + menaquinone + H2O = dimethylsulfoxide + menaquinol
For diagram of dimethyl sulfide catabolism, click here
Other name(s): DMSO reductase
Systematic name: dimethyl sulfide:menaquinone oxidoreductase
Comments: Contains molybdopterin and [4Fe-4S] clusters. Also reduces pyridine N-oxide and trimethylamine N-oxide, with lower activity, to the corresponding amines.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Simala-Grant, J.L. and Weiner, J.H. Kinetic analysis and substrate specificity of Escherichia coli dimethyl sulfoxide reductase. Microbiology 142 (1996) 3231–3239. [PMID: 8969520]
2.  Daruwala, R. and Meganathan, R. Dimethyl sulfoxide reductase is not required for trimethylamine N-oxide reduction in Escherichia coli. FEMS Microbiol. Lett. 67 (1991) 255–259. [PMID: 1769531]
3.  Miguel, L. and Meganthan, R. Electron donors and the quinone involved in dimethyl sulfoxide reduction in Escherichia coli. Curr. Microbiol. 22 (1991) 109–115.
4.  Rothery, R.A., Trieber, C.A. and Weiner, J.H. Interactions between the molybdenum cofactor and iron-sulfur clusters of Escherichia coli dimethylsulfoxide reductase. J. Biol. Chem. 274 (1999) 13002–13009. [PMID: 10224050]
[EC 1.8.5.3 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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, IUBMB, 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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+[side 1] = 2 ubiquinone + 2 H2O + n H+[side 2]
Other name(s): cytochrome bb3 oxidase; cytochrome bo oxidase; cytochrome bd-II oxidase; ubiquinol:O2 oxidoreductase (H+-transporting)
Systematic name: ubiquinol:oxygen oxidoreductase (H+-transporting)
Comments: Contains a dinuclear centre comprising two hemes, or heme and copper. This terminal oxidase enzyme generates proton motive force by two mechanisms: (1) transmembrane charge separation resulting from utilizing protons and electrons originating from opposite sides of the membrane to generate water, and (2) active pumping of protons across the membrane. The bioenergetic efficiency (the number of charges driven across the membrane per electron used to reduce oxygen to water) depends on the enzyme; for example, for the bo3 oxidase it is 2, while for the bd-II oxidase it is 1. cf. EC 1.10.3.14, ubiquinol oxidase (electrogenic, non H+-transporting).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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.  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]
3.  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]
4.  Borisov, V.B., Murali, R., Verkhovskaya, M.L., Bloch, D.A., Han, H., Gennis, R.B. and Verkhovsky, M.I. Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode. Proc. Natl. Acad. Sci. USA 108 (2011) 17320–17324. [PMID: 21987791]
[EC 1.10.3.10 created 2011, modified 2014]
 
 
EC 1.10.3.11
Accepted name: ubiquinol oxidase (non-electrogenic)
Reaction: 2 ubiquinol + O2 = 2 ubiquinone + 2 H2O
Other name(s): plant alternative oxidase; cyanide-insensitive oxidase; AOX (gene name); ubiquinol oxidase; ubiquinol:O2 oxidoreductase (non-electrogenic)
Systematic name: ubiquinol:oxygen oxidoreductase (non-electrogenic)
Comments: The enzyme, described from the mitochondria of plants and some fungi and protists, is an alternative terminal oxidase that is not sensitive to cyanide inhibition and does not generate a proton motive force. Unlike the electrogenic terminal oxidases that contain hemes (cf. EC 1.10.3.10 and EC 1.10.3.14), this enzyme contains a dinuclear non-heme iron complex. The function of this oxidase is believed to be dissipating excess reducing power, minimizing oxidative stress, and optimizing photosynthesis in response to changing conditions.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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.  Berthold, D.A., Andersson, M.E. and Nordlund, P. New insight into the structure and function of the alternative oxidase. Biochim. Biophys. Acta 1460 (2000) 241–254. [PMID: 11106766]
4.  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:e1000761 (2010). [PMID: 20169184]
5.  Gandin, A., Duffes, C., Day, D.A. and Cousins, A.B. The absence of alternative oxidase AOX1A results in altered response of photosynthetic carbon assimilation to increasing CO2 in Arabidopsis thaliana. Plant Cell Physiol 53 (2012) 1627–1637. [PMID: 22848123]
[EC 1.10.3.11 created 2011, modified 2014]
 
 
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; menaquinol:O2 oxidoreductase (H+-transporting)
Systematic name: menaquinol:oxygen 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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: 2 L-ascorbate + H2O2 + 2 H+ = L-ascorbate + L-dehydroascorbate + 2 H2O (overall reaction)
(1a) 2 L-ascorbate + H2O2 + 2 H+ = 2 monodehydroascorbate + 2 H2O
(1b) 2 monodehydroascorbate = L-ascorbate + L-dehydroascorbate (spontaneous)
Glossary: monodehydroascorbate = ascorbate radical
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-enzymic disproportionation to ascorbate and dehydroascorbate.
Links to other databases: BRENDA, EXPASY, IUBMB, 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]
5.  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]
6.  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: (1) 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol + H2O2 = 3,4-dimethoxybenzaldehyde + 2-methoxyphenol + glycolaldehyde + H2O
(2) 2 (3,4-dimethoxyphenyl)methanol + H2O2 = 2 (3,4-dimethoxyphenyl)methanol radical + 2 H2O
Glossary: veratryl alcohol = (3,4-dimethoxyphenyl)methanol
veratraldehyde = 3,4-dimethoxybenzaldehyde
2-methoxyphenol = guaiacol
Other name(s): diarylpropane oxygenase; ligninase I; diarylpropane peroxidase; LiP; diarylpropane:oxygen,hydrogen-peroxide oxidoreductase (C-C-bond-cleaving); 1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol:hydrogen-peroxide oxidoreductase (incorrect); (3,4-dimethoxyphenyl)methanol:hydrogen-peroxide oxidoreductase
Systematic name: 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol:hydrogen-peroxide oxidoreductase
Comments: A hemoprotein, involved in the oxidative breakdown of lignin by white-rot basidiomycete fungi. The reaction involves an initial oxidation of the heme iron by hydrogen peroxide, forming compound I (FeIV=O radical cation) at the active site. A single one-electron reduction of compound I by an electron derived from a substrate molecule yields compound II (FeIV=O non-radical cation), followed by a second one-electron transfer that returns the enzyme to the ferric oxidation state. The electron transfer events convert the substrate molecule into a transient cation radical intermediate that fragments spontaneously. The enzyme can act on a wide range of aromatic compounds, including methoxybenzenes and nonphenolic β-O-4 linked arylglycerol β-aryl ethers, but cannot act directly on the lignin molecule, which is too large to fit into the active site. However larger lignin molecules can be degraded in the presence of veratryl alcohol. It has been suggested that the free radical that is formed when the enzyme acts on veratryl alcohol can diffuse into the lignified cell wall, where it oxidizes lignin and other organic substrates. In the presence of high concentration of hydrogen peroxide and lack of substrate, the enzyme forms a catalytically inactive form (compound III). This form can be rescued by interaction with two molecules of the free radical products. In the case of veratryl alcohol, such an interaction yields two molecules of veratryl aldehyde.
Links to other databases: BRENDA, EXPASY, IUBMB, 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.  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]
5.  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]
6.  Khindaria, A., Yamazaki, I. and Aust, S.D. Veratryl alcohol oxidation by lignin peroxidase. Biochemistry 34 (1995) 16860–16869. [PMID: 8527462]
7.  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]
8.  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]
9.  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]
10.  Pollegioni, L., Tonin, F. and Rosini, E. Lignin-degrading enzymes. FEBS J. 282 (2015) 1190–1213. [PMID: 25649492]
[EC 1.11.1.14 created 1992, modified 2006, modified 2011, modified 2016]
 
 
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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: (1) linoleate + O2 = (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate
(2) α-linolenate + O2 = (9Z,11E,13S,15Z)-13-hydroperoxyoctadeca-9,11,15-trienoate
Glossary: linoleate = (9Z,12Z)-octadeca-9,12-dienoate
α-linolenate = (9Z,12Z,15Z)-octadeca-9,12,15-trienoate
Other name(s): 13-lipoxidase; carotene oxidase; 13-lipoperoxidase; fat oxidase; 13-lipoxydase; lionoleate:O2 13-oxidoreductase
Systematic name: linoleate:oxygen 13-oxidoreductase
Comments: Contains nonheme iron. A common plant lipoxygenase that oxidizes linoleate and α-linolenate, the two most common polyunsaturated fatty acids in plants, by inserting molecular oxygen at the C-13 position with (S)-configuration. This enzyme produces precursors for several important compounds, including the plant hormone jasmonic acid. EC 1.13.11.58, linoleate 9S-lipoxygenase, catalyses a similar reaction at the second available position of these fatty acids.
Links to other databases: BRENDA, EXPASY, IUBMB, 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, modified 2012]
 
 
EC 1.13.11.57
Accepted name: gallate dioxygenase
Reaction: 3,4,5-trihydroxybenzoate + O2 = (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
For diagram of the protocatechuate 3,4-cleavage pathway, click here
Glossary: 3,4,5-trihydroxybenzoate = gallate
Other name(s): GalA; gallate:oxygen oxidoreductase
Systematic name: 3,4,5-trihydroxybenzoate:oxygen oxidoreductase
Comments: Contains non-heme Fe2+. The enzyme is a ring-cleavage dioxygenase that acts specifically on 3,4,5-trihydroxybenzoate to produce the keto-tautomer of 4-oxalomesaconate [1,2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD
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., Jiménez-Barbero, J., Serra B., Pingarrón, J. M., García, J. L. and Díaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359–374. [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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 1.13.12.14
Transferred entry: chlorophyllide-a oxygenase. Now EC 1.14.13.122, chlorophyllide-a oxygenase
[EC 1.13.12.14 created 2006, deleted 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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, IUBMB, 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 1.14.13.122
Accepted name: chlorophyllide-a oxygenase
Reaction: chlorophyllide a + 2 O2 + 2 NADPH + 2 H+ = chlorophyllide b + 3 H2O + 2 NADP+ (overall reaction)
(1a) chlorophyllide a + O2 + NADPH + H+ = 71-hydroxychlorophyllide a + H2O + NADP+
(1b) 71-hydroxychlorophyllide a + O2 + NADPH + H+ = chlorophyllide b + 2 H2O + NADP+
For diagram of the chlorophyll cycle, click here
Other name(s): chlorophyllide a oxygenase; chlorophyll-b synthase; CAO
Systematic name: chlorophyllide-a:oxygen 71-oxidoreductase
Comments: Chlorophyll b is required for the assembly of stable light-harvesting complexes (LHCs) in the chloroplast of green algae, cyanobacteria and plants [2,3]. Contains a mononuclear iron centre [3]. The enzyme catalyses two successive hydroxylations at the 7-methyl group of chlorophyllide a. The second step yields the aldehyde hydrate, which loses H2O spontaneously to form chlorophyllide b [2]. Chlorophyll a and protochlorophyllide a are not substrates [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 216503-73-0
References:
1.  Espineda, C.E., Linford, A.S., Devine, D. and Brusslan, J.A. The AtCAO gene, encoding chlorophyll a oxygenase, is required for chlorophyll b synthesis in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 96 (1999) 10507–10511. [PMID: 10468639]
2.  Oster, U., Tanaka, R., Tanaka, A. and Rüdiger, W. Cloning and functional expression of the gene encoding the key enzyme for chlorophyll b biosynthesis (CAO) from Arabidopsis thaliana. Plant J. 21 (2000) 305–310. [PMID: 10758481]
3.  Eggink, L.L., LoBrutto, R., Brune, D.C., Brusslan, J., Yamasato, A., Tanaka, A. and Hoober, J.K. Synthesis of chlorophyll b: localization of chlorophyllide a oxygenase and discovery of a stable radical in the catalytic subunit. BMC Plant Biol. 4 (2004) 5. [PMID: 15086960]
4.  Porra, R.J., Schafer, W., Cmiel, E., Katheder, I. and Scheer, H. The derivation of the formyl-group oxygen of chlorophyll b in higher plants from molecular oxygen. Achievement of high enrichment of the 7-formyl-group oxygen from 18O2 in greening maize leaves. Eur. J. Biochem. 219 (1994) 671–679. [PMID: 8307032]
[EC 1.14.13.122 created 2006 as EC 1.13.12.14, transferred 2011 to EC 1.14.13.122, modified 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 costunolide biosynthesis, 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 1.14.13.123 is a mutifunctional enzyme with EC 1.1.1.314, germacrene A alcohol dehydrogenase [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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
Transferred entry: phenylalanine N-monooxygenase, now classified as EC 1.14.14.40, phenylalanine N-monooxygenase
[EC 1.14.13.124 created 2011, deleted 2017]
 
 
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 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 an oxime. It is still not known whether the decarboxylation is spontaneous or catalysed by the enzyme.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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
Transferred entry: vitamin D3 24-hydroxylase. Now EC 1.14.15.16, vitamin D3 24-hydroxylase
[EC 1.14.13.126 created 2011, deleted 2016]
 
 
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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
Other name(s): ndmC (gene name)
Systematic name: 7-methylxanthine:oxygen oxidoreductase (demethylating)
Comments: A non-heme iron oxygenase. The enzyme from the bacterium Pseudomonas putida prefers NADH over NADPH. The enzyme is specific for 7-methylxanthine [2]. Forms part of the caffeine degradation pathway.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD
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]
2.  Summers, R.M., Louie, T.M., Yu, C.L., Gakhar, L., Louie, K.C. and Subramanian, M. Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids. J. Bacteriol. 194 (2012) 2041–2049. [PMID: 22328667]
[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
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 133425-64-6
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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
Transferred entry: (S)-2-hydroxypropylphosphonic acid epoxidase. Now EC 1.11.1.23, (S)-2-hydroxypropylphosphonic acid epoxidase.
[EC 1.14.19.7 created 2011, deleted 2014]
 
 
EC 1.14.99.42
Accepted name: zeaxanthin 7,8-dioxygenase
Reaction: zeaxanthin + 2 O2 = crocetin dialdehyde + 2 (3S)-3-hydroxycyclocitral (overall reaction)
(1a) zeaxanthin + O2 = β-citraurin + (3S)-3-hydroxycyclocitral
(1b) β-citraurin + O2 = crocetin dialdehyde + (3S)-3-hydroxycyclocitral
For diagram of crocin biosynthesis, click here
Glossary: β-citraurin = 3-hydroxy-β-apo-8′-carotenal
Other name(s): zeaxanthin 7,8(7′,8′)-cleavage dioxygenase; CsZCD (incorrect); CCD2 (gene name)
Systematic name: zeaxanthin:oxygen oxidoreductase (7,8-cleaving)
Comments: The enzyme, characterized from the plant Crocus sativus, acts twice on zeaxanthin, cleaving 3-hydroxycyclocitral off each 3-hydroxy end group. It is part of the zeaxanthin degradation pathway in that organism, leading to the different compounds that impart the color, flavor and aroma of the saffron spice.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Frusciante, S., Diretto, G., Bruno, M., Ferrante, P., Pietrella, M., Prado-Cabrero, A., Rubio-Moraga, A., Beyer, P., Gomez-Gomez, L., Al-Babili, S. and Giuliano, G. Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis. Proc. Natl. Acad. Sci. USA 111 (2014) 12246–12251. [PMID: 25097262]
[EC 1.14.99.42 created 2011, modified 2014]
 
 
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
For diagram of soyasapogenol biosynthesis, click here
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).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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
For diagram of C30 carotenoid biosynthesis, click here
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 + AH2 + O2 = α-cryptoxanthin + A + H2O
For diagram of lutein biosynthesis, click here
Other name(s): CYP97C1; LUT1
Systematic name: α-carotene:oxygen oxidoreductase (3-hydroxylating)
Comments: A heme-thiolate protein (P-450). Also acts on zeinoxanthin to give lutein.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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, IUBMB, 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 a 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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:e884 (2010). [PMID: 21103361]
[EC 1.16.5.1 created 2011]
 
 
EC 1.16.98 With other, known, acceptors
 
EC 1.16.98.1
Transferred entry: Now EC 1.16.9.1 iron:rusticyanin reductase
[EC 1.16.98.1 created 2011, deleted 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 (ambiguous); 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-ferredoxin NAP reductase (component of naphthalene dioxygenase multicomponent enzyme system); ferredoxin-linked NAD+ reductase; NADH-ferredoxin TOL 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, IUBMB, 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 + oxidized 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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
Deleted entry: myricetin O-methyltransferase. Now covered by EC 2.1.1.267, flavonoid 3′,5′-methyltransferase.
[EC 2.1.1.149 created 2003, modified 2011, deleted 2013]
 
 
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 2.3.1.93
Accepted name: 13-hydroxylupanine O-tigloyltransferase
Reaction: (E)-2-methylcrotonoyl-CoA + 13-hydroxylupanine = CoA + 13-[(E)-2-methylcrotonoyl]oxylupanine
Glossary: (E)-2-methylcrotonoyl-CoA = tigloyl-CoA = (E)-2-methylbut-2-enoyl-CoA
Other name(s): tigloyl-CoA:13-hydroxylupanine O-tigloyltransferase; 13-hydroxylupanine acyltransferase
Systematic name: (E)-2-methylcrotonoyl-CoA:13-hydroxylupanine O-2-methylcrotonoyltransferase
Comments: Benzoyl-CoA and, more slowly, pentanoyl-CoA, 3-methylbutanoyl-CoA and butanoyl-CoA can act as acyl donors. Involved in the synthesis of lupanine alkaloids.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 85341-00-0
References:
1.  Wink, M. and Hartmann, T. Enzymatic synthesis of quinolizidine alkaloid esters: a tigloyl-CoA:13-hydroxylupanine O-tigloyl transferase from Lupinus albus L. Planta 156 (1982) 560–565.
2.  Okada, T.. Hirai, M.Y., Suzuki, H., Yamazaki, M. and Saito, K. Molecular characterization of a novel quinolizidine alkaloid O-tigloyltransferase: cDNA cloning, catalytic activity of recombinant protein and expression analysis in Lupinus plants. Plant Cell Physiol. 46 (2005) 233–244.
3.  Suzuki, H., Murakoshi, I. and Saito, K. A novel O-tigloyltransferase for alkaloid biosynthesis in plants. Purification, characterization, and distribution in Lupinus plants. J. Biol. Chem. 269 (1994) 15853–15860. [PMID: 8195240]
[EC 2.3.1.93 created 1986, modified 2011]
 
 
EC 2.3.1.196
Accepted name: benzyl alcohol O-benzoyltransferase
Reaction: benzoyl-CoA + benzyl alcohol = CoA + benzyl benzoate
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].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 2.4.1.130
Transferred entry: dolichyl-phosphate-mannose—glycolipid α-mannosyltransferase. Now covered by EC 2.4.1.258 (Dol-P-Man:Man5GlcNAc2-PP-Dol α-1,3-mannosyltransferase), EC 2.4.1.259 (Dol-P-Man:Man6GlcNAc2-PP-Dol α-1,2-mannosyltransferase), EC 2.4.1.260 (Dol-P-Man:Man7GlcNAc2-PP-Dol α-1,6-mannosyltransferase) and EC 2.4.1.261 (Dol-P-Man:Man8GlcNAc2-PP-Dol α-1,2-mannosyltransferase).
[EC 2.4.1.130 created 1984, deleted 2011]
 
 
*EC 2.4.1.131
Accepted name: GDP-Man:Man3GlcNAc2-PP-dolichol α-1,2-mannosyltransferase
Reaction: 2 GDP-α-D-mannose + α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = 2 GDP + α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol
For diagram of dolichyltetradecasaccharide biosynthesis, click here
Other name(s): ALG11; ALG11 mannosyltransferase; LEW3 (gene name); At2G40190 (gene name); gmd3 (gene name); galactomannan deficiency protein 3; GDP-mannose:glycolipid 1,2-α-D-mannosyltransferase; glycolipid 2-α-mannosyltransferase; GDP-mannose:glycolipid 2-α-D-mannosyltransferase; GDP-Man:Man3GlcNAc2-PP-Dol α-1,2-mannosyltransferase; GDP-α-D-mannose:D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol 2-α-D-mannosyltransferase
Systematic name: GDP-α-D-mannose:α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 2-α-D-mannosyltransferase (configuration-retaining)
Comments: The biosynthesis of asparagine-linked glycoproteins (N-linked protein glycosylation) utilizes a dolichyl diphosphate-linked glycosyl donor, which is assembled by the series of membrane-bound glycosyltransferases that comprise the dolichol pathway. ALG11 mannosyltransferase from Saccharomyces cerevisiae carries out two sequential steps in the formation of the lipid-linked core oligosaccharide, adding two mannose residues in α(1→2) linkages to the nascent oligosaccharide.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 74506-43-7
References:
1.  O'Reilly, M.K., Zhang, G. and Imperiali, B. In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis. Biochemistry 45 (2006) 9593–9603. [PMID: 16878994]
2.  Absmanner, B., Schmeiser, V., Kampf, M. and Lehle, L. Biochemical characterization, membrane association and identification of amino acids essential for the function of Alg11 from Saccharomyces cerevisiae, an α1,2-mannosyltransferase catalysing two sequential glycosylation steps in the formation of the lipid-linked core oligosaccharide. Biochem. J. 426 (2010) 205–217. [PMID: 19929855]
3.  Schutzbach, J.S., Springfield, J.D. and Jensen, J.W. The biosynthesis of oligosaccharide-lipids. Formation of an α-1,2-mannosyl-mannose linkage. J. Biol. Chem. 255 (1980) 4170–4175. [PMID: 6154707]
[EC 2.4.1.131 created 1984, modified 2011, modified 2012]
 
 
*EC 2.4.1.132
Accepted name: GDP-Man:Man1GlcNAc2-PP-dolichol α-1,3-mannosyltransferase
Reaction: GDP-α-D-mannose + β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = GDP + α-D-Man-(1→3)-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol
For diagram of dolichyltetradecasaccharide biosynthesis, click here
Glossary: β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = β-D-mannosyl-(1→4)-N,N′-diacetylchitobiosyldiphosphodolichol
Other name(s): Alg2 mannosyltransferase (ambiguous); ALG2 (gene name, ambiguous); glycolipid 3-α-mannosyltransferase; GDP-mannose:glycolipid 3-α-D-mannosyltransferase; GDP-Man:Man1GlcNAc2-PP-Dol α-1,3-mannosyltransferase; GDP-D-mannose:D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol 3-α-mannosyltransferase
Systematic name: GDP-α-D-mannose:β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 3-α-D-mannosyltransferase (configuration-retaining)
Comments: The biosynthesis of asparagine-linked glycoproteins utilizes a dolichyl diphosphate-linked glycosyl donor, which is assembled by the series of membrane-bound glycosyltransferases that comprise the dolichol pathway. Alg2 mannosyltransferase from Saccharomyces cerevisiae carries out an α1,3-mannosylation of D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol, followed by an α1,6-mannosylation (cf. EC 2.4.1.257), to form the first branched pentasaccharide intermediate of the dolichol pathway [1,2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 81181-76-2
References:
1.  Kampf, M., Absmanner, B., Schwarz, M. and Lehle, L. Biochemical characterization and membrane topology of Alg2 from Saccharomyces cerevisiae as a bifunctional α1,3- and 1,6-mannosyltransferase involved in lipid-linked oligosaccharide biosynthesis. J. Biol. Chem. 284 (2009) 11900–11912. [PMID: 19282279]
2.  O'Reilly, M.K., Zhang, G. and Imperiali, B. In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis. Biochemistry 45 (2006) 9593–9603. [PMID: 16878994]
[EC 2.4.1.132 created 1984, modified 2011, modified 2012]
 
 
*EC 2.4.1.191
Accepted name: luteolin-7-O-diglucuronide 4′-O-glucuronosyltransferase
Reaction: UDP-α-D-glucuronate + luteolin 7-O-[β-D-glucuronosyl-(1→2)-β-D-glucuronide] = UDP + luteolin 7-O-[β-D-glucuronosyl-(1→2)-β-D-glucuronide]-4′-O-β-D-glucuronide
For diagram of luteolin derivatives biosynthesis, click here
Other name(s): uridine diphosphoglucuronate-luteolin 7-O-diglucuronide glucuronosyltransferase; UDP-glucuronate:luteolin 7-O-diglucuronide-glucuronosyltransferase; UDPglucuronate:luteolin 7-O-diglucuronide-4′-O-glucuronosyl-transferase; LDT; UDP-glucuronate:luteolin-7-O-β-D-diglucuronide 4′-O-glucuronosyltransferase
Systematic name: UDP-α-D-glucuronate:luteolin-7-O-β-D-diglucuronide 4′-O-glucuronosyltransferase (configuration-inverting)
Comments: The enzyme participates in the biosynthesis of luteolin triglucuronide, the major flavone found in the photosynthetically-active mesophyll of the primary leaves of Secale cereale (rye).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 115490-50-1
References:
1.  Schulz, M. and Weissenböck, G. 3 specific UDP-glucuronate-flavone-glucuronosyl-transferases from primary leaves of Secale cereale. Phytochemistry 27 (1988) 1261–1267.
[EC 2.4.1.191 created 1992, modified 2011]
 
 
EC 2.4.1.256
Accepted name: dolichyl-P-Glc:Glc2Man9GlcNAc2-PP-dolichol α-1,2-glucosyltransferase
Reaction: dolichyl β-D-glucosyl phosphate + D-Glc-α-(1→3)-D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = D-Glc-α-(1→2)-D-Glc-α-(1→3)-D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate
For diagram of dolichyltetradecasaccharide biosynthesis, click here
Other name(s): ALG10; Dol-P-Glc:Glc2Man9GlcNAc2-PP-Dol α-1,2-glucosyltransferase
Systematic name: dolichyl β-D-glucosyl phosphate:D-Glc-α-(1→3)-D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol 2-α-D-glucosyltransferase
Comments: This eukaryotic enzyme performs the final step in the synthesis of the lipid-linked oligosaccharide, attaching D-glucose in an α-1,2-linkage to the outermost D-glucose in the long branch. The lipid-linked oligosaccharide is involved in N-linked protein glycosylation of selected asparagine residues of nascent polypeptide chains in eukaryotic cells.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Burda, P. and Aebi, M. The ALG10 locus of Saccharomyces cerevisiae encodes the α-1,2 glucosyltransferase of the endoplasmic reticulum: the terminal glucose of the lipid-linked oligosaccharide is required for efficient N-linked glycosylation. Glycobiology 8 (1998) 455–462. [PMID: 9597543]
[EC 2.4.1.256 created 2011, modified 2012]
 
 
EC 2.4.1.257
Accepted name: GDP-Man:Man2GlcNAc2-PP-dolichol α-1,6-mannosyltransferase
Reaction: GDP-α-D-mannose + α-D-Man-(1→3)-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = GDP + α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol
For diagram of dolichyltetradecasaccharide biosynthesis, click here
Other name(s): GDP-Man:Man2GlcNAc2-PP-Dol α-1,6-mannosyltransferase; Alg2 mannosyltransferase (ambiguous); ALG2 (gene name, ambiguous); GDP-Man:Man1GlcNAc2-PP-dolichol mannosyltransferase (ambiguous); GDP-D-mannose:D-Man-α-(1→3)-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-6-mannosyltransferase
Systematic name: GDP-α-D-mannose:α-D-Man-(1→3)-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 6-α-D-mannosyltransferase (configuration-retaining)
Comments: The biosynthesis of asparagine-linked glycoproteins utilizes a dolichyl diphosphate-linked glycosyl donor, which is assembled by the series of membrane-bound glycosyltransferases that comprise the dolichol pathway. Alg2 mannosyltransferase from Saccharomyces cerevisiae carries out an α1,3-mannosylation (cf. EC 2.4.1.132) of β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol, followed by an α1,6-mannosylation, to form the first branched pentasaccharide intermediate of the dolichol pathway [1,2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kampf, M., Absmanner, B., Schwarz, M. and Lehle, L. Biochemical characterization and membrane topology of Alg2 from Saccharomyces cerevisiae as a bifunctional α1,3- and 1,6-mannosyltransferase involved in lipid-linked oligosaccharide biosynthesis. J. Biol. Chem. 284 (2009) 11900–11912. [PMID: 19282279]
2.  O'Reilly, M.K., Zhang, G. and Imperiali, B. In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis. Biochemistry 45 (2006) 9593–9603. [PMID: 16878994]
[EC 2.4.1.257 created 2011, modified 2012]
 
 
EC 2.4.1.258
Accepted name: dolichyl-P-Man:Man5GlcNAc2-PP-dolichol α-1,3-mannosyltransferase
Reaction: dolichyl β-D-mannosyl phosphate + α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→3)-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol + dolichyl phosphate
For diagram of dolichyltetradecasaccharide biosynthesis, click here
Other name(s): Man5GlcNAc2-PP-Dol mannosyltransferase; ALG3; dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase; Not56-like protein; Alg3 α-1,3-mannosyl transferase; Dol-P-Man:Man5GlcNAc2-PP-Dol α-1,3-mannosyltransferase; dolichyl β-D-mannosyl phosphate:D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,3-mannosyltransferase
Systematic name: dolichyl β-D-mannosyl phosphate:α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 3-α-D-mannosyltransferase (configuration-inverting)
Comments: The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl diphosphate. Early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-dolichol to Man9Glc-NAc2-PP-dolichol on the lumenal side use dolichyl β-D-mannosyl phosphate. The first step of this assembly pathway on the luminal side of the endoplasmic reticulum is catalysed by ALG3.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sharma, C.B., Knauer, R. and Lehle, L. Biosynthesis of lipid-linked oligosaccharides in yeast: the ALG3 gene encodes the Dol-P-Man:Man5GlcNAc2-PP-Dol mannosyltransferase. Biol. Chem. 382 (2001) 321–328. [PMID: 11308030]
2.  Cipollo, J.F. and Trimble, R.B. The accumulation of Man(6)GlcNAc(2)-PP-dolichol in the Saccharomyces cerevisiae Δalg9 mutant reveals a regulatory role for the Alg3p α1,3-Man middle-arm addition in downstream oligosaccharide-lipid and glycoprotein glycan processing. J. Biol. Chem. 275 (2000) 4267–4277. [PMID: 10660594]
[EC 2.4.1.258 created 1976 as EC 2.4.1.130, part transferred 2011 to EC 2.4.1.258, modified 2012]
 
 
EC 2.4.1.259
Accepted name: dolichyl-P-Man:Man6GlcNAc2-PP-dolichol α-1,2-mannosyltransferase
Reaction: dolichyl β-D-mannosyl phosphate + α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→3)-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol + dolichyl phosphate
For diagram of dolichyltetradecasaccharide biosynthesis, click here
Other name(s): ALG9; ALG9 α1,2 mannosyltransferase; dolichylphosphomannose-dependent ALG9 mannosyltransferase; ALG9 mannosyltransferase; Dol-P-Man:Man6GlcNAc2-PP-Dol α-1,2-mannosyltransferase; dolichyl β-D-mannosyl phosphate:D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→3)-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,2-mannosyltransferase
Systematic name: dolichyl β-D-mannosyl phosphate:α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→3)-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 2-α-D-mannosyltransferase (configuration-inverting)
Comments: The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl diphosphate. Early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9Glc-NAc2-PP-Dol on the lumenal side use dolichyl β-D-mannosyl phosphate. ALG9 mannosyltransferase catalyses the addition of two different α-1,2-mannose residues - the addition of α-1,2-mannose to Man6GlcNAc2-PP-Dol (EC 2.4.1.259) and the addition of α-1,2-mannose to Man8GlcNAc2-PP-Dol (EC 2.4.1.261).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Vleugels, W., Keldermans, L., Jaeken, J., Butters, T.D., Michalski, J.C., Matthijs, G. and Foulquier, F. Quality control of glycoproteins bearing truncated glycans in an ALG9-defective (CDG-IL) patient. Glycobiology 19 (2009) 910–917. [PMID: 19451548]
2.  Cipollo, J.F. and Trimble, R.B. The accumulation of Man(6)GlcNAc(2)-PP-dolichol in the Saccharomyces cerevisiae Δalg9 mutant reveals a regulatory role for the Alg3p α1,3-Man middle-arm addition in downstream oligosaccharide-lipid and glycoprotein glycan processing. J. Biol. Chem. 275 (2000) 4267–4277. [PMID: 10660594]
3.  Frank, C.G. and Aebi, M. ALG9 mannosyltransferase is involved in two different steps of lipid-linked oligosaccharide biosynthesis. Glycobiology 15 (2005) 1156–1163. [PMID: 15987956]
[EC 2.4.1.259 created 1976 as EC 2.4.1.130, part transferred 2011 to EC 2.4.1.259, modified 2012]
 
 
EC 2.4.1.260
Accepted name: dolichyl-P-Man:Man7GlcNAc2-PP-dolichol α-1,6-mannosyltransferase
Reaction: dolichyl β-D-mannosyl phosphate + α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→6)]-β-D-Man-β-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = α-D-Man-α-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol + dolichyl phosphate
For diagram of dolichyltetradecasaccharide biosynthesis, click here
Other name(s): ALG12; ALG12 mannosyltransferase; ALG12 α1,6mannosyltransferase; dolichyl-P-mannose:Man7GlcNAc2-PP-dolichyl mannosyltransferase; dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl α6-mannosyltransferase; EBS4; Dol-P-Man:Man7GlcNAc2-PP-Dol α-1,6-mannosyltransferase; dolichyl β-D-mannosyl phosphate:D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,6-mannosyltransferase
Systematic name: dolichyl β-D-mannosyl phosphate:α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→6)]-β-D-Man-β-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 6-α-D-mannosyltransferase (configuration-inverting)
Comments: The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl diphosphate. Early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9Glc-NAc2-PP-Dol on the lumenal side use dolichyl β-D-mannosyl phosphate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Frank, C.G. and Aebi, M. ALG9 mannosyltransferase is involved in two different steps of lipid-linked oligosaccharide biosynthesis. Glycobiology 15 (2005) 1156–1163. [PMID: 15987956]
2.  Hong, Z., Jin, H., Fitchette, A.C., Xia, Y., Monk, A.M., Faye, L. and Li, J. Mutations of an α1,6 mannosyltransferase inhibit endoplasmic reticulum-associated degradation of defective brassinosteroid receptors in Arabidopsis. Plant Cell 21 (2009) 3792–3802. [PMID: 20023196]
3.  Cipollo, J.F. and Trimble, R.B. The Saccharomyces cerevisiae alg12δ mutant reveals a role for the middle-arm α1,2Man- and upper-arm α1,2Manα1,6Man- residues of Glc3Man9GlcNAc2-PP-Dol in regulating glycoprotein glycan processing in the endoplasmic reticulum and Golgi apparatus. Glycobiology 12 (2002) 749–762. [PMID: 12460943]
4.  Grubenmann, C.E., Frank, C.G., Kjaergaard, S., Berger, E.G., Aebi, M. and Hennet, T. ALG12 mannosyltransferase defect in congenital disorder of glycosylation type lg. Hum. Mol. Genet. 11 (2002) 2331–2339. [PMID: 12217961]
[EC 2.4.1.260 created 1976 as EC 2.4.1.130, part transferred 2011 to EC 2.4.1.160, modified 2012]
 
 
EC 2.4.1.261
Accepted name: dolichyl-P-Man:Man8GlcNAc2-PP-dolichol α-1,2-mannosyltransferase
Reaction: dolichyl β-D-mannosyl phosphate + α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol = α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol + dolichyl phosphate
For diagram of dolichyltetradecasaccharide biosynthesis, click here
Other name(s): ALG9; ALG9 α1,2 mannosyltransferase; dolichylphosphomannose-dependent ALG9 mannosyltransferase; ALG9 mannosyltransferase; Dol-P-Man:Man8GlcNAc2-PP-Dol α-1,2-mannosyltransferase; dolichyl β-D-mannosyl phosphate:D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol 2-α-D-mannosyltransferase
Systematic name: dolichyl β-D-mannosyl phosphate:α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol 2-α-D-mannosyltransferase (configuration-inverting)
Comments: The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl diphosphate. Early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9Glc-NAc2-PP-Dol on the lumenal side use dolichyl β-D-mannosyl phosphate. ALG9 mannosyltransferase catalyses the addition of two different α-1,2-mannose residues: the addition of α-1,2-mannose to Man6GlcNAc2-PP-Dol (EC 2.4.1.259) and the addition of α-1,2-mannose to Man8GlcNAc2-PP-Dol (EC 2.4.1.261).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Vleugels, W., Keldermans, L., Jaeken, J., Butters, T.D., Michalski, J.C., Matthijs, G. and Foulquier, F. Quality control of glycoproteins bearing truncated glycans in an ALG9-defective (CDG-IL) patient. Glycobiology 19 (2009) 910–917. [PMID: 19451548]
2.  Frank, C.G. and Aebi, M. ALG9 mannosyltransferase is involved in two different steps of lipid-linked oligosaccharide biosynthesis. Glycobiology 15 (2005) 1156–1163. [PMID: 15987956]
[EC 2.4.1.261 created 1976 as EC 2.4.1.130, part transferred 2011 to EC 2.4.1.261, modified 2012]
 
 
EC 2.4.1.262
Accepted name: soyasapogenol glucuronosyltransferase
Reaction: UDP-α-D-glucuronate + soyasapogenol B = UDP + soyasapogenol B 3-O-β-D-glucuronide
For diagram of soyasapogenol biosynthesis, click here
Other name(s): UGASGT; UDP-D-glucuronate:soyasapogenol 3-O-D-glucuronosyltransferase
Systematic name: UDP-α-D-glucuronate:soyasapogenol 3-O-D-glucuronosyltransferase (configuration-inverting)
Comments: Requires a divalent ion, Mg2+ better than Mn2+, better than Ca2+. Also acts on soysapogenol A and E.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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-α-D-glucose + abscisate = UDP + β-D-glucopyranosyl abscisate
For diagram of abscisic acid biosynthesis, click here
Other name(s): ABA-glucosyltransferase; ABA-GTase; AOG; UDP-D-glucose:abscisate β-D-glucosyltransferase
Systematic name: UDP-α-D-glucose:abscisate β-D-glucosyltransferase (configuration-inverting)
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 terpenoid biosynthesis, 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, IUBMB, 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 2.5.1.31
Accepted name: ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
Reaction: (2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + ditrans,octacis-undecaprenyl diphosphate
For diagram of di- and tritrans,polycis-polyprenol biosynthesis, click here
Other name(s): di-trans,poly-cis-undecaprenyl-diphosphate synthase; undecaprenyl-diphosphate synthase; bactoprenyl-diphosphate synthase; UPP synthetase; undecaprenyl diphosphate synthetase; undecaprenyl pyrophosphate synthetase; di-trans,poly-cis-decaprenylcistransferase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 8 isopentenyl units)
Comments: Undecaprenyl pyrophosphate synthase catalyses the consecutive condensation reactions of a farnesyl diphosphate with eight isopentenyl diphosphates, in which new cis-double bonds are formed, to generate undecaprenyl diphosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 52350-87-5
References:
1.  Muth, J.D. and Allen, C.M. Undecaprenyl pyrophosphate synthetase from Lactobacillus plantarum: a dimeric protein. Arch. Biochem. Biophys. 230 (1984) 49–60. [PMID: 6712246]
2.  Takahashi, I. and Ogura, K. Prenyltransferases of Bacillus subtilis: undecaprenyl pyrophosphate synthetase and geranylgeranyl pyrophosphate synthetase. J. Biochem. (Tokyo) 92 (1982) 1527–1537. [PMID: 6818223]
3.  Guo, R.T., Ko, T.P., Chen, A.P., Kuo, C.J., Wang, A.H. and Liang, P.H. Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis. J. Biol. Chem. 280 (2005) 20762–20774. [PMID: 15788389]
4.  Ko, T.P., Chen, Y.K., Robinson, H., Tsai, P.C., Gao, Y.G., Chen, A.P., Wang, A.H. and Liang, P.H. Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis. J. Biol. Chem. 276 (2001) 47474–47482. [PMID: 11581264]
5.  Fujikura, K., Zhang, Y.W., Fujihashi, M., Miki, K. and Koyama, T. Mutational analysis of allylic substrate binding site of Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase. Biochemistry 42 (2003) 4035–4041. [PMID: 12680756]
6.  Fujihashi, M., Zhang, Y.W., Higuchi, Y., Li, X.Y., Koyama, T. and Miki, K. Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase. Proc. Natl. Acad. Sci. USA 98 (2001) 4337–4342. [PMID: 11287651]
7.  Pan, J.J., Chiou, S.T. and Liang, P.H. Product distribution and pre-steady-state kinetic analysis of Escherichia coli undecaprenyl pyrophosphate synthase reaction. Biochemistry 39 (2000) 10936–10942. [PMID: 10978182]
8.  Kharel, Y., Zhang, Y.W., Fujihashi, M., Miki, K. and Koyama, T. Significance of highly conserved aromatic residues in Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase. J. Biochem. 134 (2003) 819–826. [PMID: 14769870]
[EC 2.5.1.31 created 1984, modified 2011]
 
 
*EC 2.5.1.89
Accepted name: tritrans,polycis-undecaprenyl-diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + tritrans,heptacis-undecaprenyl diphosphate
For diagram of di- and tritrans,polycis-polyprenol biosynthesis, click here
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 7 isopentenyl units)
Comments: This enzyme is involved in the biosynthesis of the glycosyl carrier lipid in some archaebacteria. Unlike EC 2.5.1.31, its counterpart in most bacteria, it prefers geranylgeranyl diphosphate to farnesyl diphosphate as the allylic substrate, resulting in production of a tritrans,polycis variant of undecaprenyl diphosphate [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hemmi, H., Yamashita, S., Shimoyama, T., Nakayama, T. and Nishino, T. Cloning, expression, and characterization of cis-polyprenyl diphosphate synthase from the thermoacidophilic archaeon Sulfolobus acidocaldarius. J. Bacteriol. 183 (2001) 401–404. [PMID: 11114943]
[EC 2.5.1.89 created 2010, modified 2011]
 
 
*EC 2.5.1.92
Accepted name: (2Z,6Z)-farnesyl diphosphate synthase
Reaction: dimethylallyl diphosphate + 2 isopentenyl diphosphate = 2 diphosphate + (2Z,6Z)-farnesyl diphosphate
For diagram of all-cis-polyprenyl diphosphate, click here
Other name(s): cis,cis-farnesyl diphosphate synthase; Z,Z-FPP synthase; zFPS; Z,Z-farnesyl pyrophosphate synthase
Systematic name: dimethylallyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 2 isopentenyl units)
Comments: This enzyme, originally characterized from wild tomato, specifically forms (2Z,6Z)-farnesyl diphosphate via neryl diphosphate and isopentenyl diphosphate. In wild tomato it is involved in the biosynthesis of several sesquiterpenes. See also EC 2.5.1.68 [(2Z,6E)-farnesyl diphosphate synthase] and EC 2.5.1.10 [(2E,6E)-farnesyl diphosphate synthase].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301–317. [PMID: 19155349]
[EC 2.5.1.92 created 2010, 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-acetylmuramate 6-phosphate
Other name(s): anhMurNAc kinase; AnmK
Systematic name: ATP:1,6-anhydro-N-acetyl-β-muramate 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. The product N-acetylmuramate 6-phosphate is produced as a 7:1 mixture of the α- and β-anomers.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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]
3.  Bacik, J.P., Whitworth, G.E., Stubbs, K.A., Yadav, A.K., Martin, D.R., Bailey-Elkin, B.A., Vocadlo, D.J. and Mark, B.L. Molecular basis of 1,6-anhydro bond cleavage and phosphoryl transfer by Pseudomonas aeruginosa 1,6-anhydro-N-acetylmuramic acid kinase. J. Biol. Chem. 286 (2011) 12283–12291. [PMID: 21288904]
[EC 2.7.1.170 created 2011, modified 2011]
 
 
*EC 2.7.8.30
Transferred entry: undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase. Now EC 2.4.2.53, undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
[EC 2.7.8.30 created 2010, modified 2011, deleted 2013]
 
 
EC 2.7.8.33
Accepted name: UDP-N-acetylglucosamine—undecaprenyl-phosphate N-acetylglucosaminephosphotransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + ditrans,octacis-undecaprenyl phosphate = UMP + N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Glossary: N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = lipid I = GlcNAc-pyrophosphorylundecaprenol = ditrans,octacis-undecaprenyl-N-acetyl-α-D-glucosaminyl diphosphate
Other name(s): UDP-N-acetylglucosamine:undecaprenyl-phosphate GlcNAc-1-phosphate transferase; WecA; WecA transferase; UDP-GIcNAc:undecaprenyl phosphate N-acetylglucosaminyl 1-P transferase; GlcNAc-P-P-Und synthase; GPT (ambiguous); TagO; UDP-GlcNAc:undecaprenyl-phosphate GlcNAc-1-phosphate transferase; UDP-N-acetyl-D-glucosamine:ditrans,octacis-undecaprenyl phosphate N-acetylglucosaminephosphotransferase
Systematic name: UDP-N-acetyl-α-D-glucosamine:ditrans,octacis-undecaprenyl phosphate N-acetyl-α-D-glucosaminephosphotransferase
Comments: This enzyme catalyses the synthesis of N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol, an essential lipid intermediate for the biosynthesis of various bacterial cell envelope components. The enzyme also initiates the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide in certain Escherichia coli strains, including K-12 [2] and of teichoic acid in certain Gram-positive bacteria [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Al-Dabbagh, B., Mengin-Lecreulx, D. and Bouhss, A. Purification and characterization of the bacterial UDP-GlcNAc:undecaprenyl-phosphate GlcNAc-1-phosphate transferase WecA. J. Bacteriol. 190 (2008) 7141–7146. [PMID: 18723618]
2.  Lehrer, J., Vigeant, K.A., Tatar, L.D. and Valvano, M.A. Functional characterization and membrane topology of Escherichia coli WecA, a sugar-phosphate transferase initiating the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide. J. Bacteriol. 189 (2007) 2618–2628. [PMID: 17237164]
3.  Rush, J.S., Rick, P.D. and Waechter, C.J. Polyisoprenyl phosphate specificity of UDP-GlcNAc:undecaprenyl phosphate N-acetylglucosaminyl 1-P transferase from E.coli. Glycobiology 7 (1997) 315–322. [PMID: 9134438]
4.  Soldo, B., Lazarevic, V. and Karamata, D. tagO is involved in the synthesis of all anionic cell-wall polymers in Bacillus subtilis 168. Microbiology 148 (2002) 2079–2087. [PMID: 12101296]
[EC 2.7.8.33 created 2011]
 
 
*EC 2.8.1.6
Accepted name: biotin synthase
Reaction: dethiobiotin + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + 2 reduced [2Fe-2S] ferredoxin = biotin + (sulfur carrier) + 2 L-methionine + 2 5′-deoxyadenosine + 2 oxidized [2Fe-2S] ferredoxin
Other name(s): dethiobiotin:sulfur sulfurtransferase
Systematic name: dethiobiotin:sulfur-(sulfur carrier) 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 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, IUBMB, 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, modified 2014]
 
 
EC 3.1.1.85
Accepted name: pimelyl-[acyl-carrier protein] methyl ester esterase
Reaction: pimeloyl-[acyl-carrier protein] methyl ester + H2O = pimeloyl-[acyl-carrier protein] + methanol
Other name(s): BioH
Systematic name: pimeloyl-[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 pimeloyl-[acyl carrier protein], terminating the part of the biotin biosynthesis pathway that is catalysed by the fatty acid elongation enzymes [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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. 6 (2010) 682–688. [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].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 3.1.2.29
Accepted name: fluoroacetyl-CoA thioesterase
Reaction: fluoroacetyl-CoA + H2O = fluoroacetate + CoA
Systematic name: fluoroacetyl-CoA hydrolase
Comments: Fluoroacetate is extremely toxic. It reacts with CoA to form fluoroacetyl-CoA, which substitutes for acetyl CoA and reacts with EC 2.3.3.1 (citrate synthase) to produce fluorocitrate, a metabolite of which binds very tightly to EC 4.2.1.3 (aconitase) and halts the TCA cycle. This enzyme hydrolyses fluoroacetyl-CoA before it can react with citrate synthase, and thus confers fluoroacetate resistance on the organisms that produce it. It has been described in the poisonous plant Dichapetalum cymosum and the bacterium Streptomyces cattleya, both of which are fluoroacetate producers.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Meyer, J.J.M., Grobbelaar, N., Vleggaar, R. and Louw, A.I. Fluoroacetyl-coenzyme-A hydrolase-like activity in Dichapetalum cymosum. J. Plant Physiol. 139 (1992) 369–372.
2.  Huang, F., Haydock, S.F., Spiteller, D., Mironenko, T., Li, T.L., O'Hagan, D., Leadlay, P.F. and Spencer, J.B. The gene cluster for fluorometabolite biosynthesis in Streptomyces cattleya: a thioesterase confers resistance to fluoroacetyl-coenzyme A. Chem. Biol. 13 (2006) 475–484. [PMID: 16720268]
3.  Dias, M.V., Huang, F., Chirgadze, D.Y., Tosin, M., Spiteller, D., Dry, E.F., Leadlay, P.F., Spencer, J.B. and Blundell, T.L. Structural basis for the activity and substrate specificity of fluoroacetyl-CoA thioesterase FlK. J. Biol. Chem. 285 (2010) 22495–22504. [PMID: 20430898]
[EC 3.1.2.29 created 2011]
 
 
*EC 3.1.3.73
Accepted name: adenosylcobalamin/α-ribazole phosphatase
Reaction: (1) adenosylcobalamin 5′-phosphate + H2O = coenzyme B12 + phosphate
(2) α-ribazole 5′-phosphate + H2O = α-ribazole + phosphate
For diagram of the enzyme’s role in corrin biosynthesis, click here
Other name(s): CobC; adenosylcobalamin phosphatase; α-ribazole phosphatase
Systematic name: adenosylcobalamin/α-ribazole-5′-phosphate phosphohydrolase
Comments: This enzyme catalyses the last step in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis, characterized in Salmonella enterica [3]. It also participates in a salvage pathway that recycles cobinamide into adenosylcobalamin [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 251991-06-7
References:
1.  O'Toole, G.A., Trzebiatowski, J.R. and Escalante-Semerena, J.C. The cobC gene of Salmonella typhimurium codes for a novel phosphatase involved in the assembly of the nucleotide loop of cobalamin. J. Biol. Chem. 269 (1994) 26503–26511. [PMID: 7929373]
2.  Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390–412. [PMID: 12195810]
3.  Zayas, C.L. and Escalante-Semerena, J.C. Reassessment of the late steps of coenzyme B12 synthesis in Salmonella enterica: evidence that dephosphorylation of adenosylcobalamin-5′-phosphate by the CobC phosphatase is the last step of the pathway. J. Bacteriol. 189 (2007) 2210–2218. [PMID: 17209023]
[EC 3.1.3.73 created 2004, modified 2011]
 
 
EC 3.1.3.84
Accepted name: ADP-ribose 1′′-phosphate phosphatase
Reaction: ADP-D-ribose 1′′-phosphate + H2O = ADP-D-ribose + phosphate
Other name(s): POA1; Appr1p phosphatase; Poa1p; ADP-ribose 1′′-phosphate phosphohydrolase
Systematic name: ADP-D-ribose 1′′-phosphate phosphohydrolase
Comments: The enzyme is highly specific for ADP-D-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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 3.2.2.1
Accepted name: purine nucleosidase
Reaction: a purine nucleoside + H2O = D-ribose + a purine base
Other name(s): nucleosidase (misleading); purine β-ribosidase; purine nucleoside hydrolase; purine ribonucleosidase; ribonucleoside hydrolase (misleading); nucleoside hydrolase (misleading); N-ribosyl purine ribohydrolase; nucleosidase g; N-D-ribosylpurine ribohydrolase; inosine-adenosine-guanosine preferring nucleoside hydrolase; purine-specific nucleoside N-ribohydrolase; IAG-nucleoside hydrolase; IAG-NH
Systematic name: purine-nucleoside ribohydrolase
Comments: The enzyme from the bacterium Ochrobactrum anthropi specifically catalyses the irreversible N-riboside hydrolysis of purine nucleosides. Pyrimidine nucleosides, purine and pyrimidine nucleotides, NAD+, NADP+ and nicotinaminde mononucleotide are not substrates [6].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 9025-44-9
References:
1.  Heppel, L.A. and Hilmoe, R.J. Phosphorolysis and hydrolysis of purine ribosides from yeast. J. Biol. Chem. 198 (1952) 683–694. [PMID: 12999785]
2.  Kalckar, H.M. Biosynthetic aspects of nucleosides and nucleic acids. Pubbl. Staz. Zool. (Napoli) 23 (1951) 87–103.
3.  Takagi, Y. and Horecker, B.L. Purification and properties of a bacterial riboside hydrolyase. J. Biol. Chem. 225 (1956) 77–86. [PMID: 13416219]
4.  Tarr, H.L.A. Fish muscle riboside hydrolases. Biochem. J. 59 (1955) 386–391. [PMID: 14363106]
5.  Parkin, D.W. Purine-specific nucleoside N-ribohydrolase from Trypanosoma brucei brucei. Purification, specificity, and kinetic mechanism. J. Biol. Chem. 271 (1996) 21713–21719. [PMID: 8702965]
6.  Ogawa, J., Takeda, S., Xie, S.X., Hatanaka, H., Ashikari, T., Amachi, T. and Shimizu, S. Purification, characterization, and gene cloning of purine nucleosidase from Ochrobactrum anthropi. Appl. Environ. Microbiol. 67 (2001) 1783–1787. [PMID: 11282633]
7.  Versées, W., Decanniere, K., Van Holsbeke, E., Devroede, N. and Steyaert, J. Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax. J. Biol. Chem. 277 (2002) 15938–15946. [PMID: 11854281]
8.  Mazumder-Shivakumar, D. and Bruice, T.C. Computational study of IAG-nucleoside hydrolase: determination of the preferred ground state conformation and the role of active site residues. Biochemistry 44 (2005) 7805–7817. [PMID: 15909995]
[EC 3.2.2.1 created 1961, modified 2006, modified 2011]
 
 
*EC 3.4.13.19
Accepted name: membrane dipeptidase
Reaction: Hydrolysis of dipeptides
Other name(s): renal dipeptidase; dehydropeptidase I (DPH I); dipeptidase (ambiguous); aminodipeptidase; dipeptide hydrolase (ambiguous); dipeptidyl hydrolase (ambiguous); nonspecific dipeptidase; glycosyl-phosphatidylinositol-anchored renal dipeptidase; MDP
Comments: A membrane-bound, zinc enzyme with broad specificity. Abundant in the kidney cortex. Inhibited by bestatin and cilastatin. Type example of peptidase family M19.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, MEROPS, PDB, CAS registry number: 9031-99-6
References:
1.  Campbell, B., Lin, H., Davis, R. and Ballew, E. The purification and properties of a particulate renal dipeptidase. Biochim. Biophys. Acta 118 (1966) 371–386. [PMID: 5961612]
2.  Campbell, B.J. Renal dipeptidase. Methods Enzymol. 19 (1970) 722–729.
3.  Kropp, H., Sundelof, J.G., Hajdu, R. and Kahan, F.M. Metabolism of thienamycin and related carbapenem antibiotics by renal dipeptidase, dehydropeptidase-I. Antimicrob. Agents Chemother. 22 (1982) 62–70. [PMID: 7125632]
4.  Hooper, N.M., Keen, J.N. and Turner, A.J. Characterization of the glycosyl-phosphatidylinositol-anchored human renal dipeptidase reveals that it is more extensively glycosylated than the pig enzyme. Biochem. J. 265 (1990) 429–433. [PMID: 2137335]
[EC 3.4.13.19 created 1961 as EC 3.4.3.1 and EC 3.4.3.2, transferred 1972 to EC 3.4.13.1 and EC 3.4.13.2, transferred 1978 to EC 3.4.13.11, part transferred 1992 to EC 3.4.13.19, modified 2011]
 
 
*EC 3.4.15.1
Accepted name: peptidyl-dipeptidase A
Reaction: Release of a C-terminal dipeptide, oligopeptide┼Xaa-Yaa, when Xaa is not Pro, and Yaa is neither Asp nor Glu. Thus, conversion of angiotensin I to angiotensin II, with increase in vasoconstrictor activity, but no action on angiotensin II
Glossary: captopril = (2S)-1-(3-mercapto-2-methylpropanoyl)-L-proline
Other name(s): dipeptidyl carboxypeptidase I; peptidase P; dipeptide hydrolase (ambiguous); peptidyl dipeptidase; angiotensin converting enzyme; kininase II; angiotensin I-converting enzyme; carboxycathepsin; dipeptidyl carboxypeptidase; peptidyl dipeptidase I; peptidyl-dipeptide hydrolase; peptidyldipeptide hydrolase; endothelial cell peptidyl dipeptidase; ACE; peptidyl dipeptidase-4; PDH; peptidyl dipeptide hydrolase; DCP
Comments: A Cl--dependent, zinc glycoprotein that is generally membrane-bound. A potent inhibitor is captopril. Important in elevation of blood pressure, through formation of angiotensin II (vasoconstrictor) and destruction of bradykinin (vasodilator). Two molecular forms exist in mammalian tissues, a widely-distributed somatic form of 150- to 180-kDa that contains two non-identical catalytic sites, and a testicular form of 90- to 100-kDa that contains only a single catalytic site. Type example of peptidase family M2
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, MEROPS, PDB, CAS registry number: 9015-82-1
References:
1.  Soubrier, F., Alhenc-Gelas, F., Hubert, C., Allegrini, J., John, M., Tregear, G. and Corvol, P. Two putative active centers in human angiotensin I-converting enzyme revealed by molecular cloning. Proc. Natl. Acad. Sci. USA 85 (1988) 9386–9390. [PMID: 2849100]
2.  Ehlers, M.R.W., Fox, E.A., Strydom, D.J. and Riordan, J.F. Molecular cloning of human testicular angiotensin-converting enzyme: the testis enzyme is identical to the C-terminal half of endothelial angiotensin-converting enzyme. Proc. Natl. Acad. Sci. USA 86 (1989) 7741–7745. [PMID: 2554286]
3.  Wei, L., Clauser, E., Alhenc-Gelas, F. and Corvol, P. The two homologous domains of human angiotensin I-converting enzyme interact differently with competitive inhibitors. J. Biol. Chem. 267 (1992) 13398–13405. [PMID: 1320019]
4.  Corvol, P., Williams, T.A. and Soubrier, F. Peptidyl dipeptidase A: angiotensin I-converting enzyme. Methods Enzymol. 248 (1995) 283–305. [PMID: 7674927]
[EC 3.4.15.1 created 1972, modified 1981, modified 1989, modified 1996, modified 2011]
 
 
*EC 3.4.16.6
Accepted name: carboxypeptidase D
Reaction: Preferential release of a C-terminal arginine or lysine residue
Other name(s): cereal serine carboxypeptidase II; Saccharomyces cerevisiae KEX1 gene product; carboxypeptidase Kex1; gene KEX1 serine carboxypeptidase; KEX1 carboxypeptidase; KEX1 proteinase; KEX1DELTAp; CPDW-II; serine carboxypeptidase (misleading); Phaseolus proteinase
Comments: A carboxypeptidase with optimum pH 4.5-6.0, inhibited by diisopropyl fluorophosphate, and sensitive to thiol-blocking reagents (reviewed in [1]). In peptidase family S10 (carboxypeptidase C family).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, MEROPS, PDB, CAS registry number: 153967-26-1
References:
1.  Breddam, K. Serine carboxypeptidases. A review. Carlsberg Res. Commun. 51 (1986) 83–128.
2.  Breddam, K., Sørensen, S.B. and Svendsen, I. Primary structure and enzymatic properties of carboxypeptidase II from wheat bran. Carlsberg Res. Commun. 52 (1987) 297–311.
3.  Dmochowska, A., Dignard, D., Henning, D., Thomas, D.Y. and Bussey, H. Yeast KEX1 gene encodes a putative protease with a carboxypeptidase B-like function involved in killer toxin and α-factor precursor processing. Cell 50 (1987) 573–584. [PMID: 3301004]
4.  Liao, D.-I., Breddam, K., Sweet, R.M., Bullock, T. and Remington, S.J. Refined atomic model of wheat serine carboxypeptidase II at 2.2-Å resolution. Biochemistry 31 (1992) 9796–9812. [PMID: 1390755]
[EC 3.4.16.6 created 1972 as EC 3.4.12.1, transferred 1978 to EC 3.4.16.1, part transferred 1993 to EC 3.4.16.6 (EC 3.4.16.3 created 1972 as EC 3.4.12.12, transferred 1978 to EC 3.4.16.3, transferred 1992 to EC 3.4.16.1), (EC 3.4.21.13 created 1972, transferred 1978 to EC 3.4.16.1), modified 2011]
 
 
*EC 3.5.1.4
Accepted name: amidase
Reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3
Other name(s): acylamidase; acylase (misleading); amidohydrolase (ambiguous); deaminase (ambiguous); fatty acylamidase; N-acetylaminohydrolase (ambiguous)
Systematic name: acylamide amidohydrolase
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, UM-BBD, CAS registry number: 9012-56-0
References:
1.  Bray, H.G., James, S.P., Raffan, I.M., Ryman, B.E. and Thorpe, W.V. The fate of certain organic acids and amides in the rabbit. 7. An amidase of rabbit liver. Biochem. J. 44 (1949) 618–625. [PMID: 16748573]
2.  Bray, H.G., James, S.P., Thorpe, W.V. and Wasdell, M.R. The fate of certain organic acids and amides in the rabbit. 11. Further observations on the hydrolysis of amides by tissue extracts. Biochem. J. 47 (1950) 294–299. [PMID: 14800883]
[EC 3.5.1.4 created 1961, modified 2011]
 
 
*EC 4.1.1.31
Accepted name: phosphoenolpyruvate carboxylase
Reaction: phosphate + oxaloacetate = phosphoenolpyruvate + HCO3-
For diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here
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, IUBMB, 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 4.1.1.52
Accepted name: 6-methylsalicylate decarboxylase
Reaction: 6-methylsalicylate = 3-methylphenol + CO2
Glossary: 3-methylphenol = 3-cresol = m-cresol
Other name(s): 6-methylsalicylic acid (2,6-cresotic acid) decarboxylase; 6-MSA decarboxylase; 6-methylsalicylate carboxy-lyase
Systematic name: 6-methylsalicylate carboxy-lyase (3-methylphenol-forming)
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 37289-50-2
References:
1.  Light, R.J. 6-Methylsalicylic acid decarboxylase from Penicillium patulum. Biochim. Biophys. Acta 191 (1969) 430–438. [PMID: 5354271]
2.  Vogel, G. and Lynen, F. 6-Methylsalicylsäure-Decarboxylase. Naturwissenschaften 57 (1970) 664.
[EC 4.1.1.52 created 1972, modified 2011]
 
 
*EC 4.1.1.77
Accepted name: 2-oxo-3-hexenedioate decarboxylase
Reaction: (3E)-2-oxohex-3-enedioate = 2-oxopent-4-enoate + CO2
For diagram of catechol catabolism (meta ring cleavage), click here
Other name(s): 4-oxalocrotonate carboxy-lyase (misleading); 4-oxalocrotonate decarboxylase (misleading); cnbF (gene name); praD (gene name); amnE (gene name); nbaG (gene name); xylI (gene name)
Systematic name: (3E)-2-oxohex-3-enedioate carboxy-lyase (2-oxopent-4-enoate-forming)
Comments: Involved in the meta-cleavage pathway for the degradation of phenols, modified phenols and catechols. The enzyme has been reported to accept multiple tautomeric forms [1-4]. However, careful analysis of the stability of the different tautomers, as well as characterization of the enzyme that produces its substrate, EC 5.3.2.6, 2-hydroxymuconate tautomerase, showed that the actual substrate for the enzyme is (3E)-2-oxohex-3-enedioate [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD, CAS registry number: 37325-55-6
References:
1.  Shingler, V., Marklund, U., Powlowski, J. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J. Bacteriol. 174 (1992) 711–724. [PMID: 1732207]
2.  Takenaka, S., Murakami, S., Shinke, R. and Aoki, K. Metabolism of 2-aminophenol by Pseudomonas sp. AP-3: modified meta-cleavage pathway. Arch. Microbiol. 170 (1998) 132–137. [PMID: 9683650]
3.  Stanley, T.M., Johnson, W.H., Jr., Burks, E.A., Whitman, C.P., Hwang, C.C. and Cook, P.F. Expression and stereochemical and isotope effect studies of active 4-oxalocrotonate decarboxylase. Biochemistry 39 (2000) 718–726. [PMID: 10651637]
4.  Wang, S.C., Johnson, W.H., Jr., Czerwinski, R.M., Stamps, S.L. and Whitman, C.P. Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions. Biochemistry 46 (2007) 11919–11929. [PMID: 17902707]
5.  Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758–6768. [PMID: 19717587]
[EC 4.1.1.77 created 1999, modified 2011, modified 2012]
 
 
*EC 4.1.3.39
Accepted name: 4-hydroxy-2-oxovalerate aldolase
Reaction: (S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
For diagram of 3-phenylpropanoate catabolism, click here, for diagram of catechol catabolism (meta ring cleavage), click here and for diagram of cinnamate catabolism, click here
Glossary: (S)-4-hydroxy-2-oxopentanoate = (S)-4-hydroxy-2-oxovalerate
Other name(s): 4-hydroxy-2-ketovalerate aldolase; HOA; DmpG; 4-hydroxy-2-oxovalerate pyruvate-lyase; 4-hydroxy-2-oxopentanoate pyruvate-lyase; BphI; 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Systematic name: (S)-4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Comments: Requires Mn2+ for maximal activity [1]. The enzyme from the bacterium Pseudomonas putida is also stimulated by NADH [1]. In some bacterial species the enzyme forms a bifunctional complex with EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 4.1.3.43, 4-hydroxy-2-oxohexanoate aldolase [4,5].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD, CAS registry number: 37325-52-3
References:
1.  Manjasetty, B.A., Powlowski, J. and Vrielink, A. Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Proc. Natl. Acad. Sci. USA 100 (2003) 6992–6997. [PMID: 12764229]
2.  Powlowski, J., Sahlman, L. and Shingler, V. Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. J. Bacteriol. 175 (1993) 377–385. [PMID: 8419288]
3.  Manjasetty, B.A., Croteau, N., Powlowski, J. and Vrielink, A. Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase—aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 582–585. [PMID: 11264589]
4.  Baker, P., Carere, J. and Seah, S.Y.K. Probing the molecular basis of substrate specificity, stereospecificity, and catalysis in the class II pyruvate aldolase, BphI. Biochemistry 50 (2011) 3559–3569. [PMID: 21425833]
5.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [PMID: 22316175]
6.  Baker, P. and Seah, S.Y.K. Rational design of stereoselectivity in the class II pyruvate aldolase BphI. J. Am. Chem. Soc. 134 (2012) 507–513. [PMID: 22081904]
[EC 4.1.3.39 created 2006, modified 2011]
 
 
*EC 4.1.99.5
Accepted name: aldehyde oxygenase (deformylating)
Reaction: a long-chain aldehyde + O2 + 2 NADPH + 2 H+ = an alkane + formate + H2O + 2 NADP+
Glossary: a long-chain aldehyde = an aldehyde derived from a fatty acid with an aliphatic chain of 13-22 carbons.
Other name(s): decarbonylase; aldehyde decarbonylase; octadecanal decarbonylase; octadecanal alkane-lyase
Systematic name: a long-chain aldehyde 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 and 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, IUBMB, 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., Nørgaard, 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]
4.  Li, N., Chang, W.C., Warui, D.M., Booker, S.J., Krebs, C. and Bollinger, J.M., Jr. Evidence for only oxygenative cleavage of aldehydes to alk(a/e)nes and formate by cyanobacterial aldehyde decarbonylases. Biochemistry 51 (2012) 7908–7916. [PMID: 22947199]
[EC 4.1.99.5 created 1989, modified 2011, modified 2013]
 
 
EC 4.1.99.16
Accepted name: geosmin synthase
Reaction: (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O = (-)-geosmin + acetone
For diagram of germacrene-derived sesquiterpenoid biosynthesis, click here. For mechanism, click here
Systematic name: germacradienol geosmin-lyase (acetone forming)
Comments: Requires Mg2+. Geosmin is the cause of the characteristic smell of moist soil. It is a bifunctional enzyme. The N-terminal part of the enzyme is EC 4.2.3.22, germacradienol synthase, and forms germacradienol from FPP. The C-terminal part of the enzyme catalyses the conversion of germacradienol to geosmin via (1S,4aS,8aS)-1,4a-dimethyl-1,2,3,4,4a,5,6,8a-octahydronaphthalene.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Jiang, J., He, X. and Cane, D.E. Geosmin biosynthesis. Streptomyces coelicolor germacradienol/germacrene D synthase converts farnesyl diphosphate to geosmin. J. Am. Chem. Soc. 128 (2006) 8128–8129. [PMID: 16787064]
2.  Cane, D.E., He, X., Kobayashi, S., Omura, S. and Ikeda, H. Geosmin biosynthesis in Streptomyces avermitilis. Molecular cloning, expression, and mechanistic study of the germacradienol/geosmin synthase. J. Antibiot. (Tokyo) 59 (2006) 471–479. [PMID: 17080683]
3.  Jiang, J., He, X. and Cane, D.E. Biosynthesis of the earthy odorant geosmin by a bifunctional Streptomyces coelicolor enzyme. Nat. Chem. Biol. 3 (2007) 711–715. [PMID: 17873868]
[EC 4.1.99.16 created 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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
For diagram of hopene biosynthesis, click here
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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
For diagram of arabidiol, camellidiol and thalianol biosynthesis, click here
Glossary: arabidiol = (13R)-malabarica-17,21-diene-3β,14-diol
Other name(s): PEN1 (gene name); (S)-squalene-2,3-epoxide hydro-lyase (arabidiol forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (arabidiol forming)
Comments: The reaction occurs in the reverse direction.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
For diagram of dammarenediol II and tirucalla-7,24-dien-3β-ol biosynthesis, click here
Other name(s): dammarenediol synthase; 2,3-oxidosqualene (20S)-dammarenediol cyclase; DDS; (S)-squalene-2,3-epoxide hydro-lyase (dammarenediol-II forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (dammarenediol-II forming)
Comments: The reaction occurs in the reverse direction.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 189354-84-5
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: (R)-lactate + N-acetyl-D-glucosamine 6-phosphate = N-acetylmuramate 6-phosphate + H2O
Other name(s): MurNAc-6-P etherase; MurQ
Systematic name: (R)-lactate hydro-lyase (adding N-acetyl-D-glucosamine 6-phosphate; N-acetylmuramate 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 4.2.3.22
Accepted name: germacradienol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
For diagram of germacrene-derived sesquiterpenoid biosynthesis, click here
Other name(s): germacradienol/germacrene-D synthase; 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase [(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol-forming]
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol-forming]
Comments: Requires Mg2+ for activity. H-1si of farnesyl diphosphate is lost in the formation of (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol. Formation of (-)-germacrene D involves a stereospecific 1,3-hydride shift of H-1si of farnesyl diphosphate. Both products are formed from a common intermediate [2]. Other enzymes produce germacrene D as the sole product using a different mechanism. The enzyme mediates a key step in the biosynthesis of geosmin (see EC 4.1.99.16 geosmin synthase), a widely occurring metabolite of many streptomycetes, bacteria and fungi [2]. Also catalyses the reaction of EC 4.2.3.75, (-)-germacrene D synthase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 211049-88-6
References:
1.  Cane, D.E. and Watt, R.M. Expression and mechanistic analysis of a germacradienol synthase from Streptomyces coelicolor implicated in geosmin biosynthesis. Proc. Natl. Acad. Sci. USA 100 (2003) 1547–1551. [PMID: 12556563]
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.  Gust, B., Challis, G.L., Fowler, K., Kieser, T. and Chater, K.F. PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc. Natl. Acad. Sci. USA 100 (2003) 1541–1546. [PMID: 12563033]
[EC 4.2.3.22 created 2006, modified 2011]
 
 
EC 4.2.3.61
Accepted name: 5-epiaristolochene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-5-epiaristolochene + diphosphate
For diagram of eremophilane and spirovetivane sesquiterpenoid biosynthesis, click here
Other name(s): 5-epi-aristolochene synthase; tobacco epiaristolochene synthase; farnesyl pyrophosphate cyclase (ambiguous); EAS; TEAS
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-5-epiaristolochene-forming]
Comments: Initial cyclization gives (+)-germacrene A in an enzyme bound form which is not released to the medium.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Back, K., Yin, S. and Chappell, J. Expression of a plant sesquiterpene cyclase gene in Escherichia coli. Arch. Biochem. Biophys. 315 (1994) 527–532. [PMID: 7986100]
2.  Starks, C.M., Back, K., Chappell, J. and Noel, J.P. Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase. Science 277 (1997) 1815–1820. [PMID: 9295271]
3.  Back, K., He, S., Kim, K.U. and Shin, D.H. Cloning and bacterial expression of sesquiterpene cyclase, a key branch point enzyme for the synthesis of sesquiterpenoid phytoalexin capsidiol in UV-challenged leaves of Capsicum annuum. Plant Cell Physiol. 39 (1998) 899–904. [PMID: 9816674]
4.  Rising, K.A., Starks, C.M., Noel, J.P. and Chappell, J. Demonstration of germacrene A as an intermediate in 5-epi-aristolochene synthase catalysis. J. Am. Chem. Soc. 122 (2000) 1861–1866.
5.  Bohlmann, J., Stauber, E.J., Krock, B., Oldham, N.J., Gershenzon, J. and Baldwin, I.T. Gene expression of 5-epi-aristolochene synthase and formation of capsidiol in roots of Nicotiana attenuata and N. sylvestris. Phytochemistry 60 (2002) 109–116. [PMID: 12009313]
6.  O'Maille, P.E., Chappell, J. and Noel, J.P. Biosynthetic potential of sesquiterpene synthases: alternative products of tobacco 5-epi-aristolochene synthase. Arch. Biochem. Biophys. 448 (2006) 73–82. [PMID: 16375847]
[EC 4.2.3.61 created 2011]
 
 
EC 4.2.3.62
Accepted name: (-)-γ-cadinene synthase [(2Z,6E)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6E)-farnesyl diphosphate = (-)-γ-cadinene + diphosphate
For diagram of ent-cadinane sesquiterpenoid biosynthesis, click here
Other name(s): (-)-γ-cadinene cyclase
Systematic name: (2Z,6E)-farnesyl-diphosphate diphosphate-lyase [(-)-γ-cadinene-forming]
Comments: Isolated from the liverwort Heteroscyphus planus. cf EC 4.2.3.92 (+)-γ-cadinene synthase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Nabeta, K., Fujita, M., Komuro, K., Katayama, K., and Takasawa, T. In vitro biosynthesis of cadinanes by cell-free extracts of cultured cells of Heteroscyphus planus. J. Chem. Soc., Perkin Trans. 1 (1997) 2065–2070.
[EC 4.2.3.62 created 2011, modified 2011]
 
 
EC 4.2.3.63
Accepted name: (+)-cubenene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-cubenene + diphosphate
For diagram of ent-cadinane sesquiterpenoid biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-cubenene-forming]
Comments: Requires Mg2+.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Nabeta, K., Kigure, K., Fujita, M., Nagoya, T., Ishikawa, T., Okuyama, H. and Takasawa, T. Bioynthesis of (+)-cubenene and (+)-epicubenol by cell-free extracts of cultured cells of Heteroscyphus planus and cyclization of [2H]farnesyl diphosphates. J. Chem. Soc., Perkin Trans. 1 (1995) 1935–1939.
2.  Nabeta, K., Fujita, M., Komuro, K., Katayama, K., and Takasawa, T. In vitro biosynthesis of cadinanes by cell-free extracts of cultured cells of Heteroscyphus planus. J. Chem. Soc., Perkin Trans. 1 (1997) 2065–2070.
[EC 4.2.3.63 created 2011]
 
 
EC 4.2.3.64
Accepted name: (+)-epicubenol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (+)-epicubenol + diphosphate
For diagram of ent-cadinane sesquiterpenoid biosynthesis, click here
Other name(s): farnesyl pyrophosphate cyclase (ambiguous)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-epicubenol-forming]
Comments: Requires Mg2+. In the bacteria Streptomyces and the liverwort Heteroscyphus the (+)-isomer is formed in contrast to higher plants where the (-)-isomer is formed.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Cane, D.E., Tandon, M., and Prabhakaran, P.C. Epicubenol synthase and the enzymatic cyclization of farnesyl diphosphate. J. Am. Chem. Soc. 115 (1993) 8103–8106.
2.  Cane, D.E. and Tandon, M. Biosynthesis of (+)-epicubenol. Tetrahedron Lett. 35 (1994) 5355–5358.
3.  Cane, D.E. and Tandon, M. Epicubenol synthase and the stereochemistry of the enzymatic cyclization of farnesyl and nerolidyl diphosphate. J. Am. Chem. Soc. 117 (1995) 5602–5603.
4.  Nabeta, K., Kigure, K., Fujita, M., Nagoya, T., Ishikawa, T., Okuyama, H. and Takasawa, T. Bioynthesis of (+)-cubenene and (+)-epicubenol by cell-free extracts of cultured cells of Heteroscyphus planus and cyclization of [2H]farnesyl diphosphates. J. Chem. Soc., Perkin Trans. 1 (1995) 1935–1939.
5.  Nabeta, K., Fujita, M., Komuro, K., Katayama, K., and Takasawa, T. In vitro biosynthesis of cadinanes by cell-free extracts of cultured cells of Heteroscyphus planus. J. Chem. Soc., Perkin Trans. 1 (1997) 2065–2070.
[EC 4.2.3.64 created 2011]
 
 
EC 4.2.3.65
Accepted name: zingiberene synthase
Reaction: (2E,6E)-farnesyl diphosphate = zingiberene + diphosphate
For diagram of bisabolene biosynthesis, click here, for diagram of bisabolene biosynthesis, click here and for diagram of γ-curcumene, β-sesquiphellandrene and zingiberene biosynthesis, click here
Other name(s): α-zingiberene synthase; ZIS
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (zingiberene-forming)
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Davidovich-Rikanati, R., Lewinsohn, E., Bar, E., Iijima, Y., Pichersky, E. and Sitrit, Y. Overexpression of the lemon basil α-zingiberene synthase gene increases both mono- and sesquiterpene contents in tomato fruit. Plant J. 56 (2008) 228–238. [PMID: 18643974]
[EC 4.2.3.65 created 2011]
 
 
EC 4.2.3.66
Accepted name: β-selinene cyclase
Reaction: (2E,6E)-farnesyl diphosphate = β-selinene + diphosphate
For diagram of eudesmol and selinene biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (β-selinene-forming)
Comments: Initial cyclization gives (+)-germacrene A in an enzyme bound form which is not released to the medium.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Belingher, L., Cartayrade, A., Pauly, G. and Gleizes, M. Partial purification and properties of the sesquiterpene β-selinene cyclase from Citrofortunella mitis. Plant Sci. 84 (1992) 129–136.
[EC 4.2.3.66 created 2011]
 
 
EC 4.2.3.67
Accepted name: cis-muuroladiene synthase
Reaction: (1) (2E,6E)-farnesyl diphosphate = cis-muurola-3,5-diene + diphosphate
(2) (2E,6E)-farnesyl diphosphate = cis-muurola-4(14),5-diene + diphosphate
For diagram of cadinane sesquiterpenoid biosynthesis, click here and for diagram of cadinene, cubebol and muuroladiene biosynthesis, click here
Other name(s): MxpSS1
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cis-muuroladiene-forming)
Comments: The recombinant enzyme from black peppermint (Mentha x piperita) gave a mixture of cis-muurola-3,5-diene (45%) and cis-muurola-4(14),5-diene (43%).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Prosser, I.M., Adams, R.J., Beale, M.H., Hawkins, N.D., Phillips, A.L., Pickett, J.A. and Field, L.M. Cloning and functional characterisation of a cis-muuroladiene synthase from black peppermint (Mentha × piperita) and direct evidence for a chemotype unable to synthesise farnesene. Phytochemistry 67 (2006) 1564–1571. [PMID: 16083926]
[EC 4.2.3.67 created 2011]
 
 
EC 4.2.3.68
Accepted name: β-eudesmol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = β-eudesmol + diphosphate
For diagram of eudesmol and selinene biosynthesis, click here and for diagram of eudesmol biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (β-eudesmol-forming)
Comments: The recombinant enzyme from ginger (Zingiber zerumbet) gives 62.6% β-eudesmol, 16.8% 10-epi-γ-eudesmol (cf. EC 4.2.3.84, 10-epi-γ-eudesmol synthase), 10% α-eudesmol (cf. EC 4.2.3.85, α-eudesmol synthase), and 5.6% aristolene.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yu, F., Harada, H., Yamasaki, K., Okamoto, S., Hirase, S., Tanaka, Y., Misawa, N. and Utsumi, R. Isolation and functional characterization of a β-eudesmol synthase, a new sesquiterpene synthase from Zingiber zerumbet Smith. FEBS Lett. 582 (2008) 565–572. [PMID: 18242187]
[EC 4.2.3.68 created 2011, modified 2011, modified 2012]
 
 
EC 4.2.3.69
Accepted name: (+)-α-barbatene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-α-barbatene + diphosphate
For diagram of barbatene biosynthesis, click here and for diagram of biosynthesis of tricyclic sesquiterpenoids derived from bisabolyl cation, click here
Other name(s): AtBS
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-α-barbatene-forming]
Comments: The recombinant enzyme from the plant Arabidopsis thaliana produces 27.3% α-barbatene, 17.8% thujopsene (cf. EC 4.2.3.79, thujopsene synthase) and 9.9% β-chamigrene (cf. EC 4.2.3.78, β-chamigrene synthase) [1] plus traces of other sesquiterpenoids [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Wu, S., Schoenbeck, M.A., Greenhagen, B.T., Takahashi, S., Lee, S., Coates, R.M. and Chappell, J. Surrogate splicing for functional analysis of sesquiterpene synthase genes. Plant Physiol. 138 (2005) 1322–1333. [PMID: 15965019]
2.  Tholl, D., Chen, F., Petri, J., Gershenzon, J. and Pichersky, E. Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J. 42 (2005) 757–771. [PMID: 15918888]
[EC 4.2.3.69 created 2011, modified 2012]
 
 
EC 4.2.3.70
Accepted name: patchoulol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = patchoulol + diphosphate
For diagram of guaiene, α-gurjunene, patchoulol and viridiflorene biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (patchoulol-forming)
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Croteau, R., Munck, S.L., Akoh, C.C., Fisk, H.J. and Satterwhite, D.M. Biosynthesis of the sesquiterpene patchoulol from farnesyl pyrophosphate in leaf extracts of Pogostemon cablin (patchouli): mechanistic considerations. Arch. Biochem. Biophys. 256 (1987) 56–68. [PMID: 3038029]
2.  Munck, S.L. and Croteau, R. Purification and characterization of the sesquiterpene cyclase patchoulol synthase from Pogostemon cablin. Arch. Biochem. Biophys. 282 (1990) 58–64. [PMID: 2171435]
3.  Faraldos, J.A., Wu, S., Chappell, J. and Coates, R.M. Doubly deuterium-labeled patchouli alcohol from cyclization of singly labeled [2-2H1]farnesyl diphosphate catalyzed by recombinant patchoulol synthase. J. Am. Chem. Soc. 132 (2010) 2998–3008. [PMID: 20148554]
[EC 4.2.3.70 created 2011]
 
 
EC 4.2.3.71
Accepted name: (E,E)-germacrene B synthase
Reaction: (2E,6E)-farnesyl diphosphate = (E,E)-germacrene B + diphosphate
For diagram of germacrene-derived sesquiterpenoid biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(E,E)-germacrene-B-forming]
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  van Der Hoeven, R.S., Monforte, A.J., Breeden, D., Tanksley, S.D. and Steffens, J.C. Genetic control and evolution of sesquiterpene biosynthesis in Lycopersicon esculentum and L. hirsutum. Plant Cell 12 (2000) 2283–2294. [PMID: 11090225]
[EC 4.2.3.71 created 2011]
 
 
EC 4.2.3.72
Accepted name: α-gurjunene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (-)-α-gurjunene + diphosphate
For diagram of guaiene, α-gurjunene, patchoulol and viridiflorene biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(-)-α-gurjunene-forming]
Comments: Initial cyclization probably gives biyclogermacrene in an enzyme bound form which is not released to the medium. The enzyme from Solidago canadensis also forms a small amount of (+)-γ-gurjunene [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Schmidt, C.O., Bouwmeester, H.J., Bulow, N. and Konig, W.A. Isolation, characterization, and mechanistic studies of (-)-α-gurjunene synthase from Solidago canadensis. Arch. Biochem. Biophys. 364 (1999) 167–177. [PMID: 10190971]
[EC 4.2.3.72 created 2011]
 
 
EC 4.2.3.73
Accepted name: valencene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-valencene + diphosphate
For diagram of eremophilane and spirovetivane sesquiterpenoid biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (valencene-forming)
Comments: The recombinant enzyme from Vitis vinifera gave 49.5% (+)-valencene and 35.5% (-)-7-epi-α-selinene. Initial cyclization gives (+)-germacrene A in an enzyme bound form which is not released to the medium.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  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]
[EC 4.2.3.73 created 2011]
 
 
EC 4.2.3.74
Accepted name: presilphiperfolanol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = presilphiperfolan-8β-ol + diphosphate
For diagram of bicyclic and tricyclic sesquiterpenoids derived from humuladienyl cation, click here and for diagram of 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 4.2.3.76
Accepted name: (+)-δ-selinene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-δ-selinene + diphosphate
For diagram of gurjunene, patchoulol and selinene biosynthesis, 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 germacrene sesquiterpenoid biosynthesis, 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).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 4.3.1.20
Accepted name: erythro-3-hydroxy-L-aspartate ammonia-lyase
Reaction: erythro-3-hydroxy-L-aspartate = oxaloacetate + NH3
Other name(s): erythro-β-hydroxyaspartate dehydratase; erythro-3-hydroxyaspartate dehydratase; erythro-3-hydroxy-Ls-aspartate hydro-lyase (deaminating); erythro-3-hydroxy-Ls-aspartate ammonia-lyase
Systematic name: erythro-3-hydroxy-L-aspartate ammonia-lyase (oxaloacetate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, which was characterized from the bacterium Paracoccus denitrificans NCIMB 8944, is highly specific for the L-isomer of erythro-3-hydroxyaspartate. Different from EC 4.3.1.16, threo-3-hydroxy-L-aspartate ammonia-lyase and EC 4.3.1.27, threo-3-hydroxy-D-aspartate ammonia-lyase. Requires a divalent cation such as Mn2+, Mg2+, and Ca2+.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 37290-74-7
References:
1.  Gibbs, R.G. and Morris, J.G. Purification and properties of erythro-β-hydroxyaspartate dehydratase from Micrococcus denitrificans. Biochem. J. 97 (1965) 547–554. [PMID: 16749162]
[EC 4.3.1.20 created 1972 as EC 4.2.1.38, transferred 2001 to EC 4.3.1.20, modified 2011]
 
 
EC 5.3.3.16
Transferred entry: 4-oxalomesaconate tautomerase. Now EC 5.3.2.8, 4-oxalomesaconate tautomerase
[EC 5.3.3.16 created 2011, modified 2011, deleted 2013]
 
 
EC 5.4.99.31
Accepted name: thalianol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = thalianol
Other name(s): (S)-2,3-epoxysqualene mutase (cyclizing, thalianol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, thalianol-forming)
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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: (3S)-2,3-epoxy-2,3-dihydrosqualene = (17Z)-protosta-17(20),24-dien-3β-ol
For diagram of cucurbitadienol, cycloartenol, lanosterol and prostadienol biosynthesis, click here
Other name(s): PdsA; (S)-2,3-epoxysqualene mutase [cyclizing, (17Z)-protosta-17(20),24-dien-3β-ol-forming]
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene 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.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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: (3S)-2,3-epoxy-2,3-dihydrosqualene = cucurbitadienol
For diagram of cucurbitadienol, cycloartenol, lanosterol and prostadienol biosynthesis, click here
Other name(s): CPQ (gene name); (S)-2,3-epoxysqualene mutase (cyclizing, cucurbitadienol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, cucurbitadienol-forming)
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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: (3S)-2,3-epoxy-2,3-dihydrosqualene = germanicol
For diagram of α-amyrin, α-seco-amyrin and germanicol biosynthesis, click here
Other name(s): RsM1; (S)-2,3-epoxysqualene mutase (cyclizing, germanicol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualenee mutase (cyclizing, germanicol-forming)
Comments: The enzyme produces germanicol, β-amyrin and lupeol in the ratio 63:33:4.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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: (3S)-2,3-epoxy-2,3-dihydrosqualene = taraxerol
For diagram of friedelin, glutinol, isomultiflorenol and taraxerol biosynthesis, click here
Other name(s): RsM2; (S)-2,3-epoxysqualene mutase (cyclizing, taraxerol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, taraxerol-forming)
Comments: The enzyme gives taraxerol, β-amyrin and lupeol in the ratio 70:17:13.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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: (3S)-2,3-epoxy-2,3-dihydrosqualene = isomultiflorenol
For diagram of friedelin, glutinol, isomultiflorenol and taraxerol biosynthesis, click here
Other name(s): LcIMS1; (S)-2,3-epoxysqualene mutase (cyclizing, isomultiflorenol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualenee mutase (cyclizing, isomultiflorenol-forming)
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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 6.3.2.31
Accepted name: coenzyme F420-0:L-glutamate ligase
Reaction: GTP + coenzyme F420-0 + L-glutamate = GDP + phosphate + coenzyme F420-1
For diagram of coenzyme F420 biosynthesis, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-0 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to cofactor F420 by two distinct and independent reactions. In the reaction described here the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction (EC 6.3.2.34, coenzyme F420-1—γ-L-glutamate ligase) it catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771–9778. [PMID: 12911320]
2.  Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456–469. [PMID: 17669425]
[EC 6.3.2.31 created 2010]
 
 
EC 6.3.2.37
Accepted name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—D-lysine ligase
Reaction: ATP + UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate + D-lysine = ADP + phosphate + UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-Nε-D-lysine
Glossary: muramic acid = 2-amino-3-O-[(R)-1-carboxyethyl]-2-deoxy-D-glucose
Other name(s): UDP-MurNAc-L-Ala-D-Glu:D-Lys ligase; D-lysine-adding enzyme
Systematic name: UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate:D-lysine γ-ligase (ADP-forming)
Comments: Involved in the synthesis of cell-wall peptidoglycan. The D-lysine is attached to the peptide chain at the N6 position. The enzyme from Thermotoga maritima also performs the reaction of EC 6.3.2.7, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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, modified 2015]
 
 
EC 6.4.1.8
Accepted name: acetophenone carboxylase
Reaction: 2 ATP + acetophenone + HCO3- + H2O + H+ = 2 ADP + 2 phosphate + 3-oxo-3-phenylpropanoate
Systematic name: acetophenone:carbon-dioxide ligase (ADP-forming)
Comments: The enzyme is involved in anaerobic degradation of ethylbenzene. No activity with acetone, butanone, 4-hydroxy-acetophenone or 4-amino-acetophenone.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD
References:
1.  Jobst, B., Schuhle, K., Linne, U. and Heider, J. ATP-dependent carboxylation of acetophenone by a novel type of carboxylase. J. Bacteriol. 192 (2010) 1387–1394. [PMID: 20047908]
[EC 6.4.1.8 created 2011]
 
 


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