The Enzyme Database

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EC 2.5.1.121     Relevance: 100%
Accepted name: 5,10-dihydrophenazine-1-carboxylate 9-dimethylallyltransferase
Reaction: prenyl diphosphate + 5,10-dihydrophenazine-1-carboxylate = diphosphate + 9-prenyl-5,10-dihydrophenazine-1-carboxylate
Glossary: 9-prenyl-5,10-dihydrophenazine-1-carboxylate = 9-(3-methylbut-2-en-1-yl)-5,10-dihydrophenazine-1-carboxylate
Other name(s): PpzP; dihydrophenazine-1-carboxylate dimethylallyltransferase; 5,10-dihydrophenazine 1-carboxylate dimethylallyltransferase; dimethylallyl diphosphate:5,10-dihydrophenazine-1-carboxylate 9-dimethylallyltransferase
Systematic name: prenyl-diphosphate:5,10-dihydrophenazine-1-carboxylate 9-prenyltransferase
Comments: The enzyme is involved in the biosynthesis of prenylated phenazines by the bacterium Streptomyces anulatus. It is specific for both prenyl diphosphate and 5,10-dihydrophenazine-1-carboxylate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Saleh, O., Gust, B., Boll, B., Fiedler, H.P. and Heide, L. Aromatic prenylation in phenazine biosynthesis: dihydrophenazine-1-carboxylate dimethylallyltransferase from Streptomyces anulatus. J. Biol. Chem. 284 (2009) 14439–14447. [DOI] [PMID: 19339241]
[EC 2.5.1.121 created 2014]
 
 
EC 1.10.3.16     Relevance: 56.1%
Accepted name: dihydrophenazinedicarboxylate synthase
Reaction: (1) (1R,6R)-1,4,5,5a,6,9-hexahydrophenazine-1,6-dicarboxylate + O2 = (1R,10aS)-1,4,10,10a-tetrahydrophenazine-1,6-dicarboxylate + H2O2
(2) (1R,10aS)-1,4,10,10a-tetrahydrophenazine-1,6-dicarboxylate + O2 = (5aS)-5,5a-dihydrophenazine-1,6-dicarboxylate + H2O2
(3) (1R,10aS)-1,4,10,10a-tetrahydrophenazine-1-carboxylate + O2 = (10aS)-10,10a-dihydrophenazine-1-carboxylate + H2O2
(4) (1R)-1,4,5,10-tetrahydrophenazine-1-carboxylate + O2 = (10aS)-5,10-dihydrophenazine-1-carboxylate + H2O2
For diagram of enediyne antitumour antibiotic biosynthesis and pyocyanin biosynthesis, click here
Other name(s): phzG (gene name)
Systematic name: 1,4,5a,6,9,10a-hexahydrophenazine-1,6-dicarboxylate:oxygen oxidoreductase
Comments: Requires FMN. The enzyme, isolated from the bacteria Pseudomonas fluorescens 2-79 and Burkholderia lata 383, is involved in biosynthesis of the reduced forms of phenazine, phenazine-1-carboxylate, and phenazine-1,6-dicarboxylate, where it catalyses multiple reactions.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Xu, N., Ahuja, E.G., Janning, P., Mavrodi, D.V., Thomashow, L.S. and Blankenfeldt, W. Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 69 (2013) 1403–1413. [DOI] [PMID: 23897464]
[EC 1.10.3.16 created 2016]
 
 
EC 1.14.13.85      
Transferred entry: glyceollin synthase. Now EC 1.14.14.135, glyceollin synthase
[EC 1.14.13.85 created 2004, deleted 2018]
 
 
EC 1.14.20.3     Relevance: 28%
Accepted name: (5R)-carbapenem-3-carboxylate synthase
Reaction: (3S,5S)-carbapenam-3-carboxylate + 2-oxoglutarate + O2 = (5R)-carbapen-2-em-3-carboxylate + succinate + CO2 + H2O
Glossary: (3S,5S)-carbapenam-3-carboxylate = (2S,5S)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylate
(5R)-carbapen-2-em-3-carboxylate = (5R)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylate
Other name(s): carC (gene name)
Systematic name: (3S,5S)-carbapenam-3-carboxylate,2-oxoglutarate:oxygen oxidoreductase (dehydrating)
Comments: Requires Fe2+. The enzyme is involved in the biosynthesis of the carbapenem β-lactam antibiotic (5R)-carbapen-2-em-3-carboxylate in the bacterium Pectobacterium carotovorum. It catalyses a stereoinversion at C-5 and introduces a double bond between C-2 and C-3.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Clifton, I.J., Doan, L.X., Sleeman, M.C., Topf, M., Suzuki, H., Wilmouth, R.C. and Schofield, C.J. Crystal structure of carbapenem synthase (CarC). J. Biol. Chem. 278 (2003) 20843–20850. [DOI] [PMID: 12611886]
2.  Stapon, A., Li, R. and Townsend, C.A. Carbapenem biosynthesis: confirmation of stereochemical assignments and the role of CarC in the ring stereoinversion process from L-proline. J. Am. Chem. Soc. 125 (2003) 8486–8493. [DOI] [PMID: 12848554]
3.  Sleeman, M.C., Smith, P., Kellam, B., Chhabra, S.R., Bycroft, B.W. and Schofield, C.J. Biosynthesis of carbapenem antibiotics: new carbapenam substrates for carbapenem synthase (CarC). ChemBioChem 5 (2004) 879–882. [DOI] [PMID: 15174175]
[EC 1.14.20.3 created 2013]
 
 
EC 1.14.13.130     Relevance: 27.1%
Accepted name: pyrrole-2-carboxylate monooxygenase
Reaction: pyrrole-2-carboxylate + NADH + H+ + O2 = 5-hydroxypyrrole-2-carboxylate + NAD+ + H2O
Other name(s): pyrrole-2-carboxylate oxygenase
Systematic name: pyrrole-2-carboxylate,NADH:oxygen oxidoreductase (5-hydroxylating)
Comments: A flavoprotein (FAD). The enzyme initiates the degradation of pyrrole-2-carboxylate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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]
 
 
EC 2.5.1.34     Relevance: 26.5%
Accepted name: 4-dimethylallyltryptophan synthase
Reaction: prenyl diphosphate + L-tryptophan = diphosphate + 4-(3-methylbut-2-en-1-yl)-L-tryptophan
For diagram of ergot alkaloid biosynthesis, click here
Glossary: prenyl diphosphate = dimethylallyl diphosphate
Other name(s): dimethylallylpyrophosphate:L-tryptophan dimethylallyltransferase; dimethylallyltryptophan synthetase; dimethylallylpyrophosphate:tryptophan dimethylallyl transferase; DMAT synthetase; 4-(γ,gamma-dimethylallyl)tryptophan synthase; tryptophan dimethylallyltransferase; dimethylallyl-diphosphate:L-tryptophan 4-dimethylallyltransferase
Systematic name: prenyl-diphosphate:L-tryptophan 4-prenyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 55127-01-0
References:
1.  Lee, S.L., Floss, H.G. and Heinstein, P. Purification and properties of dimethylallylpyrophosphate:tryptophan dimethylallyl transferase, the first enzyme of ergot alkaloid biosynthesis in Claviceps sp. SD 58. Arch. Biochem. Biophys. 177 (1976) 84–94. [DOI] [PMID: 999297]
[EC 2.5.1.34 created 1984, modified 2010]
 
 
EC 1.5.1.1     Relevance: 25.8%
Accepted name: 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H]
Reaction: (1) L-pipecolate + NAD(P)+ = 1-piperideine-2-carboxylate + NAD(P)H + H+
(2) L-proline + NAD(P)+ = 1-pyrroline-2-carboxylate + NAD(P)H + H+
Other name(s): Δ1-pyrroline-2-carboxylate reductase; DELTA1-pyrroline-2-carboxylate reductase; DELTA1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (ambiguous); AbLhpI; pyrroline-2-carboxylate reductase; L-proline:NAD(P)+ 2-oxidoreductase
Systematic name: L-pipecolate/L-proline:NAD(P)+ 2-oxidoreductase
Comments: The enzymes, characterized from the bacterium Azospirillum brasilense, is involved in trans-3-hydroxy-L-proline metabolism. In contrast to EC 1.5.1.21, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH), which is specific for NADPH, this enzyme shows similar activity with NADPH and NADH.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9029-16-7
References:
1.  Meister, A., Radhakrishnan, A.N. and Buckley, S.D. Enzymatic synthesis of L-pipecolic acid and L-proline. J. Biol. Chem. 229 (1957) 789–800. [PMID: 13502341]
2.  Watanabe, S., Tanimoto, Y., Yamauchi, S., Tozawa, Y., Sawayama, S. and Watanabe, Y. Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Δ1-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria. FEBS Open Bio 4 (2014) 240–250. [DOI] [PMID: 24649405]
[EC 1.5.1.1 created 1961, modified 2015]
 
 
EC 2.5.1.111     Relevance: 25.6%
Accepted name: 4-hydroxyphenylpyruvate 3-dimethylallyltransferase
Reaction: prenyl diphosphate + 3-(4-hydroxyphenyl)pyruvate = diphosphate + 3-(4-hydroxy-3-prenylphenyl)pyruvate
For diagram of 3-dimethylallyl-4-hydroxybenzoate biosynthesis, click here and for diagram of 4-hydroxyphenylpyruvate metabolites, click here
Glossary: 3-dimethylallyl-4-hydroxyphenylpyruvate = 3-[4-hydroxy-3-(3-methylbut-2-en-1-yl)phenyl]-2-oxopropanoate
Other name(s): CloQ; 4HPP dimethylallyltransferase; NovQ; dimethylallyl diphosphate:4-hydroxyphenylpyruvate 3-dimethylallyltransferase
Systematic name: prenyl-diphosphate:3-(4-hydroxyphenyl)pyruvate 3′-prenyltransferase
Comments: The enzyme's product feeds into the biosynthesis of the aminocoumarin antibiotics clorobiocin and novobiocin [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Pojer, F., Wemakor, E., Kammerer, B., Chen, H., Walsh, C.T., Li, S.M. and Heide, L. CloQ, a prenyltransferase involved in clorobiocin biosynthesis. Proc. Natl. Acad. Sci. USA 100 (2003) 2316–2321. [DOI] [PMID: 12618544]
2.  Keller, S., Pojer, F., Heide, L. and Lawson, D.M. Crystallization and preliminary X-ray analysis of the aromatic prenyltransferase CloQ from the clorobiocin biosynthetic cluster of Streptomyces roseochromogenes. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (2006) 1153–1155. [DOI] [PMID: 17077503]
3.  Metzger, U., Keller, S., Stevenson, C.E., Heide, L. and Lawson, D.M. Structure and mechanism of the magnesium-independent aromatic prenyltransferase CloQ from the clorobiocin biosynthetic pathway. J. Mol. Biol. 404 (2010) 611–626. [DOI] [PMID: 20946900]
4.  Ozaki, T., Mishima, S., Nishiyama, M. and Kuzuyama, T. NovQ is a prenyltransferase capable of catalyzing the addition of a dimethylallyl group to both phenylpropanoids and flavonoids. J. Antibiot. (Tokyo) 62 (2009) 385–392. [DOI] [PMID: 19557032]
[EC 2.5.1.111 created 2013]
 
 
EC 1.17.3.5     Relevance: 25.6%
Accepted name: 4-oxocyclohexanecarboxylate 2-dehydrogenase
Reaction: 4-oxocyclohexane-1-carboxylate + O2 = 4-oxocyclohex-2-ene-1-carboxylate + H2O2
Glossary: 4-oxocyclohexane-1-carboxylate = 4-oxocyclohexanecarboxylate
Other name(s): chcC1 (gene name); 4-oxocyclohexanecarboxylate desaturase I; 4-oxocyclohexanecarboxylate 2-desaturase
Systematic name: 4-oxocyclohexane-1-carboxylate:oxygen oxidoreductase (4-oxocyclohex-2-ene-1-carboxylate-forming)
Comments: Contains FAD. The enzyme, characterized from the bacterium Corynebacterium cyclohexanicum, participates in a cyclohexane-1-carboxylate degradation pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kaneda, T., Obata, H. and Tokumoto, M. Aromatization of 4-oxocyclohexanecarboxylic acid to 4-hydroxybenzoic acid by two distinctive desaturases from Corynebacterium cyclohexanicum. Properties of two desaturases. Eur. J. Biochem. 218 (1993) 997–1003. [DOI] [PMID: 8281951]
2.  Yamamoto, T., Hasegawa, Y., Lau, P.CK. and Iwaki, H. Identification and characterization of a chc gene cluster responsible for the aromatization pathway of cyclohexanecarboxylate degradation in Sinomonas cyclohexanicum ATCC 51369. J. Biosci. Bioeng. 132 (2021) 621–629. [DOI] [PMID: 34583900]
[EC 1.17.3.5 created 2024]
 
 
EC 1.5.1.21     Relevance: 24.7%
Accepted name: 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH)
Reaction: (1) L-pipecolate + NADP+ = 1-piperideine-2-carboxylate + NADPH + H+
(2) L-proline + NADP+ = 1-pyrroline-2-carboxylate + NADPH + H+
Glossary: 1-piperideine-2-carboxylate = 3,4,5,6-tetrahydropyridine-2-carboxylate
Other name(s): Pyr2C reductase; 1,2-didehydropipecolate reductase; P2C reductase; 1,2-didehydropipecolic reductase; DELTA1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (ambiguous); L-pipecolate:NADP+ 2-oxidoreductase; DELTA1-piperideine-2-carboxylate reductase; Δ1-piperideine-2-carboxylate reductase
Systematic name: L-pipecolate/L-proline:NADP+ 2-oxidoreductase
Comments: The enzyme is involved in the catabolism of D-lysine and D-proline in bacteria that belong to the Pseudomonas genus. In contrast to EC 1.5.1.1, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H], which shows similar activity with NADPH and NADH, this enzyme is specific for NADPH.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 52037-88-4
References:
1.  Payton, C.W. and Chang, Y.-F. Δ1-Piperideine-2-carboxylate reductase of Pseudomonas putida. J. Bacteriol. 149 (1982) 864–871. [PMID: 6801013]
2.  Muramatsu, H., Mihara, H., Kakutani, R., Yasuda, M., Ueda, M., Kurihara, T. and Esaki, N. The putative malate/lactate dehydrogenase from Pseudomonas putida is an NADPH-dependent Δ1-piperideine-2-carboxylate/Δ1-pyrroline-2-carboxylate reductase involved in the catabolism of D-lysine and D-proline. J. Biol. Chem. 280 (2005) 5329–5335. [DOI] [PMID: 15561717]
3.  Watanabe, S., Tanimoto, Y., Yamauchi, S., Tozawa, Y., Sawayama, S. and Watanabe, Y. Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Δ1-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria. FEBS Open Bio 4 (2014) 240–250. [DOI] [PMID: 24649405]
[EC 1.5.1.21 created 1984 (EC 1.5.1.14 created 1976, incorporated 1989), modified 2015]
 
 
EC 2.5.1.27     Relevance: 24.6%
Accepted name: adenylate dimethylallyltransferase (AMP-dependent)
Reaction: prenyl diphosphate + AMP = diphosphate + N6-prenyladenosine 5′-phosphate
For diagram of N6-(Dimethylallyl)adenosine phosphates biosynthesis, click here
Glossary: prenyl = 3-methylbut-2-en-1-yl = dimethylallyl (ambiguous)
Other name(s): cytokinin synthase (ambiguous); isopentenyltransferase (ambiguous); 2-isopentenyl-diphosphate:AMP Δ2-isopentenyltransferase; adenylate isopentenyltransferase (ambiguous); IPT; adenylate dimethylallyltransferase; dimethylallyl-diphosphate:AMP dimethylallyltransferase
Systematic name: prenyl-diphosphate:AMP prenyltransferase
Comments: Involved in the biosynthesis of cytokinins in plants. Some isoforms from the plant Arabidopsis thaliana are specific for AMP while others also have the activity of EC 2.5.1.112, adenylate dimethylallyltransferase (ADP/ATP-dependent).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 72840-95-0
References:
1.  Chen, C.-M. and Melitz, D.K. Cytokinin biosynthesis in a cell-free system from cytokinin-autotrophic tobacco tissue cultures. FEBS Lett. 107 (1979) 15–20. [DOI] [PMID: 499537]
2.  Takei, K., Sakakibara, H. and Sugiyama, T. Identification of genes encoding adenylate isopentenyltransferase, a cytokinin biosynthesis enzyme, in Arabidopsis thaliana. J. Biol. Chem. 276 (2001) 26405–26410. [DOI] [PMID: 11313355]
3.  Sakano, Y., Okada, Y., Matsunaga, A., Suwama, T., Kaneko, T., Ito, K., Noguchi, H. and Abe, I. Molecular cloning, expression, and characterization of adenylate isopentenyltransferase from hop (Humulus lupulus L.). Phytochemistry 65 (2004) 2439–2446. [DOI] [PMID: 15381407]
[EC 2.5.1.27 created 1984, modified 2002, modified 2013]
 
 
EC 2.5.1.107     Relevance: 24.5%
Accepted name: verruculogen prenyltransferase
Reaction: prenyl diphosphate + verruculogen = diphosphate + fumitremorgin A
For diagram of fumitremorgin alkaloid biosynthesis (part 2), click here
Glossary: prenyl diphosphate = dimethylallyl diphosphate
verruculogen = (5R,10S,10aR,14aS,15bS)-10,10a-dihydroxy-6-methoxy-2,2-dimethyl-5-(2-methylprop-1-en-1-yl)-1,10,10a,14,14a,15b-hexahydro-12H-3,4-dioxa-5a,11a,15a-triazacycloocta[1,2,3-lm]indeno[5,6-b]fluorene-11,15(2H,13H)-dione
fumitremorgin A = (5R,10S,10aR,14aS,15bS)-10a-hydroxy-7-methoxy-2,2-dimethyl-10-[(3-methylbut-2-en-1-yl)oxy]-5-(2-methylprop-1-en-1-yl)-1,10,10a,14,14a,15b-hexahydro-12H-3,4-dioxa-5a,11a,15a-triazacycloocta[1,2,3-lm]indeno[5,6-b]fluorene-11,15(H,13H)-dione
Other name(s): FtmPT3; dimethylallyl-diphosphate:verruculogen dimethylallyl-O-transferase
Systematic name: prenyl-diphosphate:verruculogen dimethylallyl-O-transferase
Comments: Found in a number of fungi. Catalyses the last step in the biosynthetic pathway of the indole alkaloid fumitremorgin A. The enzyme from the fungus Neosartorya fischeri is also active with fumitremorgin B and 12α,13α-dihydroxyfumitremorgin C.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Mundt, K., Wollinsky, B., Ruan, H.L., Zhu, T. and Li, S.M. Identification of the verruculogen prenyltransferase FtmPT3 by a combination of chemical, bioinformatic and biochemical approaches. ChemBioChem 13 (2012) 2583–2592. [DOI] [PMID: 23109474]
[EC 2.5.1.107 created 2013]
 
 
EC 1.1.1.438     Relevance: 24.3%
Accepted name: cis-4-hydroxycyclohexanecarboxylate dehydrogenase
Reaction: cis-4-hydroxycyclohexane-1-carboxylate + NAD+ = 4-oxocyclohexane-1-carboxylate + NADH + H+
Glossary: cis-4-hydroxycyclohexane-1-carboxylate = cis-4-hydroxycyclohexanecarboxylate
4-oxocyclohexane-1-carboxylate = 4-oxocyclohexanecarboxylate
Other name(s): chcB2 (gene name)
Systematic name: cis-4-hydroxycyclohexane-1-carboxylate:NAD+ 4-oxidoreductase
Comments: The enzyme from Corynebacterium cyclohexanicum is highly specific for the cis-4-hydroxy derivative. cf. EC 1.1.1.226, trans-4-hydroxycyclohexanecarboxylate dehydrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yamamoto, T., Hasegawa, Y., Lau, P.CK. and Iwaki, H. Identification and characterization of a chc gene cluster responsible for the aromatization pathway of cyclohexanecarboxylate degradation in Sinomonas cyclohexanicum ATCC 51369. J. Biosci. Bioeng. 132 (2021) 621–629. [DOI] [PMID: 34583900]
[EC 1.1.1.438 created 2024]
 
 
EC 2.5.1.122     Relevance: 24.1%
Accepted name: 4-O-dimethylallyl-L-tyrosine synthase
Reaction: prenyl diphosphate + L-tyrosine = diphosphate + 4-O-prenyl-L-tyrosine
Other name(s): SirD; dimethylallyl diphosphate:L-tyrosine 4-O-dimethylallyltransferase
Systematic name: prenyl-diphosphate:L-tyrosine 4-O-prenyltransferase
Comments: The enzyme is involved in biosynthesis of the phytotoxin sirodesmin PL by the phytopathogenic ascomycete Leptosphaeria maculans.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kremer, A. and Li, S.M. A tyrosine O-prenyltransferase catalyses the first pathway-specific step in the biosynthesis of sirodesmin PL. Microbiology 156 (2010) 278–286. [DOI] [PMID: 19762440]
2.  Zou, H.X., Xie, X., Zheng, X.D. and Li, S.M. The tyrosine O-prenyltransferase SirD catalyzes O-, N-, and C-prenylations. Appl. Microbiol. Biotechnol. 89 (2011) 1443–1451. [DOI] [PMID: 21038099]
[EC 2.5.1.122 created 2014]
 
 
EC 2.5.1.112     Relevance: 23.7%
Accepted name: adenylate dimethylallyltransferase (ADP/ATP-dependent)
Reaction: (1) prenyl diphosphate + ADP = diphosphate + N6-prenyladenosine 5′-diphosphate
(2) prenyl diphosphate + ATP = diphosphate + N6-prenyladenosine 5′-triphosphate
For diagram of N6-(Dimethylallyl)adenosine phosphates biosynthesis, click here
Other name(s): cytokinin synthase (ambiguous); isopentenyltransferase (ambiguous); 2-isopentenyl-diphosphate:ADP/ATP Δ2-isopentenyltransferase; adenylate isopentenyltransferase (ambiguous); dimethylallyl diphosphate:ATP/ADP isopentenyltransferase: IPT; dimethylallyl-diphosphate:ADP/ATP dimethylallyltransferase
Systematic name: prenyl-diphosphate:ADP/ATP prenyltransferase
Comments: Involved in the biosynthesis of cytokinins in plants. The IPT4 isoform from the plant Arabidopsis thaliana is specific for ADP and ATP [1]. Other isoforms, such as IPT1 from Arabidopsis thaliana [1,2] and the enzyme from the common hop, Humulus lupulus [3], also have a lower activity with AMP (cf. EC 2.5.1.27, adenylate dimethylallyltransferase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Kakimoto, T. Identification of plant cytokinin biosynthetic enzymes as dimethylallyl diphosphate:ATP/ADP isopentenyltransferases. Plant Cell Physiol. 42 (2001) 677–685. [PMID: 11479373]
2.  Takei, K., Sakakibara, H. and Sugiyama, T. Identification of genes encoding adenylate isopentenyltransferase, a cytokinin biosynthesis enzyme, in Arabidopsis thaliana. J. Biol. Chem. 276 (2001) 26405–26410. [DOI] [PMID: 11313355]
3.  Sakano, Y., Okada, Y., Matsunaga, A., Suwama, T., Kaneko, T., Ito, K., Noguchi, H. and Abe, I. Molecular cloning, expression, and characterization of adenylate isopentenyltransferase from hop (Humulus lupulus L.). Phytochemistry 65 (2004) 2439–2446. [DOI] [PMID: 15381407]
[EC 2.5.1.112 created 2013]
 
 
EC 1.5.1.49     Relevance: 23.6%
Accepted name: 1-pyrroline-2-carboxylate reductase [NAD(P)H]
Reaction: L-proline + NAD(P)+ = 1-pyrroline-2-carboxylate + NAD(P)H + H+
Systematic name: L-proline:NAD(P)+ 2-oxidoreductase
Comments: The enzyme from the bacterium Colwellia psychrerythraea is involved in trans-3-hydroxy-L-proline metabolism. In contrast to EC 1.5.1.1, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H], which shows similar activity with 1-piperideine-2-carboxylate and 1-pyrroline-2-carboxylate, this enzyme is specific for the latter. While the enzyme is active with both NADH and NADPH, activity is higher with NADPH.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Watanabe, S., Tanimoto, Y., Yamauchi, S., Tozawa, Y., Sawayama, S. and Watanabe, Y. Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Δ1-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria. FEBS Open Bio 4 (2014) 240–250. [DOI] [PMID: 24649405]
[EC 1.5.1.49 created 2015]
 
 
EC 2.5.1.35     Relevance: 22.9%
Accepted name: aspulvinone dimethylallyltransferase
Reaction: 2 prenyl diphosphate + aspulvinone E = 2 diphosphate + aspulvinone H
Other name(s): dimethylallyl pyrophosphate:aspulvinone dimethylallyltransferase; dimethylallyl-diphosphate:aspulvinone-E dimethylallyltransferase
Systematic name: prenyl-diphosphate:aspulvinone-E prenyltransferase
Comments: This enzyme will also use as acceptor aspulvinone G, a hydroxylated derivative of the complex phenolic pigment aspulvinone E.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 67584-68-3
References:
1.  Takahashi, I., Ojima, N., Ogura, K. and Seto, S. Purification and characterization of dimethylallyl pyrophosphate: aspulvinone dimethylallyltransferase from Aspergillus terreus. Biochemistry 17 (1978) 2696–2702. [PMID: 678538]
[EC 2.5.1.35 created 1984]
 
 
EC 2.5.1.36     Relevance: 22.8%
Accepted name: trihydroxypterocarpan dimethylallyltransferase
Reaction: (1) prenyl diphosphate + (6aS,11aS)-3,6a,9-trihydroxypterocarpan = diphosphate + (6aS,11aS)-3,6a,9-trihydroxy-2-prenylpterocarpan
(2) prenyl diphosphate + (6aS,11aS)-3,6a,9-trihydroxypterocarpan = diphosphate + (6aS,11aS)-3,6a,9-trihydroxy-4-prenylpterocarpan
For diagram of glyceollin biosynthesis (part 2), click here
Other name(s): glyceollin synthase; dimethylallylpyrophosphate:3,6a,9-trihydroxypterocarpan dimethylallyltransferase; dimethylallylpyrophosphate:trihydroxypterocarpan dimethylallyl transferase; dimethylallyl-diphosphate:(6aS,11aS)-3,6a,9-trihydroxypterocarpan dimethyltransferase; dimethylallyl-diphosphate:(6aS,11aS)-3,6a,9-trihydroxypterocarpan dimethylallyltransferase
Systematic name: prenyl-diphosphate:(6aS,11aS)-3,6a,9-trihydroxypterocarpan prenyltransferase
Comments: Part of the glyceollin biosynthesis system in soy bean.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 70851-94-4
References:
1.  Leube, J. and Grisebach, H. Further studies on induction of enzymes of phytoalexin synthesis in soybean and cultured soybean cells. Z. Naturforsch. C: Biosci. 38 (1983) 730–735.
2.  Zähringer, U., Schaller, E. and Grisebach, H. Induction of phytoalexin synthesis in soybean. Structure and reactions of naturally occurring and enzymatically prepared prenylated pterocarpans from elicitor-treated cotyledons and cell cultures of soybean. Z. Natursforsch. C: Biosci. 36 (1981) 234–241.
[EC 2.5.1.36 created 1989]
 
 
EC 6.3.1.16      
Transferred entry: carbapenam-3-carboxylate synthetase. The enzyme was discovered at the public-review stage to have been misclassified and so was withdrawn. See EC 6.3.3.6, carbapenam-3-carboxylate synthase
[EC 6.3.1.16 created 2013, deleted 2013]
 
 
EC 1.5.1.25     Relevance: 22.5%
Accepted name: thiomorpholine-carboxylate dehydrogenase
Reaction: thiomorpholine 3-carboxylate + NAD(P)+ = 3,4-dehydro-thiomorpholine-3-carboxylate + NAD(P)H + H+
For diagram of reaction, click here
Other name(s): ketimine reductase; ketimine-reducing enzyme
Systematic name: thiomorpholine-3-carboxylate:NAD(P)+ 5,6-oxidoreductase
Comments: The product is the cyclic imine of the 2-oxoacid corresponding to S-(2-aminoethyl)cysteine. In the reverse direction, a number of other cyclic unsaturated compounds can act as substrates, but more slowly.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 115232-54-7
References:
1.  Nardini, M., Ricci, G., Caccuri, A.M., Solinas, S.P., Vesci, L. and Cavallini, D. Purification and characterization of a ketimine-reducing enzyme. Eur. J. Biochem. 173 (1988) 689–694. [DOI] [PMID: 3371353]
[EC 1.5.1.25 created 1990]
 
 
EC 1.1.1.226     Relevance: 22.3%
Accepted name: trans-4-hydroxycyclohexanecarboxylate dehydrogenase
Reaction: trans-4-hydroxycyclohexane-1-carboxylate + NAD+ = 4-oxocyclohexane-1-carboxylate + NADH + H+
Glossary: trans-4-hydroxycyclohexane-1-carboxylate = trans-4-hydroxycyclohexanecarboxylate
4-oxocyclohexane-1-carboxylate = 4-oxocyclohexanecarboxylate
Other name(s): 4-hydroxycyclohexanecarboxylate dehydrogenase (ambiguous); chcB1 (gene name)
Systematic name: trans-4-hydroxycyclohexane-1-carboxylate:NAD+ 4-oxidoreductase
Comments: The enzyme from Corynebacterium cyclohexanicum is highly specific for the trans-4-hydroxy derivative. cf. EC 1.1.1.438, cis-4-hydroxycyclohexanecarboxylate dehydrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 67272-36-0
References:
1.  Obata, H., Uebayashi, M. and Kaneda, T. Purification and properties of 4-hydroxycyclohexanecarboxylate dehydrogenase from Corynebacterium cyclohexanicum. Eur. J. Biochem. 174 (1988) 451–458. [DOI] [PMID: 3292236]
2.  Yamamoto, T., Hasegawa, Y., Lau, P.CK. and Iwaki, H. Identification and characterization of a chc gene cluster responsible for the aromatization pathway of cyclohexanecarboxylate degradation in Sinomonas cyclohexanicum ATCC 51369. J. Biosci. Bioeng. 132 (2021) 621–629. [DOI] [PMID: 34583900]
[EC 1.1.1.226 created 1990, modified 2024]
 
 
EC 1.3.1.25     Relevance: 22.3%
Accepted name: 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase
Reaction: (1R,6S)-1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate + NAD+ = catechol + CO2 + NADH + H+
For diagram of benzoate metabolism, click here
Other name(s): 3,5-cyclohexadiene-1,2-diol-1-carboxylate dehydrogenase; 3,5-cyclohexadiene-1,2-diol-1-carboxylic acid dehydrogenase; dihydrodihydroxybenzoate dehydrogenase; DHBDH; cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase; 2-hydro-1,2-dihydroxybenzoate dehydrogenase; cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate:NAD+ oxidoreductase; dihydrodihydroxybenzoate dehydrogenase; (1R,6R)-1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate:NAD+ oxidoreductase (decarboxylating)
Systematic name: (1R,6S)-1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate:NAD+ oxidoreductase (decarboxylating)
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 60496-16-4
References:
1.  Reiner, A.M. Metabolism of aromatic compounds in bacteria. Purification and properties of the catechol-forming enzyme, 3,5-cyclohexadiene-1,2-diol-1-carboxylic acid (NAD+) oxidoreductase (decarboxylating). J. Biol. Chem. 247 (1972) 4960–4965. [PMID: 4341530]
2.  Neidle, E., Hartnett, C., Ornston, L.N., Bairoch, A., Rekik, M. and Harayama, S. cis-Diol dehydrogenases encoded by the TOL pWW0 plasmid xylL gene and the Acinetobacter calcoaceticus chromosomal benD gene are members of the short-chain alcohol dehydrogenase superfamily. Eur. J. Biochem. 204 (1992) 113–120. [DOI] [PMID: 1740120]
[EC 1.3.1.25 created 1976, modified 2004 (EC 1.3.1.55 created 1999, incorporated 2004)]
 
 
EC 4.1.1.93     Relevance: 22.1%
Accepted name: pyrrole-2-carboxylate decarboxylase
Reaction: (1) pyrrole-2-carboxylate = pyrrole + CO2
(2) pyrrole-2-carboxylate + H2O = pyrrole + HCO3-
Systematic name: pyrrole-2-carboxylate carboxy-lyase
Comments: The enzyme catalyses both the carboxylation and decarboxylation reactions. However, while bicarbonate is the preferred substrate for the carboxylation reaction, decarboxylation produces carbon dioxide. The enzyme is activated by carboxylic acids.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc
References:
1.  Wieser, M., Fujii, N., Yoshida, T. and Nagasawa, T. Carbon dioxide fixation by reversible pyrrole-2-carboxylate decarboxylase from Bacillus megaterium PYR2910. Eur. J. Biochem. 257 (1998) 495–499. [DOI] [PMID: 9826198]
2.  Omura, H., Wieser, M. and Nagasawa, T. Pyrrole-2-carboxylate decarboxylase from Bacillus megaterium PYR2910, an organic-acid-requiring enzyme. Eur. J. Biochem. 253 (1998) 480–484. [DOI] [PMID: 9654100]
3.  Wieser, M., Yoshida, T. and Nagasawa, T. Microbial synthesis of pyrrole-2-carboxylate by Bacillus megaterium PYR2910. Tetrahedron Lett. 39 (1998) 4309–4310.
[EC 4.1.1.93 created 2011]
 
 
EC 1.3.99.19     Relevance: 22%
Accepted name: quinoline-4-carboxylate 2-oxidoreductase
Reaction: quinoline-4-carboxylate + acceptor + H2O = 2-oxo-1,2-dihydroquinoline-4-carboxylate + reduced acceptor
For diagram of reaction, click here
Other name(s): quinaldic acid 4-oxidoreductase; quinoline-4-carboxylate:acceptor 2-oxidoreductase (hydroxylating)
Systematic name: quinoline-4-carboxylate:acceptor 2-oxidoreductase (hydroxylating)
Comments: A molybdenum—iron—sulfur flavoprotein with molybdopterin cytosine dinucleotide as the molybdenum cofactor. Quinoline, 4-methylquinoline and 4-chloroquinoline can also serve as substrates for the enzyme from Agrobacterium sp. 1B. Iodonitrotetrazolium chloride, thionine, menadione and 2,6-dichlorophenolindophenol can act as electron acceptors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 175780-18-4
References:
1.  Bauer, G. and Lingens, F. Microbial metabolism of quinoline and related compounds. XV. Quinoline-4-carboxylic acid oxidoreductase from Agrobacterium spec.1B: a molybdenum-containing enzyme. Biol. Chem. Hoppe-Seyler 373 (1992) 699–705. [PMID: 1418685]
[EC 1.3.99.19 created 1999, modified 2006]
 
 
EC 2.3.1.315     Relevance: 21.7%
Accepted name: succinyl-CoA:cyclohexane-1-carboxylate CoA transferase
Reaction: succinyl-CoA + cyclohexane-1-carboxylate = succinate + cyclohexane-1-carbonyl-CoA
Other name(s): Gmet_3304 (locus name)
Systematic name: succinyl-CoA—cyclohexane-1-carboxylate CoA-transferase
Comments: The enzyme, characterized from the bacterium Geobacter metallireducens, participates in an anaerobic degradation pathway for cyclohexane-1-carboxylate. In vitro, the enzyme can use butanoyl-coA as a CoA donor with greater efficiency than succinyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kung, J.W., Meier, A.K., Mergelsberg, M. and Boll, M. Enzymes involved in a novel anaerobic cyclohexane carboxylic acid degradation pathway. J. Bacteriol. 196 (2014) 3667–3674. [DOI] [PMID: 25112478]
[EC 2.3.1.315 created 2024]
 
 
EC 1.5.3.7     Relevance: 21.6%
Accepted name: L-pipecolate oxidase
Reaction: L-pipecolate + O2 = (S)-2,3,4,5-tetrahydropyridine-2-carboxylate + H2O2
Glossary: L-1-piperideine 6-carboxylate = (S)-2,3,4,5-tetrahydropyridine-2-carboxylate = (S)-1,6-didehydropiperidine-2-carboxylate
(S)-2-amino-6-oxohexanoate = L-2-aminoadipate 6-semialdehyde = L-allysine
Other name(s): pipecolate oxidase; L-pipecolic acid oxidase
Systematic name: L-pipecolate:oxygen 1,6-oxidoreductase
Comments: The product reacts with water to form (S)-2-amino-6-oxohexanoate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 81669-65-0
References:
1.  Baginsky, B.L. and Rodwell, V.W. Metabolism of pipecolic acid in a Pseudomonas species. V. Pipecolate oxidase and dehydrogenase. J. Bacteriol. 94 (1967) 1034–1039. [PMID: 6051341]
2.  Kinzel, J.J. and Bhattacharjee, J.K. Lysine biosynthesis in Rhodotorula glutinis: properties of pipecolic acid oxidase. J. Bacteriol. 151 (1982) 1073–1077. [PMID: 6809728]
[EC 1.5.3.7 created 1986, modified 2011]
 
 
EC 4.1.1.92     Relevance: 21.5%
Accepted name: indole-3-carboxylate decarboxylase
Reaction: indole-3-carboxylate = indole + CO2
Systematic name: indole-3-carboxylate carboxy-lyase
Comments: Activated by Zn2+, Mn2+ or Mg2+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yoshida, T., Fujita, K. and Nagasawa, T. Novel reversible indole-3-carboxylate decarboxylase catalyzing nonoxidative decarboxylation. Biosci. Biotechnol. Biochem. 66 (2002) 2388–2394. [PMID: 12506977]
[EC 4.1.1.92 created 2011]
 
 
EC 4.8.1.1     Relevance: 21.5%
Accepted name: L-piperazate synthase
Reaction: N5-hydroxy-L-ornithine = (3S)-1,2-diazinane-3-carboxylate + H2O
Glossary: (3S)-1,2-diazinane-3-carboxylate = (3S)-pyridazin-3-carboxylate = L-piperazate
Other name(s): ktzT (gene name)
Systematic name: (3S)-1,2-diazinane-3-carboxylate hydrolase (N5-hydroxy-L-ornithine-forming)
Comments: Contains a heme b cofactor. The enzyme, characterized from the bacterium Kutzneria sp. 744, is one of very few enzymes known to result in the formation of an N-N bond. (3S)-1,2-diazinane-3-carboxylate (piperazate) is known to be incorporated into assorted secondary products that are produced by nonribosomal peptide synthetase or nonribosomal peptide synthetase/polyketide synthase hybrid pathways, such as the kutznerides, padanamides, himastatins, and sanglifehrins.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Du, Y.L., He, H.Y., Higgins, M.A. and Ryan, K.S. A heme-dependent enzyme forms the nitrogen-nitrogen bond in piperazate. Nat. Chem. Biol. 13 (2017) 836–838. [DOI] [PMID: 28628093]
[EC 4.8.1.1 created 2021]
 
 
EC 2.1.1.327     Relevance: 21.4%
Accepted name: phenazine-1-carboxylate N-methyltransferase
Reaction: S-adenosyl-L-methionine + phenazine-1-carboxylate = S-adenosyl-L-homocysteine + 5-methylphenazine-1-carboxylate
For diagram of enediyne antitumour antibiotic biosynthesis and pyocyanin biosynthesis, click here
Other name(s): phzM (gene name)
Systematic name: S-adenosyl-L-methionine:phenazine-1-carboxylate 5-methyltransferase
Comments: The enzyme, characterized from the bacterium Pseudomonas aeruginosa, is involved in the biosynthesis of pyocyanin, a toxin produced and secreted by the organism. The enzyme is active in vitro only in the presence of EC 1.14.13.218, 5-methylphenazine-1-carboxylate 1-monooxygenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Parsons, J.F., Greenhagen, B.T., Shi, K., Calabrese, K., Robinson, H. and Ladner, J.E. Structural and functional analysis of the pyocyanin biosynthetic protein PhzM from Pseudomonas aeruginosa. Biochemistry 46 (2007) 1821–1828. [DOI] [PMID: 17253782]
[EC 2.1.1.327 created 2016]
 
 
EC 3.6.1.76     Relevance: 21.2%
Accepted name: prenyl-diphosphate phosphatase
Reaction: (1) prenyl diphosphate + H2O = prenyl phosphate + phosphate
(2) 3-methylbut-3-en-1-yl diphosphate + H2O = 3-methylbut-3-en-1-yl phosphate + phosphate
Glossary: isopentenyl = 3-methylbut-3-en-1-yl
prenyl = 3-methylbut-2-en-1-yl = dimethylallyl
dimethylallyl diphosphate = DMAPP
isopentenyl diphosphate = IPP
Systematic name: prenyl diphosphate/3-methylbut-3-en-1-yl diphosphate phosphohydrolase
Comments: The enzyme, characterized from the methanogenic archaeon Methanosarcina mazei, belongs to the Nudix hydrolase family (a superfamily of hydrolytic enzymes capable of cleaving nucleoside diphosphates linked to a moiety). Its main purpose is to provide the substrate for EC 2.5.1.129, flavin prenyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ishibashi, Y., Matsushima, N., Ito, T. and Hemmi, H. Isopentenyl diphosphate/dimethylallyl diphosphate-specific Nudix hydrolase from the methanogenic archaeon Methanosarcina mazei. Biosci. Biotechnol. Biochem. 86 (2022) 246–253. [DOI] [PMID: 34864834]
[EC 3.6.1.76 created 2022]
 
 
EC 6.3.3.6     Relevance: 21.1%
Accepted name: carbapenam-3-carboxylate synthase
Reaction: ATP + (2S,5S)-5-carboxymethylproline = AMP + diphosphate + (3S,5S)-carbapenam 3-carboxylate
Other name(s): CarA (ambiguous); CPS (ambiguous); carbapenam-3-carboxylate ligase; 6-methyl-(2S,5S)-5-carboxymethylproline cyclo-ligase (AMP-forming)
Systematic name: (2S,5S)-5-carboxymethylproline cyclo-ligase (AMP-forming)
Comments: The enzyme is involved in the biosynthesis of the carbapenem β-lactam antibiotic (5R)-carbapen-2-em-3-carboxylate in the bacterium Pectobacterium carotovorum.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Gerratana, B., Stapon, A. and Townsend, C.A. Inhibition and alternate substrate studies on the mechanism of carbapenam synthetase from Erwinia carotovora. Biochemistry 42 (2003) 7836–7847. [DOI] [PMID: 12820893]
2.  Miller, M.T., Gerratana, B., Stapon, A., Townsend, C.A. and Rosenzweig, A.C. Crystal structure of carbapenam synthetase (CarA). J. Biol. Chem. 278 (2003) 40996–41002. [DOI] [PMID: 12890666]
3.  Raber, M.L., Arnett, S.O. and Townsend, C.A. A conserved tyrosyl-glutamyl catalytic dyad in evolutionarily linked enzymes: carbapenam synthetase and β-lactam synthetase. Biochemistry 48 (2009) 4959–4971. [DOI] [PMID: 19371088]
4.  Arnett, S.O., Gerratana, B. and Townsend, C.A. Rate-limiting steps and role of active site Lys443 in the mechanism of carbapenam synthetase. Biochemistry 46 (2007) 9337–9345. [DOI] [PMID: 17658887]
[EC 6.3.3.6 created 2013 as 6.3.1.16, transferred 2013 to EC 6.3.3.6]
 
 
EC 1.1.1.166     Relevance: 21.1%
Accepted name: hydroxycyclohexanecarboxylate dehydrogenase
Reaction: (1S,3R,4S)-3,4-dihydroxycyclohexane-1-carboxylate + NAD+ = (1S,4S)-4-hydroxy-3-oxocyclohexane-1-carboxylate + NADH + H+
Other name(s): dihydroxycyclohexanecarboxylate dehydrogenase; (-)t-3,t-4-dihydroxycyclohexane-c-1-carboxylate-NAD+ oxidoreductase
Systematic name: (1S,3R,4S)-3,4-dihydroxycyclohexane-1-carboxylate:NAD+ 3-oxidoreductase
Comments: Acts on hydroxycyclohexanecarboxylates that have an equatorial carboxy group at C-1, an axial hydroxy group at C-3 and an equatorial hydroxy or carbonyl group at C-4, including (-)-quinate and (-)-shikimate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 55467-53-3
References:
1.  Whiting, G.C. and Coggins, R.A. A new nicotinamide-adenine dinucleotide-dependent hydroaromatic dehydrogenase of Lactobacillus plantarum and its role in formation of (-)t-3,t-4-dihydroxycyclohexane-c-1-carboxylate. Biochem. J. 141 (1974) 35–42. [PMID: 4375976]
[EC 1.1.1.166 created 1976]
 
 
EC 2.3.1.226     Relevance: 21.1%
Accepted name: carboxymethylproline synthase
Reaction: malonyl-CoA + (S)-1-pyrroline-5-carboxylate + H2O = CoA + (2S,5S)-5-carboxymethylproline + CO2
Other name(s): CarB (ambiguous)
Systematic name: malonyl-CoA:(S)-1-pyrroline-5-carboxylate malonyltransferase (cyclizing)
Comments: The enzyme is involved in the biosynthesis of the carbapenem β-lactam antibiotic (5R)-carbapen-2-em-3-carboxylate in the bacterium Pectobacterium carotovorum.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Sleeman, M.C. and Schofield, C.J. Carboxymethylproline synthase (CarB), an unusual carbon-carbon bond-forming enzyme of the crotonase superfamily involved in carbapenem biosynthesis. J. Biol. Chem. 279 (2004) 6730–6736. [DOI] [PMID: 14625287]
2.  Gerratana, B., Arnett, S.O., Stapon, A. and Townsend, C.A. Carboxymethylproline synthase from Pectobacterium carotorova: a multifaceted member of the crotonase superfamily. Biochemistry 43 (2004) 15936–15945. [DOI] [PMID: 15595850]
3.  Sorensen, J.L., Sleeman, M.C. and Schofield, C.J. Synthesis of deuterium labelled L- and D-glutamate semialdehydes and their evaluation as substrates for carboxymethylproline synthase (CarB)—implications for carbapenem biosynthesis. Chem. Commun. (Camb.) (2005) 1155–1157. [DOI] [PMID: 15726176]
4.  Sleeman, M.C., Sorensen, J.L., Batchelar, E.T., McDonough, M.A. and Schofield, C.J. Structural and mechanistic studies on carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily catalyzing the first step in carbapenem biosynthesis. J. Biol. Chem. 280 (2005) 34956–34965. [DOI] [PMID: 16096274]
5.  Batchelar, E.T., Hamed, R.B., Ducho, C., Claridge, T.D., Edelmann, M.J., Kessler, B. and Schofield, C.J. Thioester hydrolysis and C-C bond formation by carboxymethylproline synthase from the crotonase superfamily. Angew. Chem. Int. Ed. Engl. 47 (2008) 9322–9325. [DOI] [PMID: 18972478]
6.  Hamed, R.B., Gomez-Castellanos, J.R., Thalhammer, A., Harding, D., Ducho, C., Claridge, T.D. and Schofield, C.J. Stereoselective C-C bond formation catalysed by engineered carboxymethylproline synthases. Nat. Chem. 3 (2011) 365–371. [DOI] [PMID: 21505494]
[EC 2.3.1.226 created 2013]
 
 
EC 2.5.1.75     Relevance: 21.1%
Accepted name: tRNA dimethylallyltransferase
Reaction: prenyl diphosphate + adenosine37 in tRNA = diphosphate + N6-(3-methylbut-2-en-1-yl)-adenosine37 in tRNA
For diagram of N6-(Dimethylallyl)adenosine37 modified tRNA biosynthesis, click here
Glossary: N6-(3-methylbut-2-en-1-yl)-adenine37 in tRNA = N6-dimethylallyladenine37 in tRNA
Other name(s): tRNA prenyltransferase; MiaA; transfer ribonucleate isopentenyltransferase (incorrect); Δ2-isopentenyl pyrophosphate:tRNA-Δ2-isopentenyl transferase (incorrect); Δ2-isopentenyl pyrophosphate:transfer ribonucleic acid Δ2-isopentenyltransferase (incorrect); dimethylallyl-diphosphate: tRNA dimethylallyltransferase; dimethylallyl-diphosphate:adenine37 in tRNA dimethylallyltransferase
Systematic name: prenyl-diphosphate:adenine37 in tRNA prenyltransferase
Comments: Formerly known as tRNA isopentenyltransferase, but it is now known that prenyl diphosphate, rather than isopentenyl diphosphate, is the substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Leung, H.C., Chen, Y. and Winkler, M.E. Regulation of substrate recognition by the MiaA tRNA prenyltransferase modification enzyme of Escherichia coli K-12. J. Biol. Chem. 272 (1997) 13073–13083. [DOI] [PMID: 9148919]
2.  Soderberg, T. and Poulter, C.D. Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: essential elements for recognition of tRNA substrates within the anticodon stem-loop. Biochemistry 39 (2000) 6546–6553. [DOI] [PMID: 10828971]
3.  Moore, J.A., Mathis, J.R. and Poulter, C.D. Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: pre-steady-state kinetic studies. Biochim. Biophys. Acta 1479 (2000) 166–174. [DOI] [PMID: 11004538]
[EC 2.5.1.75 created 1972 as EC 2.5.1.8, transferred 2009 to EC 2.5.1.75]
 
 
EC 4.2.1.171     Relevance: 21%
Accepted name: cis-L-3-hydroxyproline dehydratase
Reaction: cis-3-hydroxy-L-proline = 1-pyrroline-2-carboxylate + H2O
Glossary: 1-pyrroline-2-carboxylate = 4,5-dihydro-3H-pyrrole-2-carboxylate
Other name(s): cis-L-3-hydroxyproline hydro-lyase; c3LHypD
Systematic name: cis-3-hydroxy-L-proline hydro-lyase (1-pyrroline-2-carboxylate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Zhang, X., Kumar, R., Vetting, M.W., Zhao, S., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. A unique cis-3-hydroxy-L-proline dehydratase in the enolase superfamily. J. Am. Chem. Soc. 137 (2015) 1388–1391. [DOI] [PMID: 25608448]
[EC 4.2.1.171 created 2017]
 
 
EC 3.5.4.22     Relevance: 21%
Accepted name: 1-pyrroline-4-hydroxy-2-carboxylate deaminase
Reaction: 1-pyrroline-4-hydroxy-2-carboxylate + H2O = 2,5-dioxopentanoate + NH3
Other name(s): HPC deaminase; 1-pyrroline-4-hydroxy-2-carboxylate aminohydrolase (decyclizing)
Systematic name: 1-pyrroline-4-hydroxy-2-carboxylate aminohydrolase (ring-opening)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9054-77-7
References:
1.  Singh, R.M.M. and Adams, E. Enzymatic deamination of Δ1-pyrroline-4-hydroxy-2-carboxylate to 2,5-dioxovalerate (α-ketoglutaric semialdehyde). J. Biol. Chem. 240 (1965) 4344–4351. [PMID: 5845838]
2.  Singh, R.M.M. and Adams, E. Isolation and identification of 2,5-dioxovalerate, an intermediate in the bacterial oxidation of hydroxyproline. J. Biol. Chem. 240 (1965) 4352–4356. [PMID: 5845839]
[EC 3.5.4.22 created 1976]
 
 
EC 1.5.1.12      
Transferred entry: 1-pyrroline-5-carboxylate dehydrogenase. Now EC 1.2.1.88, L-glutamate γ-semialdehyde dehydrogenase.
[EC 1.5.1.12 created 1972, modified 2008, deleted 2013]
 
 
EC 1.5.99.3     Relevance: 20.9%
Accepted name: L-pipecolate dehydrogenase
Reaction: L-pipecolate + acceptor = (S)-2,3,4,5-tetrahydropyridine-2-carboxylate + reduced acceptor
Glossary: (S)-2-amino-6-oxohexanoate = L-2-aminoadipate 6-semialdehyde = L-allysine
L-1-piperideine 6-carboxylate = (S)-2,3,4,5-tetrahydropyridine-2-carboxylate = (S)-1,6-didehydropiperidine-2-carboxylate
Other name(s): L-pipecolate:(acceptor) 1,6-oxidoreductase
Systematic name: L-pipecolate:acceptor 1,6-oxidoreductase
Comments: The product reacts with water to form (S)-2-amino-6-oxohexanoate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9076-63-5
References:
1.  Baginsky, B.L. and Rodwell, V.W. Metabolism of pipecolic acid in a Pseudomonas species. V. Pipecolate oxidase and dehydrogenase. J. Bacteriol. 94 (1967) 1034–1039. [PMID: 6051341]
[EC 1.5.99.3 created 1972, modified 1986, modified 2011]
 
 
EC 4.1.1.66     Relevance: 20.9%
Accepted name: uracil-5-carboxylate decarboxylase
Reaction: uracil 5-carboxylate = uracil + CO2
Other name(s): uracil-5-carboxylic acid decarboxylase; uracil-5-carboxylate carboxy-lyase
Systematic name: uracil-5-carboxylate carboxy-lyase (uracil-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 59299-01-3
References:
1.  Palmatier, R.D., McCroskey, R.P. and Abbott, M.T. The enzymatic conversion of uracil 5-carboxylic acid to uracil and carbon dioxide. J. Biol. Chem. 245 (1970) 6706–6710. [PMID: 5482775]
[EC 4.1.1.66 created 1976]
 
 
EC 1.14.13.218     Relevance: 20.8%
Accepted name: 5-methylphenazine-1-carboxylate 1-monooxygenase
Reaction: 5-methylphenazine-1-carboxylate + NADH + O2 = pyocyanin + NAD+ + CO2 + H2O
For diagram of enediyne antitumour antibiotic biosynthesis and pyocyanin biosynthesis, click here
Glossary: pyocyanin = 1-hydroxy-5-methylphenazin-5-ium
Other name(s): phzS (gene name)
Systematic name: 5-methylphenazine-1-carboxylate,NADH:oxygen oxidoreductase (1-hydroxylating, decarboxylating)
Comments: The enzyme, characterized from the bacterium Pseudomonas aeruginosa, is involved in the biosynthesis of pyocyanin, a toxin produced and secreted by the organism. It can also act on phenazine-1-carboxylate, converting it into phenazin-1-ol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Mavrodi, D.V., Bonsall, R.F., Delaney, S.M., Soule, M.J., Phillips, G. and Thomashow, L.S. Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PAO1. J. Bacteriol. 183 (2001) 6454–6465. [DOI] [PMID: 11591691]
2.  Parsons, J.F., Greenhagen, B.T., Shi, K., Calabrese, K., Robinson, H. and Ladner, J.E. Structural and functional analysis of the pyocyanin biosynthetic protein PhzM from Pseudomonas aeruginosa. Biochemistry 46 (2007) 1821–1828. [DOI] [PMID: 17253782]
3.  Greenhagen, B.T., Shi, K., Robinson, H., Gamage, S., Bera, A.K., Ladner, J.E. and Parsons, J.F. Crystal structure of the pyocyanin biosynthetic protein PhzS. Biochemistry 47 (2008) 5281–5289. [DOI] [PMID: 18416536]
[EC 1.14.13.218 created 2016]
 
 
EC 1.14.12.4      
Transferred entry: 3-hydroxy-2-methylpyridinecarboxylate dioxygenase. Now EC 1.14.13.242, 3-hydroxy-2-methylpyridinecarboxylate monooxygenase
[EC 1.14.12.4 created 1972, deleted 2018]
 
 
EC 1.5.1.2     Relevance: 20.5%
Accepted name: pyrroline-5-carboxylate reductase
Reaction: L-proline + NAD(P)+ = 1-pyrroline-5-carboxylate + NAD(P)H + H+
For diagram of proline biosynthesis, click here
Other name(s): proline oxidase; L-proline oxidase; 1-pyrroline-5-carboxylate reductase; NADPH-L-Δ1-pyrroline carboxylic acid reductase; L-proline-NAD(P)+ 5-oxidoreductase
Systematic name: L-proline:NAD(P)+ 5-oxidoreductase
Comments: Also reduces 1-pyrroline-3-hydroxy-5-carboxylate to L-hydroxyproline.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9029-17-8
References:
1.  Adams, E. and Goldstone, A. Hydroxyproline metabolism. III. Enzymatic synthesis of hydroxyproline from Δ1-pyrroline-3-hydroxy-5-carboxylate. J. Biol. Chem. 235 (1960) 3499–3503. [PMID: 13681369]
2.  Meister, A., Radhakrishnan, A.N. and Buckley, S.D. Enzymatic synthesis of L-pipecolic acid and L-proline. J. Biol. Chem. 229 (1957) 789–800. [PMID: 13502341]
3.  Smith, M.E. and Greenberg, D.M. Characterization of an enzyme reducing pyrroline-5-carboxylate to proline. Nature (Lond.) 177 (1956) 1130. [PMID: 13334497]
4.  Yura, T. and Vogel, H.J. Pyrroline-5-carboxylate reductase of Neurospora crassa: partial purification and some properties. J. Biol. Chem. 234 (1959) 335–338. [PMID: 13630905]
[EC 1.5.1.2 created 1961]
 
 
EC 1.2.1.88     Relevance: 20.5%
Accepted name: L-glutamate γ-semialdehyde dehydrogenase
Reaction: L-glutamate 5-semialdehyde + NAD+ + H2O = L-glutamate + NADH + H+
For diagram of reaction, click here
Glossary: L-glutamate 5-semialdehyde = L-glutamate γ-semialdehyde = (S)-2-amino-5-oxopentanoate
Other name(s): 1-pyrroline-5-carboxylate dehydrogenase; Δ1-pyrroline-5-carboxylate dehydrogenase; 1-pyrroline dehydrogenase; pyrroline-5-carboxylate dehydrogenase; pyrroline-5-carboxylic acid dehydrogenase; L-pyrroline-5-carboxylate-NAD+ oxidoreductase; 1-pyrroline-5-carboxylate:NAD+ oxidoreductase; Δ1-pyrroline-5-carboxylic acid dehydrogenase
Systematic name: L-glutamate γ-semialdehyde:NAD+ oxidoreductase
Comments: This enzyme catalyses the irreversible oxidation of glutamate-γ-semialdehyde to glutamate as part of the proline degradation pathway. (S)-1-pyrroline-5-carboxylate, the product of the first enzyme of the pathway (EC 1.5.5.2, proline dehydrogenase) is in spontaneous equilibrium with its tautomer L-glutamate γ-semialdehyde. In many bacterial species, both activities are carried out by a single bifunctional enzyme [3,4].The enzyme can also oxidize other 1-pyrrolines, e.g. 3-hydroxy-1-pyrroline-5-carboxylate is converted into 4-hydroxyglutamate and (R)-1-pyrroline-5-carboxylate is converted into D-glutamate. NADP+ can also act as acceptor, but with lower activity [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9054-82-4
References:
1.  Adams, E. and Goldstone, A. Hydroxyproline metabolism. IV. Enzymatic synthesis of γ-hydroxyglutamate from Δ1-pyrroline-3-hydroxy-5-carboxylate. J. Biol. Chem. 235 (1960) 3504–3512. [PMID: 13681370]
2.  Strecker, H.J. The interconversion of glutamic acid and proline. III. Δ1-Pyrroline-5-carboxylic acid dehydrogenase. J. Biol. Chem. 235 (1960) 3218–3223.
3.  Forlani, G., Scainelli, D. and Nielsen, E. Δ1-Pyrroline-5-carboxylate dehydrogenase from cultured cells of potato (purification and properties). Plant Physiol. 113 (1997) 1413–1418. [PMID: 12223682]
4.  Brown, E.D. and Wood, J.M. Redesigned purification yields a fully functional PutA protein dimer from Escherichia coli. J. Biol. Chem. 267 (1992) 13086–13092. [PMID: 1618807]
5.  Inagaki, E., Ohshima, N., Sakamoto, K., Babayeva, N.D., Kato, H., Yokoyama, S. and Tahirov, T.H. New insights into the binding mode of coenzymes: structure of Thermus thermophilus Δ1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63 (2007) 462–465. [DOI] [PMID: 17554163]
[EC 1.2.1.88 created 1972 as EC 1.5.1.12, modified 2008, transferred 2013 to EC 1.2.1.88]
 
 
EC 1.3.1.67     Relevance: 20.1%
Accepted name: cis-1,2-dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylate dehydrogenase
Reaction: cis-1,2-dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylate + NAD(P)+ = 4-methylcatechol + NAD(P)H + CO2
Systematic name: cis-1,2-dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylate:NAD(P)+ oxidoreductase (decarboxylating)
Comments: Involved in the p-xylene degradation pathway in bacteria.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc
References:
1.  Whited, G.M., McCombie, W.R., Kwart, L.D. and Gibson, D.T. Identification of cis-diols as intermediates in the oxidation of aromatic acids by a strain of Pseudomonas putida that contains a TOL plasmid. J. Bacteriol. 166 (1986) 1028–1039. [DOI] [PMID: 3711022]
[EC 1.3.1.67 created 2000]
 
 
EC 2.5.1.106     Relevance: 19.7%
Accepted name: tryprostatin B synthase
Reaction: prenyl diphosphate + brevianamide F = diphosphate + tryprostatin B
For diagram of fumitremorgin alkaloid biosynthesis (part 1), click here
Glossary: brevianamide F = (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
tryprostatin B = (3S,8aS)-3-{[2-(3-methylbut-2-en-1-yl)-1H-indol-3-yl]methyl}hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
Other name(s): ftmPT1 (gene name); brevianamide F prenyltransferase (ambiguous); dimethylallyl-diphosphate:brevianamide-F dimethylallyl-C-2-transferase
Systematic name: prenyl-diphosphate:brevianamide-F prenyl-C-2-transferase
Comments: The enzyme from the fungus Aspergillus fumigatus can also prenylate other tryptophan-containing cyclic dipeptides. Prenylation occurs mainly at C-2 [1], but also at C-3 [2]. Involved in the biosynthetic pathways of several indole alkaloids such as tryprostatins, cyclotryprostatins, spirotryprostatins, fumitremorgins and verruculogen.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Grundmann, A. and Li, S.M. Overproduction, purification and characterization of FtmPT1, a brevianamide F prenyltransferase from Aspergillus fumigatus. Microbiology 151 (2005) 2199–2207. [DOI] [PMID: 16000710]
2.  Wollinsky, B., Ludwig, L., Xie, X. and Li, S.M. Breaking the regioselectivity of indole prenyltransferases: identification of regular C3-prenylated hexahydropyrrolo[2,3-b]indoles as side products of the regular C2-prenyltransferase FtmPT1. Org. Biomol. Chem. 10 (2012) 9262–9270. [DOI] [PMID: 23090579]
[EC 2.5.1.106 created 2013]
 
 
EC 2.5.1.70     Relevance: 19.6%
Accepted name: naringenin 8-dimethylallyltransferase
Reaction: prenyl diphosphate + (–)-(2S)-naringenin = diphosphate + sophoraflavanone B
For diagram of sophoraflavanone G biosynthesis, click here
Glossary: dimethylallyl = prenyl = 3-methylbut-2-en-1-yl
(–)-(2S)-naringenin = (–)-(2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-2,3-dihydrochromen-4-one
sophoraflavanone B = (–)-(2S)-8-prenylnaringenin = (–)-(2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-en-1-yl)-2,3-dihydrochromen-4-one
Other name(s): N8DT; dimethylallyl-diphosphate:naringenin 8-dimethylallyltransferase
Systematic name: prenyl-diphosphate:naringenin 8-prenyltransferase
Comments: Requires Mg2+. This membrane-bound protein is located in the plastids [2]. In addition to naringenin, the enzyme can prenylate several other flavanones at the C-8 position, but more slowly. Along with EC 1.14.14.142 (8-dimethylallylnaringenin 2′-hydroxylase) and EC 2.5.1.71 (leachianone-G 2′′-dimethylallyltransferase), this enzyme forms part of the sophoraflavanone-G-biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yamamoto, H., Senda, M. and Inoue, K. Flavanone 8-dimethylallyltransferase in Sophora flavescens cell suspension cultures. Phytochemistry 54 (2000) 649–655. [DOI] [PMID: 10975499]
2.  Zhao, P., Inoue, K., Kouno, I. and Yamamoto, H. Characterization of leachianone G 2′′-dimethylallyltransferase, a novel prenyl side-chain elongation enzyme for the formation of the lavandulyl group of sophoraflavanone G in Sophora flavescens Ait. cell suspension cultures. Plant Physiol. 133 (2003) 1306–1313. [DOI] [PMID: 14551337]
[EC 2.5.1.70 created 2007]
 
 
EC 3.5.99.7     Relevance: 19.4%
Accepted name: 1-aminocyclopropane-1-carboxylate deaminase
Reaction: 1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanoate + NH3 (overall reaction)
(1a) 1-aminocyclopropane-1-carboxylate = 2-aminobut-2-enoate
(1b) 2-aminobut-2-enoate = 2-iminobutanoate (spontaneous)
(1c) 2-iminobutanoate + H2O = 2-oxobutanoate + NH3 (spontaneous)
Other name(s): 1-aminocyclopropane-1-carboxylate endolyase (deaminating); ACC deaminase; 1-aminocyclopropane carboxylic acid deaminase
Systematic name: 1-aminocyclopropane-1-carboxylate aminohydrolase (isomerizing)
Comments: A pyridoxal 5′-phosphate enzyme. The enzyme, found in certain soil bacteria and fungi, catalyses the ring opening of 1-aminocyclopropane-1-carboxylate, the immediate precursor to ethylene, an important plant hormone that regulates fruit ripening and other processes. The enzyme releases an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. The enzyme has been used to make fruit ripening dependent on externally added ethylene, as it removes the substrate for endogenous ethylene formation.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 69553-48-6
References:
1.  Honma, M. and Shimomura, T. Metabolism of 1-aminocyclopropane-1-carboxylic acid. Agric. Biol. Chem. 42 (1978) 1825–1831.
2.  Yao, M., Ose, T., Sugimoto, H., Horiuchi, A., Nakagawa, A., Wakatsuki, S., Yokoi, D., Murakami, T., Honma, M. and Tanaka, I. Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus. J. Biol. Chem. 275 (2000) 34557–34565. [DOI] [PMID: 10938279]
3.  Thibodeaux, C.J. and Liu, H.W. Mechanistic studies of 1-aminocyclopropane-1-carboxylate deaminase: characterization of an unusual pyridoxal 5′-phosphate-dependent reaction. Biochemistry 50 (2011) 1950–1962. [DOI] [PMID: 21244019]
[EC 3.5.99.7 created 1981 as EC 4.1.99.4, transferred 2002 to EC 3.5.99.7, modified 2014]
 
 
EC 2.5.1.109     Relevance: 19.2%
Accepted name: brevianamide F prenyltransferase (deoxybrevianamide E-forming)
Reaction: prenyl diphosphate + brevianamide F = diphosphate + deoxybrevianamide E
For diagram of fumitremorgin alkaloid biosynthesis (part 1), click here
Glossary: brevianamide F = (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
deoxybrevianamide E = (3S,8aS)-3-{[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-octahydropyrrolo[1,2-a]piperazine-1,4-dione
Other name(s): NotF; BrePT; brevianamide F reverse prenyltransferase; dimethylallyl-diphosphate:brevianamide-F tert-dimethylallyl-C-2-transferase
Systematic name: prenyl-diphosphate:brevianamide-F 2-methylbut-3-en-2-yl-C-2-transferase
Comments: The enzyme from the fungus Aspergilus sp. MF297-2 is specific for brevianamide F [1], while the enzyme from Aspergillus versicolor accepts a broad range of trytophan-containing cyclic dipeptides [2]. Involved in the biosynthetic pathways of several indole alkaloids such as paraherquamides and malbrancheamides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ding, Y., de Wet, J.R., Cavalcoli, J., Li, S., Greshock, T.J., Miller, K.A., Finefield, J.M., Sunderhaus, J.D., McAfoos, T.J., Tsukamoto, S., Williams, R.M. and Sherman, D.H. Genome-based characterization of two prenylation steps in the assembly of the stephacidin and notoamide anticancer agents in a marine-derived Aspergillus sp. J. Am. Chem. Soc. 132 (2010) 12733–12740. [DOI] [PMID: 20722388]
2.  Yin, S., Yu, X., Wang, Q., Liu, X.Q. and Li, S.M. Identification of a brevianamide F reverse prenyltransferase BrePT from Aspergillus versicolor with a broad substrate specificity towards tryptophan-containing cyclic dipeptides. Appl. Microbiol. Biotechnol. 97 (2013) 1649–1660. [DOI] [PMID: 22660767]
[EC 2.5.1.109 created 2013]
 
 
EC 1.4.1.18     Relevance: 19.2%
Accepted name: lysine 6-dehydrogenase
Reaction: L-lysine + NAD+ = (S)-2,3,4,5-tetrahydropyridine-2-carboxylate + NADH + H+ + NH3 (overall reaction)
(1a) L-lysine + NAD+ + H2O = (S)-2-amino-6-oxohexanoate + NADH + H+ + NH3
(1b) (S)-2-amino-6-oxohexanoate = (S)-2,3,4,5-tetrahydropyridine-2-carboxylate + H2O (spontaneous)
For diagram of reaction, click here and for diagram of L-lysine synthesis, click here
Glossary: (S)-2-amino-6-oxohexanoate = L-2-aminoadipate 6-semialdehyde = L-allysine
L-1-piperideine 6-carboxylate = (S)-2,3,4,5-tetrahydropyridine-2-carboxylate = (S)-1,6-didehydropiperidine-2-carboxylate
Other name(s): L-lysine ε-dehydrogenase; L-lysine 6-dehydrogenase; LysDH
Systematic name: L-lysine:NAD+ 6-oxidoreductase (deaminating)
Comments: The enzyme is highly specific for L-lysine as substrate, although S-(2-aminoethyl)-L-cysteine can act as a substrate, but more slowly. While the enzyme from Agrobacterium tumefaciens can use only NAD+, that from the thermophilic bacterium Geobacillus stearothermophilus can also use NADP+, but more slowly [1,4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 89400-30-6
References:
1.  Misono, H. and Nagasaki, S. Occurrence of L-lysine ε-dehydrogenase in Agrobacterium tumefaciens. J. Bacteriol. 150 (1982) 398–401. [PMID: 6801024]
2.  Misono, H., Uehigashi, H., Morimoto, E. and Nagasaki, S. Purification and properties of L-lysine ε-dehydrogenase from Agrobacterium tumefaciens. Agric. Biol. Chem. 49 (1985) 2253–2255.
3.  Misono, H., Hashimoto, H., Uehigashi, H., Nagata, S. and Nagasaki, S. Properties of L-lysine ε-dehydrogenase from Agrobacterium tumefaciens. J. Biochem. (Tokyo) 105 (1989) 1002–1008. [PMID: 2768207]
4.  Heydari, M., Ohshima, T., Nunoura-Kominato, N. and Sakuraba, H. Highly stable L-lysine 6-dehydrogenase from the thermophile Geobacillus stearothermophilus isolated from a Japanese hot spring: characterization, gene cloning and sequencing, and expression. Appl. Environ. Microbiol. 70 (2004) 937–942. [DOI] [PMID: 14766574]
[EC 1.4.1.18 created 1989, modified 2006, modified 2011]
 
 
EC 4.4.1.14     Relevance: 19.2%
Accepted name: 1-aminocyclopropane-1-carboxylate synthase
Reaction: S-adenosyl-L-methionine = 1-aminocyclopropane-1-carboxylate + S-methyl-5′-thioadenosine
For diagram of ethylene biosynthesis, click here
Glossary: S-methyl-5′-thioadenosine = 5′-deoxy-5′-(methylsulfanyl)adenosine
Other name(s): 1-aminocyclopropanecarboxylate synthase; 1-aminocyclopropane-1-carboxylic acid synthase; 1-aminocyclopropane-1-carboxylate synthetase; aminocyclopropanecarboxylic acid synthase; aminocyclopropanecarboxylate synthase; ACC synthase; S-adenosyl-L-methionine methylthioadenosine-lyase; S-adenosyl-L-methionine methylthioadenosine-lyase (1-aminocyclopropane-1-carboxylate-forming)
Systematic name: S-adenosyl-L-methionine S-methyl-5′-thioadenosine-lyase (1-aminocyclopropane-1-carboxylate-forming)
Comments: A pyridoxal 5′-phosphate protein. The enzyme catalyses an α,γ-elimination.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 72506-68-4
References:
1.  Boller, T., Herner, R.C. and Kende, H. Assay for and enzymatic formation of an ethylene precursor, 1-aminocyclopropane-1-carboxylic acid. Planta 145 (1979) 293–303. [DOI] [PMID: 24317737]
2.  Yu, Y.-B., Adams, D.O. and Yang, S.F. 1-Aminocyclopropanecarboxylate synthase, a key enzyme in ethylene biosynthesis. Arch. Biochem. Biophys. 198 (1979) 280–296. [DOI] [PMID: 507845]
[EC 4.4.1.14 created 1984, modified 2021]
 
 


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