Proposed Changes to the Enzyme List

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. [DOI] [PMID: 11073908]

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

1.1.1.313

Accepted name:

sulfoacetaldehyde reductase (NADPH)

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. cf. EC 1.1.1.433, sulfoacetaldehyde reductase (NADH).

Links to other databases:

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. [DOI] [PMID: 20133363]

[EC 1.1.1.313 created 2011, modified 2022]

1.1.1.314

Deleted entry:

germacrene A alcohol dehydrogenase. Now known to be catalyzed by EC 1.14.14.95, germacrene A hydroxylase

[EC 1.1.1.314 created 2011, deleted 2018]

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]

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:

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. [DOI] [PMID: 20693281]

[EC 1.2.1.81 created 2011]

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:

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. [DOI] [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. [DOI] [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, Gene, KEGG, PDB, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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, Gene, 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]

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, EAWAG-BBD, EXPASY, Gene, KEGG

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]

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, Gene, KEGG, PDB, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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]

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:

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. [DOI] [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. [DOI] [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. [DOI] [PMID: 15503129]

[EC 1.3.5.5 created 2011]

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, EAWAG-BBD, EXPASY, Gene, KEGG, 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. [DOI] [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. [DOI] [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]

1.3.7.9

Transferred entry:

4-hydroxybenzoyl-CoA reductase. Now classified as EC 1.1.7.1, 4-hydroxybenzoyl-CoA reductase.

[EC 1.3.7.9 created 2000 as EC 1.3.99.20, transferred 2011 to EC 1.3.7.9, deleted 2020]

1.3 Acting on the CH-CH group of donors

1.3.8 With a flavin as acceptor

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 a tightly-bound FAD cofactor. 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, EAWAG-BBD, EXPASY, Gene, GTD, KEGG, PDB, 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. (Ed.), 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. [DOI] [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]

1.3 Acting on the CH-CH group of donors

1.3.98 With other, known, acceptors

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, Gene, KEGG, PDB, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 19932077]

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

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]

1.3.99.15

Transferred entry:

benzoyl-CoA reductase. Now EC 1.3.7.8.

[EC 1.3.99.15 created 1999, deleted 2011]

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]

1.4 Acting on the CH-NH₂ group of donors

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]

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

Transferred entry:

NADH:ubiquinone reductase (H⁺-translocating). Now EC 7.1.1.2, NADH:ubiquinone reductase (H⁺-translocating)

[EC 1.6.5.3 created 1961, deleted 1965, reinstated 1983, modified 2011, modified 2013, deleted 2018]

1.6.5.9

Accepted name:

NADH:quinone reductase (non-electrogenic)

Reaction:

NADH + H⁺ + a quinone = NAD⁺ + a quinol

Other name(s):

type II NAD(P)H:quinone oxidoreductase; NDE2 (gene name); ndh (gene name); NDH-II; NDH-2; NADH dehydrogenase (quinone) (ambiguous); 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); NADH:ubiquinone oxidoreductase; NADH:ubiquinone reductase (non-electrogenic)

Systematic name:

NADH:quinone oxidoreductase

Comments:

A flavoprotein (FAD or FMN). Occurs in mitochondria of yeast and plants, and in aerobic bacteria. Has low activity with NADPH. Unlike EC 7.1.1.2, NADH:ubiquinone reductase (H⁺-translocating), this enzyme does not pump proteons of sodium ions across the membrane. It is also not sensitive to rotenone.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9028-04-0

References:

1.	Bergsma, J., Strijker, R., Alkema, J.Y., Seijen, H.G. and Konings, W.N. NADH dehydrogenase and NADH oxidation in membrane vesicle from Bacillus subtilis. Eur. J. Biochem. 120 (1981) 599–606. [PMID: 6800784]
2.	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. [DOI]
3.	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. [DOI] [PMID: 3138118]
4.	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]
5.	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. [DOI] [PMID: 15725055]
6.	Melo, A.M., Bandeiras, T.M. and Teixeira, M. New insights into type II NAD(P)H:quinone oxidoreductases. Microbiol. Mol. Biol. Rev. 68 (2004) 603–616. [PMID: 15590775]

[EC 1.6.5.9 created 2011 (EC 1.6.5.11 created 1972 as EC 1.6.99.5, transferred 2015 to EC 1.6.5.11, incorporated 2019), modified 2019]

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 P450_nor; 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:

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 P450_nor with nitric oxide. Implication for its nitric oxide reduction mechanism. J. Biol. Chem. 270 (1995) 1617–1623. [DOI] [PMID: 7829493]
3.	Zhang, L., Kudo, T., Takaya, N. and Shoun, H. The B′ helix determines cytochrome P450_nor specificity for the electron donors NADH and NADPH. J. Biol. Chem. 277 (2002) 33842–33847. [DOI] [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 P450_nor. J. Mol. Biol. 342 (2004) 207–217. [DOI] [PMID: 15313618]

[EC 1.7.1.14 created 2011]

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, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, 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. [DOI] [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. [DOI] [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. [DOI] [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]

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

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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 21109633]

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

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:

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. [DOI] [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. [DOI] [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. [DOI] [PMID: 15491156]

[EC 1.7.5.2 created 2011]

1.7.99.6

Transferred entry:

nitrous-oxide reductase. Now EC 1.7.2.4.

[EC 1.7.99.6 created 1989, modified 1999, deleted 2011]

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]

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:

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. [DOI] [PMID: 11807567]

[EC 1.8.1.17 created 2011]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 10809687]

[EC 1.8.2.3 created 2011]

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:

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. [DOI] [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. [DOI] [PMID: 12067345]

[EC 1.8.2.4 created 2011]

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:

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. [DOI] [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. [DOI] [PMID: 17425716]

[EC 1.8.3.6 created 2011]

1.8.5.3

Accepted name:

respiratory dimethylsulfoxide reductase

Reaction:

dimethylsulfide + menaquinone + H₂O = dimethylsulfoxide + menaquinol

For diagram of dimethyl sulfide catabolism, click here

Other name(s):

dmsABC (gene names); DMSO reductase (ambiguous); dimethylsulfoxide reductase (ambiguous)

Systematic name:

dimethyl sulfide:menaquinone oxidoreductase

Comments:

The enzyme participates in bacterial electron transfer pathways in which dimethylsulfoxide (DMSO) is the terminal electron acceptor. It is composed of three subunits - DmsA contains a bis(guanylyl molybdopterin) cofactor and a [4Fe-4S] cluster, DmsB is an iron-sulfur protein, and DmsC is a transmembrane protein that anchors the enzyme and accepts electrons from the quinol pool. The electrons are passed through DmsB to DmsA and on to DMSO. The enzyme can also reduce pyridine-N-oxide and trimethylamine N-oxide to the corresponding amines with lower activity.

Links to other databases:

References:

1.	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]
2.	Miguel, L. and Meganthan, R. Electron donors and the quinone involved in dimethyl sulfoxide reduction in Escherichia coli. Curr. Microbiol. 22 (1991) 109–115.
3.	Simala-Grant, J.L. and Weiner, J.H. Kinetic analysis and substrate specificity of Escherichia coli dimethyl sulfoxide reductase. Microbiology 142 (1996) 3231–3239. [DOI] [PMID: 8969520]
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. [DOI] [PMID: 10224050]

[EC 1.8.5.3 created 2011, modified 2019]

1.8.5.4

Accepted name:

bacterial sulfide:quinone reductase

Reaction:

n HS^- + n quinone = polysulfide + n quinol

Other name(s):

sqr (gene name); sulfide:quinone reductase (ambiguous); sulfide:quinone oxidoreductase

Systematic name:

sulfide:quinone oxidoreductase (polysulfide-producing)

Comments:

Contains FAD. Ubiquinone, plastoquinone or menaquinone can act as acceptor in different species. In some organisms the enzyme catalyses the formation of sulfur globules. It repeats the catalytic cycle without releasing the product, producing a polysulfide of up to 10 sulfur atoms. The reaction stops when the maximum length of the polysulfide that can be accommodated in the sulfide oxidation pocket is achieved. The enzyme also plays an important role in anoxygenic bacterial photosynthesis. cf. EC 1.8.5.8, sulfide quinone oxidoreductase.

Links to other databases:

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. [DOI] [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. [DOI] [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. [DOI] [PMID: 20691146]
7.	Xin, Y., Liu, H., Cui, F., Liu, H. and Xun, L. Recombinant Escherichia coli with sulfide:quinone oxidoreductase and persulfide dioxygenase rapidly oxidises sulfide to sulfite and thiosulfate via a new pathway. Environ. Microbiol. 18 (2016) 5123–5136. [PMID: 27573649]

[EC 1.8.5.4 created 2011, modified 2017, modified 2019]

*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, Gene, 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. [DOI] [PMID: 13787201]
2.	Stark, G.R. and Dawson, C.R. Ascorbic acid oxidase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), 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. [DOI] [PMID: 1548698]

[EC 1.10.3.3 created 1961, modified 2011]

1.10.3.9

Accepted name:

photosystem II

Reaction:

2 H₂O + 2 plastoquinone + 4 hν = 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:

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. [DOI] [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. [DOI] [PMID: 19219048]

[EC 1.10.3.9 created 2011]

1.10.3.10

Transferred entry:

ubiquinol oxidase (H⁺-transporting). Now EC 7.1.1.3, ubiquinol oxidase (H⁺-transporting)

[EC 1.10.3.10 created 2011, modified 2014, deleted 2018]

*EC

1.10.3.11 – private review period expired (01 July 2024) [Last modified: 2011-06-18 20:06:03]

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 7.1.1.3 and EC 7.1.1.7), 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, Gene, KEGG, MetaCyc

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. [DOI] [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. [DOI] [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). [DOI] [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. [DOI] [PMID: 22848123]

[EC 1.10.3.11 created 2011, modified 2014]

1.10.3.12

Transferred entry:

menaquinol oxidase (H⁺-transporting). Now EC 7.1.1.5, menaquinol oxidase (H⁺-transporting)

[EC 1.10.3.12 created 2011, deleted 2018]

*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, Gene, 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. [DOI] [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. [DOI] [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. [DOI] [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 (Fe^IV=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 (Fe^IV=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, EAWAG-BBD, EXPASY, KEGG, PDB, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 9790672]
10.	Pollegioni, L., Tonin, F. and Rosini, E. Lignin-degrading enzymes. FEBS J. 282 (2015) 1190–1213. [DOI] [PMID: 25649492]

[EC 1.11.1.14 created 1992, modified 2006, modified 2011, modified 2016]

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:

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. [DOI] [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. [DOI] [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. [DOI] [PMID: 20434429]

[EC 1.11.1.21 created 2011]

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:

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. [DOI] [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. [DOI] [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, Gene, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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]

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, EAWAG-BBD, EXPASY, Gene, KEGG

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. [DOI] [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. [DOI] [PMID: 21219457]

[EC 1.13.11.57 created 2011]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 18949503]

[EC 1.13.11.58 created 2011]

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]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, 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. [DOI] [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]

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]

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, Gene, 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. [DOI] [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. [DOI] [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. [DOI] [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]

1.14.13.123

Transferred entry:

germacrene A hydroxylase. Now EC 1.14.14.95, germacrene A hydroxylase

[EC 1.14.13.123 created 2011, deleted 2018]

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]

1.14.13.125

Transferred entry:

tryptophan N-monooxygenase. Now EC 1.14.14.156, tryptophan N-monooxygenase

[EC 1.14.13.125 created 2011, deleted 2018]

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]

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:

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. [DOI] [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. [DOI] [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]

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, EAWAG-BBD, EXPASY, KEGG

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. [DOI] [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. [DOI] [PMID: 22328667]

[EC 1.14.13.128 created 2011]

1.14.13.129

Transferred entry:

β-carotene 3-hydroxylase. Now EC 1.14.15.24, β-carotene 3-hydroxylase.

[EC 1.14.13.129 created 2011, deleted 2017]

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:

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. [DOI] [PMID: 9395321]

[EC 1.14.13.130 created 2011]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 17444606]

[EC 1.14.18.3 created 2011]

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]

1.14.99.42

Transferred entry:

zeaxanthin 7,8-dioxygenase. Now EC 1.13.11.84, crocetin dialdehyde synthase

[EC 1.14.99.42 created 2011, modified 2014, deleted 2017]

1.14.99.43

Transferred entry:

β-amyrin 24-hydroxylase. Now EC 1.14.14.134, β-amyrin 24-hydroxylase

[EC 1.14.99.43 created 2011, deleted 2018]

1.14.99.44

Accepted name:

diapolycopene oxygenase

Reaction:

4,4′-diapolycopene + 4 reduced acceptor + 4 O₂ = 4,4′-diapolycopenedial + 4 acceptor + 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:

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. [DOI] [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. [DOI] [PMID: 15933032]

[EC 1.14.99.44 created 2011]

1.14.99.45

Transferred entry:

carotene ε-monooxygenase. Now EC 1.14.14.158, carotene ε-monooxygenase

[EC 1.14.99.45 created 2011, deleted 2018]

*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, Gene, 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. [DOI] [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. [DOI] [PMID: 14751926]

[EC 1.16.3.1 created 1972, modified 2011]

1.16 Oxidizing metal ions

1.16.5 With a quinone or similar compound as acceptor

1.16.5.1

Transferred entry:

ascorbate ferrireductase (transmembrane). Now EC 7.2.1.3, ascorbate ferrireductase (transmembrane)

[EC 1.16.5.1 created 2011, deleted 2018]

1.16 Oxidizing metal ions

1.16.98 With other, known, acceptors

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, Gene, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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]

1.97.7.1

Accepted name:

photosystem I

Reaction:

reduced plastocyanin + oxidized ferredoxin + hν = 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:

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. [DOI] [PMID: 10504244]
3.	Chitnis, P.R. Photosystem I: function and physiology. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52 (2001) 593–626. [DOI] [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. [DOI] [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]

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 tRNA^Leu = S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2′-O-methyluridine³⁴ in tRNA^Leu

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 tRNA^LeuCmAA and tRNA^Leucmnm⁵UmAA. The enzyme is selective for the two tRNA^Leu 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:

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. [DOI] [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, 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. [PMID: 24272737]
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. [PMID: 15659437]
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]

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:

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. [DOI] [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. [DOI] [PMID: 12226525]

[EC 2.3.1.196 created 2011]

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, Gene, KEGG, PDB, 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. [DOI] [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. [DOI] [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, Gene, 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. [DOI] [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. [DOI] [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, 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]

2.4.1.256

Accepted name:

dolichyl-P-Glc:Glc₂Man₉GlcNAc₂-PP-dolichol α-1,2-glucosyltransferase

Reaction:

dolichyl β-D-glucosyl phosphate + α-D-Glc-(1→3)-α-D-Glc-(1→3)-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 + α-D-Glc-(1→2)-α-D-Glc-(1→3)-α-D-Glc-(1→3)-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

For diagram of dolichyltetradecasaccharide biosynthesis, click here

Other name(s):

ALG10; Dol-P-Glc:Glc₂Man₉GlcNAc₂-PP-Dol α-1,2-glucosyltransferase; 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

Systematic name:

dolichyl β-D-glucosyl-phosphate:α-D-Glc-(1→3)-α-D-Glc-(1→3)-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 α-1,2-glucosyltransferase (configuration-retaining)

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:

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. [DOI] [PMID: 9597543]

[EC 2.4.1.256 created 2011, modified 2012]

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:

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. [DOI] [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. [DOI] [PMID: 16878994]

[EC 2.4.1.257 created 2011, modified 2012]

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:

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. [DOI] [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. [DOI] [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]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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]

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:

Links to other databases:

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. [DOI] [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. [DOI] [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. [DOI] [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]

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:

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. [DOI] [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. [DOI] [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]

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:

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. [DOI] [PMID: 12172845]

[EC 2.4.1.262 created 2011]

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:

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. [DOI] [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, Gene, 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, Gene, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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:

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. [DOI] [PMID: 11114943]

[EC 2.5.1.89 created 2010, modified 2011]

*EC

2.5.1.92

Accepted name:

(2Z,6Z)-farnesyl diphosphate synthase

Reaction:

prenyl diphosphate + 2 isopentenyl diphosphate = 2 diphosphate + (2Z,6Z)-farnesyl diphosphate
(1a) prenyl diphosphate + isopentenyl diphosphate = diphosphate + neryl diphosphate
(1b) neryl diphosphate + isopentenyl diphosphate = diphosphate + (2Z,6Z)-farnesyl diphosphate

For diagram of all-cis-polyprenyl diphosphate, click here

Glossary:

prenyl diphosphate = dimethylallyl diphosphate

Other name(s):

cis,cis-farnesyl diphosphate synthase; Z,Z-FPP synthase; zFPS; Z,Z-farnesyl pyrophosphate synthase; dimethylallyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 2 isopentenyl units)

Systematic name:

prenyl-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:

References:

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. [DOI] [PMID: 19155349]

[EC 2.5.1.92 created 2010, modified 2011]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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

Glossary:

biotin = 5[(3aS,4S,6aR)-2-oxohexahydro(4H-thieno[4,5-d]imidazol-4-yl)]pentanoate
4,5-secobiotin = 6-[(4R,5R)-2-oxo-5-(sulfanylmethyl)imidazolidin-4-yl]hexanoate = 9-mercaptodethiobiotin

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. The first reaction produces 5′-deoxyadenosine and 4,5-secobiotin. Reaction with another equivalent of AdoMet results in abstraction of the C-6 methylene pro-S hydrogen atom from 4,5-secobiotin, and the resulting carbon radical is quenched via formation of an intramolecular C-S bond, thus closing the biotin tetrahydrothiophene 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, Gene, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 19821612]

[EC 2.8.1.6 created 1999, modified 2006, modified 2011, modified 2014]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 20693992]

[EC 3.1.1.85 created 2011]

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:

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. [DOI] [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]

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:

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. [DOI] [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. [DOI] [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 = adenosylcobalamin + phosphate
(2) α-ribazole 5′-phosphate + H₂O = α-ribazole + phosphate

For diagram of corrin biosynthesis (part 8), 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, Gene, KEGG, PDB, 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. [DOI] [PMID: 17209023]

[EC 3.1.3.73 created 2004, modified 2011]

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:

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. [DOI] [PMID: 15684411]

[EC 3.1.3.84 created 2011]

3.2.1.170

Accepted name:

mannosylglycerate hydrolase

Reaction:

2-O-(α-D-mannopyranosyl)-D-glycerate + H₂O = D-mannopyranose + D-glycerate

Other name(s):

MgH

Systematic name:

2-O-(α-D-mannopyranosyl)-D-glycerate D-mannohydrolase

Comments:

The enzyme occurs in thermophilic bacteria and has been characterized in Thermus thermophilus and Rubrobacter radiotolerans. It also has been identified in the moss Selaginella moellendorffii.

Links to other databases:

References:

1.	Alarico, S., Empadinhas, N. and da Costa, M.S. A new bacterial hydrolase specific for the compatible solutes α-D-mannopyranosyl-(1→2)-D-glycerate and α-D-glucopyranosyl-(1→2)-D-glycerate. Enzyme Microb. Technol. 52 (2013) 77–83. [DOI] [PMID: 23273275]
2.	Nobre, A., Empadinhas, N., Nobre, M.F., Lourenco, E.C., Maycock, C., Ventura, M.R., Mingote, A. and da Costa, M.S. The plant Selaginella moellendorffii possesses enzymes for synthesis and hydrolysis of the compatible solutes mannosylglycerate and glucosylglycerate. Planta 237 (2013) 891–901. [DOI] [PMID: 23179444]

[EC 3.2.1.170 created 2011, modified 2018]

*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, Gene, KEGG, PDB, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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, Gene, 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-(2-methyl-3-sulfanylpropanoyl)-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, Gene, 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. [DOI] [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. [DOI] [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, Gene, 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. [DOI] [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, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, 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, Gene, 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. [DOI] [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, Gene, 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. [DOI] [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, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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, Gene, KEGG, PDB, 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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 22947199]

[EC 4.1.99.5 created 1989, modified 2011, modified 2013]

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 geosmin biosynthesis, click here and for diagram of germacrene sesquiterpenoid biosynthesis, 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:

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. [DOI] [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. [DOI] [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. [DOI] [PMID: 17873868]

[EC 4.1.99.16 created 2011]

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 K_m for indole than the β subunit of EC 4.2.1.20.

Links to other databases:

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. [DOI] [PMID: 11756459]

[EC 4.2.1.122 created 2011]

4.2.1.123

Accepted name:

tetrahymanol synthase

Reaction:

tetrahymanol = squalene + H₂O

For diagram of hopene and tetrahymanol biosynthesis, click here

Glossary:

tetrahymanol = gammaceran-3β-ol

Systematic name:

squalene hydro-lyase (tetrahymanol-forming)

Comments:

The reaction occurs in the reverse direction.

Links to other databases:

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. [DOI] [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. [DOI] [PMID: 15959594]

[EC 4.2.1.123 created 2011]

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-3,14-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:

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. [DOI] [PMID: 16774269]

[EC 4.2.1.124 created 2011]

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, 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. [DOI] [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. [DOI] [PMID: 17088293]

[EC 4.2.1.125 created 2011]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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, Gene, 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. [DOI] [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. [DOI] [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. [DOI] [PMID: 12563033]

[EC 4.2.3.22 created 2006, modified 2011]

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:

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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 16375847]

[EC 4.2.3.61 created 2011]

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:

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]

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:

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]

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:

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]

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:

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. [DOI] [PMID: 18643974]

[EC 4.2.3.65 created 2011]

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:

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]

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:

References:

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. [DOI] [PMID: 16083926]

[EC 4.2.3.67 created 2011]

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:

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. [DOI] [PMID: 18242187]

[EC 4.2.3.68 created 2011, modified 2011, modified 2012]

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:

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. [DOI] [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. [DOI] [PMID: 15918888]

[EC 4.2.3.69 created 2011, modified 2012]

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:

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. [DOI] [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. [DOI] [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. [DOI] [PMID: 20148554]

[EC 4.2.3.70 created 2011]

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:

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]

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:

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. [DOI] [PMID: 10190971]

[EC 4.2.3.72 created 2011]

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:

References:

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. [DOI] [PMID: 15464152]

[EC 4.2.3.73 created 2011]

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:

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. [DOI] [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. [DOI] [PMID: 19476353]

[EC 4.2.3.74 created 2011]

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:

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. [DOI] [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. [DOI] [PMID: 12051690]

[EC 4.2.3.76 created 2011]

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:

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. [DOI] [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-L_s-aspartate hydro-lyase (deaminating); erythro-3-hydroxy-L_s-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, 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]

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]

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:

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. [DOI] [PMID: 15125655]

[EC 5.4.99.31 created 2011]

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:

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. [DOI] [PMID: 19216560]

[EC 5.4.99.32 created 2011]

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:

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]

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:

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. [DOI] [PMID: 17803686]

[EC 5.4.99.34 created 2011]

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:

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. [DOI] [PMID: 17803686]

[EC 5.4.99.35 created 2011]

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:

References:

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. [DOI] [PMID: 11733028]

[EC 5.4.99.36 created 2011]

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 factor F₄₂₀ (coenzyme 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:

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. [DOI] [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. [DOI] [PMID: 17669425]

[EC 6.3.2.31 created 2010]

6.3.2.37

Accepted name:

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

Reaction:

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

Glossary:

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

Other name(s):

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

Systematic name:

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

Comments:

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

Links to other databases: