The Enzyme Database

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EC 1.3.99.3      
Transferred entry: acyl-CoA dehydrogenase, now 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
[EC 1.3.99.3 created 1961 as EC 1.3.2.2, transferred 1964 to EC 1.3.99.3, deleted 2012]
 
 
EC 1.3.99.30     
Accepted name: phytoene desaturase (3,4-didehydrolycopene-forming)
Reaction: 15-cis-phytoene + 5 acceptor = all-trans-3,4-didehydrolycopene + 5 reduced acceptor (overall reaction)
(1a) 15-cis-phytoene + acceptor = all-trans-phytofluene + reduced acceptor
(1b) all-trans-phytofluene + acceptor = all-trans-ζ-carotene + reduced acceptor
(1c) all-trans-ζ-carotene + acceptor = all-trans-neurosporene + reduced acceptor
(1d) all-trans-neurosporene + acceptor = all-trans-lycopene + reduced acceptor
(1e) all-trans-lycopene + acceptor = all-trans-3,4-didehydrolycopene + reduced acceptor
For diagram of carotenoid biosynthesis, click here
Other name(s): 5-step phytoene desaturase; five-step phytoene desaturase; phytoene desaturase (ambiguous); Al-1
Systematic name: 15-cis-phytoene:acceptor oxidoreductase (3,4-didehydrolycopene-forming)
Comments: This enzyme is involved in carotenoid biosynthesis and catalyses up to five desaturation steps (cf. EC 1.3.99.28 [phytoene desaturase (neurosporene-forming)], EC 1.3.99.29 [phytoene desaturase (ζ-carotene-forming)] and EC 1.3.99.31 [phytoene desaturase (lycopene-forming)]).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hausmann, A. and Sandmann, G. A single five-step desaturase is involved in the carotenoid biosynthesis pathway to β-carotene and torulene in Neurospora crassa. Fungal Genet. Biol. 30 (2000) 147–153. [DOI] [PMID: 11017770]
2.  Estrada, A.F., Maier, D., Scherzinger, D., Avalos, J. and Al-Babili, S. Novel apocarotenoid intermediates in Neurospora crassa mutants imply a new biosynthetic reaction sequence leading to neurosporaxanthin formation. Fungal Genet. Biol. 45 (2008) 1497–1505. [DOI] [PMID: 18812228]
[EC 1.3.99.30 created 2011]
 
 
EC 1.3.99.31     
Accepted name: phytoene desaturase (lycopene-forming)
Reaction: 15-cis-phytoene + 4 acceptor = all-trans-lycopene + 4 reduced acceptor (overall reaction)
(1a) 15-cis-phytoene + acceptor = all-trans-phytofluene + reduced acceptor
(1b) all-trans-phytofluene + acceptor = all-trans-ζ-carotene + reduced acceptor
(1c) all-trans-ζ-carotene + acceptor = all-trans-neurosporene + reduced acceptor
(1d) all-trans-neurosporene + acceptor = all-trans-lycopene + reduced acceptor
For diagram of carotenoid biosynthesis, click here
Other name(s): 4-step phytoene desaturase; four-step phytoene desaturase; phytoene desaturase (ambiguous); CrtI (ambiguous)
Systematic name: 15-cis-phytoene:acceptor oxidoreductase (lycopene-forming)
Comments: Requires FAD. The enzyme is involved in carotenoid biosynthesis and catalyses up to four desaturation steps (cf. EC 1.3.99.28 [phytoene desaturase (neurosporene-forming)], EC 1.3.99.29 [phytoene desaturase (ζ-carotene-forming)] and EC 1.3.99.30 [phytoene desaturase (3,4-didehydrolycopene-forming)]).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Fraser, P.D., Misawa, N., Linden, H., Yamano, S., Kobayashi, K. and Sandmann, G. Expression in Escherichia coli, purification, and reactivation of the recombinant Erwinia uredovora phytoene desaturase. J. Biol. Chem. 267 (1992) 19891–19895. [PMID: 1400305]
[EC 1.3.99.31 created 2011]
 
 
EC 1.3.99.32     
Accepted name: glutaryl-CoA dehydrogenase (acceptor)
Reaction: glutaryl-CoA + acceptor = (E)-glutaconyl-CoA + reduced acceptor
Glossary: (E)-glutaconyl-CoA = (2E)-4-carboxybut-2-enoyl-CoA
Other name(s): GDHDes; nondecarboxylating glutaryl-coenzyme A dehydrogenase; nondecarboxylating glutaconyl-coenzyme A-forming GDH; glutaryl-CoA dehydrogenase (non-decarboxylating)
Systematic name: glutaryl-CoA:acceptor 2,3-oxidoreductase (non-decarboxylating)
Comments: The enzyme contains FAD. The anaerobic, sulfate-reducing bacterium Desulfococcus multivorans contains two glutaryl-CoA dehydrogenases: a decarboxylating enzyme (EC 1.3.8.6), and a nondecarboxylating enzyme (this entry). The two enzymes cause different structural changes around the glutaconyl carboxylate group, primarily due to the presence of either a tyrosine or a valine residue, respectively, at the active site.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wischgoll, S., Taubert, M., Peters, F., Jehmlich, N., von Bergen, M. and Boll, M. Decarboxylating and nondecarboxylating glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately anaerobic bacteria. J. Bacteriol. 191 (2009) 4401–4409. [DOI] [PMID: 19395484]
2.  Wischgoll, S., Demmer, U., Warkentin, E., Gunther, R., Boll, M. and Ermler, U. Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme A dehydrogenases. Biochemistry 49 (2010) 5350–5357. [DOI] [PMID: 20486657]
[EC 1.3.99.32 created 2012, modified 2013]
 
 
EC 1.3.99.33     
Accepted name: urocanate reductase
Reaction: dihydrourocanate + acceptor = urocanate + reduced acceptor
For diagram of histidine catabolism, click here
Glossary: urocanate = 3-(1H-imidazol-4-yl)prop-2-enoate
dihydrourocanate = 3-(1H-imidazol-4-yl)propanoate
Other name(s): urdA (gene name)
Systematic name: dihydrourocanate:acceptor oxidoreductase
Comments: The enzyme from the bacterium Shewanella oneidensis MR-1 contains a noncovalently-bound FAD and a covalently-bound FMN. It functions as part of an anaerobic electron transfer chain that utilizes urocanate as the terminal electron acceptor. The activity has been demonstrated with the artificial donor reduced methylviologen.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bogachev, A.V., Bertsova, Y.V., Bloch, D.A. and Verkhovsky, M.I. Urocanate reductase: identification of a novel anaerobic respiratory pathway in Shewanella oneidensis MR-1. Mol. Microbiol. 86 (2012) 1452–1463. [DOI] [PMID: 23078170]
[EC 1.3.99.33 created 2013]
 
 
EC 1.3.99.34      
Transferred entry: 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor). Now classified as EC 1.3.7.11, 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase.
[EC 1.3.99.34 created 2013, deleted 2015]
 
 
EC 1.3.99.35      
Transferred entry: chlorophyllide a reductase. Now EC 1.3.7.15, chlorophyllide a reductase
[EC 1.3.99.35 created 2014, deleted 2016]
 
 
EC 1.3.99.36     
Accepted name: cypemycin cysteine dehydrogenase (decarboxylating)
Reaction: cypemycin(1-18)-L-Cys-L-Leu-L-Val-L-Cys + acceptor = C3.19,S21-cyclocypemycin(1-18)-L-Ala-L-Leu-N-thioethenyl-L-valinamide + CO2 + H2S + reduced acceptor
For diagram of reaction, click here
Other name(s): cypemycin decarboxylase; CypD
Systematic name: cypemycin(1-18)-L-Cys-L-Leu-L-Val-L-Cys:acceptor oxidoreductase (decarboxylating, cyclizing)
Comments: Cypemycin, isolated from the bacterium Streptomyces sp. OH-4156, is a peptide antibiotic, member of the linaridins, a class of posttranslationally modified ribosomally synthesized peptides. The enzyme decarboxylates and reduces the C-terminal L-cysteine residue, producing a reactive ethenethiol group that reacts with a dethiolated cysteine upstream to form an aminovinyl-methyl-cysteine loop that is important for the antibiotic activity of the mature peptide.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Claesen, J. and Bibb, M. Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides. Proc. Natl. Acad. Sci. USA 107 (2010) 16297–16302. [DOI] [PMID: 20805503]
[EC 1.3.99.36 created 2014]
 
 
EC 1.3.99.37     
Accepted name: 1-hydroxy-2-isopentenylcarotenoid 3,4-desaturase
Reaction: (1) dihydroisopentenyldehydrorhodopin + acceptor = isopentenyldehydrorhodopin + reduced acceptor
(2) dihydrobisanhydrobacterioruberin + acceptor = bisanhydrobacterioruberin + reduced acceptor
For diagram of bacterioruberin biosynthesis, click here
Glossary: bisanhydrobacterioruberin = (2S,2S′)-2,2′-bis(3-methylbut-2-en-1-yl)-3,4-didehydro-1,1′,2,2′-tetrahydro-ψ,ψ-carotene-1,1′-diol
dihydrobisanhydrobacterioruberin = (2S,2S′)-2,2′-bis(3-methylbut-2-en-1-yl)-3,3′,4,4′-tetradehydro-1,1′,2,2′-tetrahydro-ψ,ψ-carotene-1,1′-diol
dihydroisopentenyldehydrorhodopin = (2S)-2-(3-methylbut-2-en-1-yl)-3,4-didehydro-1,2-dihydro-ψ,ψ-caroten-1-ol
isopentenyldehydrorhodopin = (2S)-2-(3-methylbut-2-en-1-yl)-1,2-dihydro-ψ,ψ-caroten-1-ol
Other name(s): crtD (gene name)
Systematic name: dihydroisopentenyldehydrorhodopin:acceptor 3,4-oxidoreductase
Comments: The enzyme, isolated from the archaeon Haloarcula japonica, is involved in the biosynthesis of the C50 carotenoid bacterioruberin. In this pathway it catalyses the desaturation of the C-3,4 double bond in dihydroisopentenyldehydrorhodopin and the desaturation of the C-3′,4′ double bond in dihydrobisanhydrobacterioruberin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yang, Y., Yatsunami, R., Ando, A., Miyoko, N., Fukui, T., Takaichi, S. and Nakamura, S. Complete biosynthetic pathway of the C50 carotenoid bacterioruberin from lycopene in the extremely halophilic archaeon Haloarcula japonica. J. Bacteriol. 197 (2015) 1614–1623. [DOI] [PMID: 25712483]
[EC 1.3.99.37 created 2015]
 
 
EC 1.3.99.38     
Accepted name: menaquinone-9 β-reductase
Reaction: menaquinone-9 + reduced acceptor = β-dihydromenaquinone-9 + acceptor
For diagram of vitamin K biosynthesis, click here
Glossary: β-dihydromenaquinone-9 = MK-9(II-H2) = 2-methyl-3-[(2E,10E,14E,18E,22E,26E,30E,33E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,10,14,18,22,26,30,33-octaen-1-yl]naphthalene-1,4-dione
Other name(s): MenJ
Systematic name: menaquinone-9 oxidoreductase (β-dihydromenaquinone-9-forming)
Comments: The enzyme from the bacterium Mycobacterium tuberculosis reduces the β-isoprene unit of menaquinone-9, forming the predominant form of menaquinone found in mycobacteria. Contains FAD.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Upadhyay, A., Fontes, F.L., Gonzalez-Juarrero, M., McNeil, M.R., Crans, D.C., Jackson, M. and Crick, D.C. Partial saturation of menaquinone in Mycobacterium tuberculosis: function and essentiality of a novel reductase, MenJ. ACS Cent. Sci. 1 (2015) 292–302. [DOI] [PMID: 26436137]
[EC 1.3.99.38 created 2017]
 
 
EC 1.3.99.39     
Accepted name: carotenoid φ-ring synthase
Reaction: carotenoid β-end group + 2 acceptor = carotenoid φ-end group + 2 reduced acceptor
For diagram of aromatic carotenoid biosynthesis, click here
Glossary: chlorobactene = φ,ψ-carotene
β-isorenieratene = φ,β-carotene
isorenieratene = φ,φ-carotene
Other name(s): crtU (gene name)
Systematic name: carotenoid β-ring:acceptor oxidoreductase/methyltranferase (φ-ring forming)
Comments: The enzyme, found in green sulfur bacteria, some cyanobacteria and some actinobacteria, introduces additional double bonds to the carotenoid β-end group, leading to aromatization of the ionone ring. As a result, one of the methyl groups at C-1 is transferred to position C-2. It is involved in the biosynthesis of carotenoids with φ-type aromatic end groups such as chlorobactene, β-isorenieratene, and isorenieratene.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Moshier, S.E. and Chapman, D.J. Biosynthetic studies on aromatic carotenoids. Biosynthesis of chlorobactene. Biochem. J. 136 (1973) 395–404. [PMID: 4774401]
2.  Krugel, H., Krubasik, P., Weber, K., Saluz, H.P. and Sandmann, G. Functional analysis of genes from Streptomyces griseus involved in the synthesis of isorenieratene, a carotenoid with aromatic end groups, revealed a novel type of carotenoid desaturase. Biochim. Biophys. Acta 1439 (1999) 57–64. [PMID: 10395965]
3.  Frigaard, N.U., Maresca, J.A., Yunker, C.E., Jones, A.D. and Bryant, D.A. Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. J. Bacteriol. 186 (2004) 5210–5220. [PMID: 15292122]
[EC 1.3.99.39 created 2018]
 
 


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