The Enzyme Database

Displaying entries 51-100 of 127.

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EC 5.3.2.8     Relevance: 100%
Accepted name: 4-oxalomesaconate tautomerase
Reaction: (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate = (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate
For diagram of the protocatechuate 3,4-cleavage pathway, click here
Glossary: (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate = keto tautomer of 4-oxalomesaconate
(1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate = one of the enol tautomers of 4-oxalomesaconate
Other name(s): GalD
Systematic name: 4-oxalomesaconate keto—enol-isomerase
Comments: This enzyme has been characterized from the bacterium Pseudomonas putida KT2440 and is involved in the degradation pathway of syringate and 3,4,5-trihydroxybenzoate. It catalyses the interconversion of two of the tautomers of 4-oxalomesaconate, a reaction that can also occur spontaneously.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  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 5.3.2.8 created 2011 as EC 5.3.3.16, modified 2011, transferred 2012 to EC 5.3.2.8]
 
 
EC 4.2.3.215     Relevance: 99.7%
Accepted name: δ-araneosene synthase
Reaction: geranylgeranyl diphosphate = δ-araneosene + diphosphate
Glossary: δ-araneosene = (3aR,5E,9E)-3a,6,10-trimethyl-1-(propan-2-yl)-2,3,3a,4,7,8,11,12-octahydrocyclopenta[11]annulene
Systematic name: geranylgeranyl-diphosphate diphosphate-lyase [cyclizing, δ-araneosene-forming]
Comments: Isolated from the fungus Colletotrichum gloeosporioidea. δ-Araneosene may be involved in the biosynthesis of dolasta-1(15),8-diene (see EC 4.2.3.214, dolasta-1(15),8-diene synthase) and cycloaraneosene (see EC 4.2.3.191, cycloaraneosene synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bian, G., Rinkel, J., Wang, Z., Lauterbach, L., Hou, A., Yuan, Y., Deng, Z., Liu, T. and Dickschat, J.S. A clade II-D fungal chimeric diterpene synthase from Colletotrichum gloeosporioides produces dolasta-1(15),8-diene. Angew. Chem. Int. Ed. Engl. 57 (2018) 15887–15890. [DOI] [PMID: 30277637]
[EC 4.2.3.215 created 2023]
 
 
EC 4.2.99.20     Relevance: 99.4%
Accepted name: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
Reaction: 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate = (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate + pyruvate
For diagram of reaction, click here and for diagram of vitamin K biosynthesis, click here
Other name(s): 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase; 6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate synthase; SHCHC synthase; MenH; YfbB
Systematic name: 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate pyruvate-lyase [(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate-forming]
Comments: This enzyme is involved in the biosynthesis of vitamin K2 (menaquinone). In most anaerobes and all Gram-positive aerobes, menaquinone is the sole electron transporter in the respiratory chain and is essential for their survival. It had previously been thought that the reactions carried out by this enzyme and EC 2.2.1.9, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase, were carried out by a single enzyme but this has since been disproved [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 122007-88-9
References:
1.  Jiang, M., Chen, X., Guo, Z.F., Cao, Y., Chen, M. and Guo, Z. Identification and characterization of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase in the menaquinone biosynthesis of Escherichia coli. Biochemistry 47 (2008) 3426–3434. [DOI] [PMID: 18284213]
2.  Jiang, M., Cao, Y., Guo, Z.F., Chen, M., Chen, X. and Guo, Z. Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity. Biochemistry 46 (2007) 10979–10989. [DOI] [PMID: 17760421]
[EC 4.2.99.20 created 2008 (EC 2.5.1.64 created 2003, part-incorporated 2008)]
 
 
EC 3.7.1.17     Relevance: 98.7%
Accepted name: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
Reaction: (1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate + H2O = 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate + (2Z,4Z)-2-hydroxyhexa-2,4-dienoate
Other name(s): tesD (gene name); hsaD (gene name)
Systematic name: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase ( (2Z,4Z)-2-hydroxyhexa-2,4-dienoate-forming)
Comments: The enzyme is involved in the bacterial degradation of the steroid ring structure, and is involved in degradation of multiple steroids, such as testosterone [1], cholesterol [2], and sitosterol.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Horinouchi, M., Hayashi, T., Koshino, H., Kurita, T. and Kudo, T. Identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in Comamonas testosteroni TA441. Appl. Environ. Microbiol. 71 (2005) 5275–5281. [DOI] [PMID: 16151114]
2.  Van der Geize, R., Yam, K., Heuser, T., Wilbrink, M.H., Hara, H., Anderton, M.C., Sim, E., Dijkhuizen, L., Davies, J.E., Mohn, W.W. and Eltis, L.D. A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc. Natl. Acad. Sci. USA 104 (2007) 1947–1952. [DOI] [PMID: 17264217]
3.  Lack, N., Lowe, E.D., Liu, J., Eltis, L.D., Noble, M.E., Sim, E. and Westwood, I.M. Structure of HsaD, a steroid-degrading hydrolase, from Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 2–7. [DOI] [PMID: 18097091]
4.  Lack, N.A., Yam, K.C., Lowe, E.D., Horsman, G.P., Owen, R.L., Sim, E. and Eltis, L.D. Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. J. Biol. Chem. 285 (2010) 434–443. [DOI] [PMID: 19875455]
[EC 3.7.1.17 created 2012]
 
 
EC 1.3.99.15      
Transferred entry: benzoyl-CoA reductase. Now EC 1.3.7.8.
[EC 1.3.99.15 created 1999, deleted 2011]
 
 
EC 1.3.7.8     Relevance: 96.5%
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, KEGG, MetaCyc, 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]
 
 
EC 1.1.1.243     Relevance: 96.3%
Accepted name: carveol dehydrogenase
Reaction: (–)-trans-carveol + NADP+ = (–)-carvone + NADPH + H+
For diagram of (–)-carvone, perillyl aldehyde and pulegone biosynthesis, click here
Other name(s): (–)-trans-carveol dehydrogenase
Systematic name: (–)-trans-carveol:NADP+ oxidoreductase
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 122653-66-1
References:
1.  Gershenzon, J., Maffei, M. and Croteau, R. Biochemical and histochemical-localization of monoterpene biosynthesis in the glandular trichomes of spearmint (Mentha spicata). Plant Physiol. 89 (1989) 1351–1357. [PMID: 16666709]
[EC 1.1.1.243 created 1992]
 
 
EC 1.14.14.176     Relevance: 95.7%
Accepted name: taxadiene 5α-hydroxylase
Reaction: taxa-4,11-diene + [reduced NADPH—hemoprotein reductase] + O2 = taxa-4(20),11-dien-5α-ol + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of taxadiene hydroxylation, click here
Systematic name: taxa-4,11-diene,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (5α-hydroxylating)
Comments: This microsomal cytochrome-P-450 (heme-thiolate) enzyme is involved in the biosynthesis of the diterpenoid antineoplastic drug taxol (paclitaxel). The reaction includes rearrangement of the 4(5)-double bond to a 4(20)-double bond, possibly through allylic oxidation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9035-51-2
References:
1.  Hefner, J., Rubenstein, S.M., Ketchum, R.E., Gibson, D.M., Williams, R.M. and Croteau, R. Cytochrome P450-catalyzed hydroxylation of taxa-4(5),11(12)-diene to taxa-4(20),11(12)-dien-5α-ol: the first oxygenation step in taxol biosynthesis. Chem. Biol. 3 (1996) 479–489. [DOI] [PMID: 8807878]
[EC 1.14.14.176 created 2002 as 1.14.99.37, transferred 2020 to EC 1.14.14.176]
 
 
EC 1.1.1.295     Relevance: 95.1%
Accepted name: momilactone-A synthase
Reaction: 3β-hydroxy-9β-pimara-7,15-diene-19,6β-olide + NAD(P)+ = momilactone A + NAD(P)H + H+
For diagram of the biosynthesis of diterpenoids from syn-copalyl diphosphate, click here
Other name(s): momilactone A synthase; OsMAS
Systematic name: 3β-hydroxy-9β-pimara-7,15-diene-19,6β-olide:NAD(P)+ oxidoreductase
Comments: The rice phytoalexin momilactone A is a diterpenoid secondary metabolite that is involved in the defense mechanism of the plant. Momilactone A is produced in response to attack by a pathogen through the perception of elicitor signal molecules such as chitin oligosaccharide, or after exposure to UV irradiation. The enzyme, which catalyses the last step in the biosynthesis of momilactone A, can use both NAD+ and NADP+ but activity is higher with NAD+ [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Atawong, A., Hasegawa, M. and Kodama, O. Biosynthesis of rice phytoalexin: enzymatic conversion of 3β-hydroxy-9β-pimara-7,15-dien-19,6β-olide to momilactone A. Biosci. Biotechnol. Biochem. 66 (2002) 566–570. [DOI] [PMID: 12005050]
2.  Shimura, K., Okada, A., Okada, K., Jikumaru, Y., Ko, K.W., Toyomasu, T., Sassa, T., Hasegawa, M., Kodama, O., Shibuya, N., Koga, J., Nojiri, H. and Yamane, H. Identification of a biosynthetic gene cluster in rice for momilactones. J. Biol. Chem. 282 (2007) 34013–34018. [DOI] [PMID: 17872948]
[EC 1.1.1.295 created 2008]
 
 
EC 5.5.1.28     Relevance: 92.3%
Accepted name: (–)-kolavenyl diphosphate synthase
Reaction: geranylgeranyl diphosphate = (–)-kolavenyl diphosphate
For diagram of (–)-kolavenyl diphosphate derived diterpenoids, click here
Glossary: (–)-kolavenyl diphosphate = (2E)-5-[(1R,2S,4aS,8aS)-1,2,4a,5-tetramethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-1-yl]-3-methylpent-2-en-1-yl diposphate
Other name(s): SdKPS; TwTPS14; TwTPS10/KPS; SdCPS2; clerodienyl diphosphate synthase; CLPP
Systematic name: (–)-kolavenyl diphosphate lyase (ring-opening)
Comments: Isolated from the hallucinogenic plant Salvia divinorum (seer’s sage) and the medicinal plant Tripterygium wilfordii (thunder god vine).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hansen, N.L., Heskes, A.M., Hamberger, B., Olsen, C.E., Hallstrom, B.M., Andersen-Ranberg, J. and Hamberger, B. The terpene synthase gene family in Tripterygium wilfordii harbors a labdane-type diterpene synthase among the monoterpene synthase TPS-b subfamily. Plant J. 89 (2017) 429–441. [DOI] [PMID: 27801964]
2.  Chen, X., Berim, A., Dayan, F.E. and Gang, D.R. A (–)-kolavenyl diphosphate synthase catalyzes the first step of salvinorin A biosynthesis in Salvia divinorum. J. Exp. Bot. 68 (2017) 1109–1122. [DOI] [PMID: 28204567]
[EC 5.5.1.28 created 2017]
 
 
EC 4.2.3.186     Relevance: 92.3%
Accepted name: ent-13-epi-manoyl oxide synthase
Reaction: ent-8α-hydroxylabd-13-en-15-yl diphosphate = ent-13-epi-manoyl oxide + diphosphate
For diagram of (–)-kolavenyl diphosphate derived diterpenoids, click here
Glossary: Ent-13-epi-manoyl oxide = (13R)-ent-8,13-epoxylabd-14-ene
Other name(s): SmKSL2; ent-LDPP synthase
Systematic name: ent-8α-hydroxylabd-13-en-15-yl-diphosphate diphosphate-lyase (cyclizing, ent-13-epi-manoyl-oxide-forming)
Comments: Isolated from the plant Salvia miltiorrhiza (red sage).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cui, G., Duan, L., Jin, B., Qian, J., Xue, Z., Shen, G., Snyder, J.H., Song, J., Chen, S., Huang, L., Peters, R.J. and Qi, X. Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza. Plant Physiol. 169 (2015) 1607–1618. [DOI] [PMID: 26077765]
[EC 4.2.3.186 created 2017]
 
 
EC 1.14.14.70     Relevance: 91.8%
Accepted name: ent-sandaracopimaradiene 3-hydroxylase
Reaction: ent-sandaracopimaradiene + [reduced NADPH—hemoprotein reductase] + O2 = ent-sandaracopimaradien-3β-ol + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of oryzalexins biosynthesis, click here
Glossary: ent-sandaracopimaradiene = ent-13α-pimara-8(14),15-diene = (4aR,4bR,7S,10aR)-7-ethenyl-1,1,4a,7-tetramethyl-1,2,3,4,4a,4b,5,6,7,9,10,10a-dodecahydrophenanthrene
Other name(s): CYP701A; OsKOL4
Systematic name: ent-sandaracopimaradiene,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (ent-sandaracopimaradien-3β-ol-forming)
Comments: A cytochrome P-450 (heme-thiolate) protein isolated from Oryza sativa (rice). Participates in the pathway for the biosynthesis of oryzalexins, a group of related phytoalexins produced by rice. Can also use 9β-pimara-7,15-diene as substrate (cf. EC 1.14.14.68, syn-pimaradiene 3-monooxygenase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wang, Q., Hillwig, M.L., Wu, Y. and Peters, R.J. CYP701A8: a rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism. Plant Physiol. 158 (2012) 1418–1425. [DOI] [PMID: 22247270]
2.  Wu, Y., Wang, Q., Hillwig, M.L. and Peters, R.J. Picking sides: distinct roles for CYP76M6 and CYP76M8 in rice oryzalexin biosynthesis. Biochem. J. 454 (2013) 209–216. [DOI] [PMID: 23795884]
[EC 1.14.14.70 created 2014 as EC 1.14.13.191, transferred 2018 to EC 1.14.14.70]
 
 
EC 4.2.3.95     Relevance: 91.7%
Accepted name: (-)-α-cuprenene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (-)-α-cuprenene + diphosphate
For diagram of biosynthesis of bicyclic sesquiterpenoids derived from bisabolyl cation, click here and for diagram of trichodiene and (–)-α-cuprenene biosynthesis, click here
Other name(s): Cop6
Systematic name: (-)-α-cuprenene hydrolase [cyclizing, (-)-α-cuprenene-forming]
Comments: The enzyme from the fungus Coprinopsis cinerea produces (-)-α-cuprenene with high selectivity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lopez-Gallego, F., Agger, S.A., Abate-Pella, D., Distefano, M.D. and Schmidt-Dannert, C. Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers. ChemBioChem 11 (2010) 1093–1106. [DOI] [PMID: 20419721]
[EC 4.2.3.95 created 2012]
 
 
EC 4.2.3.103     Relevance: 91.7%
Accepted name: ent-isokaurene synthase
Reaction: ent-copalyl diphosphate = ent-isokaurene + diphosphate
For diagram of biosynthesis of diterpenoids from ent-copalyl diphosphate, click here and for diagram of ent-kaurene and ent-isokaurene, click here
Other name(s): OsKSL5i; OsKSL6
Systematic name: ent-copalyl-diphosphate diphosphate-lyase (cyclizing, ent-isokaurene-forming)
Comments: Two enzymes of the rice sub-species Oryza sativa ssp. indica, OsKSL5 and OsKSL6, produce ent-isokaurene. A variant of OsKSL5 from the sub-species Oryza sativa ssp. japonica produces ent-pimara-8(14),15-diene instead [cf. EC 4.2.3.30, ent-pimara-8(14),15-diene synthase].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Xu, M., Wilderman, P.R., Morrone, D., Xu, J., Roy, A., Margis-Pinheiro, M., Upadhyaya, N.M., Coates, R.M. and Peters, R.J. Functional characterization of the rice kaurene synthase-like gene family. Phytochemistry 68 (2007) 312–326. [DOI] [PMID: 17141283]
2.  Xu, M., Wilderman, P.R. and Peters, R.J. Following evolution’s lead to a single residue switch for diterpene synthase product outcome. Proc. Natl. Acad. Sci. USA 104 (2007) 7397–7401. [DOI] [PMID: 17456599]
[EC 4.2.3.103 created 2012]
 
 
EC 4.2.3.132     Relevance: 89.9%
Accepted name: neoabietadiene synthase
Reaction: (+)-copalyl diphosphate = neoabietadiene + diphosphate
For diagram of abietane diterpenoids biosynthesis, click here
Glossary: neoabietadiene = abieta-8(14),13(15)-diene
Other name(s): TPS-LAS
Systematic name: (+)-copaly-diphosphate diphosphate-lyase (cyclizing, neoabietadiene-forming)
Comments: Isolated from Abies grandis (grand fir) [1]. This class I enzyme forms about equal proportions of abietadiene, levopimaradiene and neoabietadiene. See also EC 4.2.3.18, abieta-7,13-diene synthase and EC 4.2.3.32, levopimaradiene synthase. An X-ray study of this multifunctional enzyme showed that the class I activity is in the α domain, while (+)-copalyl diphosphate synthase activity (EC 5.5.1.12, a class II activity) is in the β and γ domains [2]. In Pinus taeda (loblolly pine) the major product is levopimaradiene, with less abietadiene and neoabietadiene [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Peters, R.J., Flory, J.E., Jetter, R., Ravn, M.M., Lee, H.J., Coates, R.M. and Croteau, R.B. Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. Biochemistry 39 (2000) 15592–15602. [DOI] [PMID: 11112547]
2.  Zhou, K., Gao, Y., Hoy, J.A., Mann, F.M., Honzatko, R.B. and Peters, R.J. Insights into diterpene cyclization from structure of bifunctional abietadiene synthase from Abies grandis. J. Biol. Chem. 287 (2012) 6840–6850. [DOI] [PMID: 22219188]
3.  Ro, D.K. and Bohlmann, J. Diterpene resin acid biosynthesis in loblolly pine (Pinus taeda): functional characterization of abietadiene/levopimaradiene synthase (PtTPS-LAS) cDNA and subcellular targeting of PtTPS-LAS and abietadienol/abietadienal oxidase (PtAO, CYP720B1). Phytochemistry 67 (2006) 1572–1578. [DOI] [PMID: 16497345]
[EC 4.2.3.132 created 2012]
 
 
EC 4.2.3.6     Relevance: 88.6%
Accepted name: trichodiene synthase
Reaction: (2E,6E)-farnesyl diphosphate = trichodiene + diphosphate
For diagram of biosynthesis of bicyclic sesquiterpenoids derived from bisabolyl cation, click here and for diagram of trichodiene and (–)-α-cuprenene biosynthesis, click here
Other name(s): trichodiene synthetase; sesquiterpene cyclase; trans,trans-farnesyl-diphosphate sesquiterpenoid-lyase
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, trichodiene-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 101915-76-8
References:
1.  Hohn, T.M. and Vanmiddlesworth, F. Purification and characterization of the sesquiterpene cyclase trichodiene synthetase from Fusarium sporotrichioides. Arch. Biochem. Biophys. 251 (1986) 756–761. [DOI] [PMID: 3800398]
2.  Hohn, T.M. and Beremand, P.D. Isolation and nucleotide sequence of a sesquiterpene cyclase gene from the trichothecene-producing fungus Fusarium sporotrichioides. Gene 79 (1989) 131–138. [DOI] [PMID: 2777086]
3.  Rynkiewicz, M.J., Cane, D.E. and Christianson, D.W. Structure of trichodiene synthase from Fusarium sporotrichioides provides mechanistic inferences on the terpene cyclization cascade. Proc. Natl. Acad. Sci. USA 98 (2001) 13543–13548. [DOI] [PMID: 11698643]
[EC 4.2.3.6 created 1989 as EC 4.1.99.6, transferred 2000 to EC 4.2.3.6]
 
 
EC 1.14.13.104      
Transferred entry: (+)-menthofuran synthase. Now EC 1.14.14.143, (+)-menthofuran synthase
[EC 1.14.13.104 created 2008, deleted 2018]
 
 
EC 1.3.99.25     Relevance: 87.5%
Accepted name: carvone reductase
Reaction: (1) (+)-dihydrocarvone + acceptor = (–)-carvone + reduced acceptor
(2) (–)-isodihydrocarvone + acceptor = (+)-carvone + reduced acceptor
For diagram of (–)-carvone catabolism, click here
Glossary: (+)-dihydrocarvone = (1S,4R)-menth-8-en-2-one
(+)-isodihydrocarvone = (1S,4R)-menth-8-en-2-one
(–)-carvone = (4R)-mentha-1(6),8-dien-6-one = (5R)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-en-1-one
Systematic name: (+)-dihydrocarvone:acceptor 1,6-oxidoreductase
Comments: This enzyme participates in the carveol and dihydrocarveol degradation pathway of the Gram-positive bacterium Rhodococcus erythropolis DCL14. The enzyme has not been purified, and requires an unknown cofactor, which is different from NAD+, NADP+ or a flavin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  van der Werf, M.J. and Boot, A.M. Metabolism of carveol and dihydrocarveol in Rhodococcus erythropolis DCL14. Microbiology 146 (2000) 1129–1141. [DOI] [PMID: 10832640]
[EC 1.3.99.25 created 2008]
 
 
EC 4.2.1.83     Relevance: 87%
Accepted name: 4-oxalomesaconate hydratase
Reaction: 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate + H2O
For diagram of the protocatechuate 3,4-cleavage pathway, click here
Other name(s): 4-oxalmesaconate hydratase; 4-carboxy-2-oxohexenedioate hydratase; 4-carboxy-2-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase; oxalmesaconate hydratase; γ-oxalmesaconate hydratase; 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase; LigJ; GalB
Systematic name: (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate 1,2-hydro-lyase (2-hydroxy-4-oxobutane-1,2,4-tricarboxylate-forming)
Comments: This enzyme participates in the degradation of 3,4-dihydroxybenzoate (via the meta-cleavage pathway), syringate and 3,4,5-trihydroxybenzoate, catalysing the reaction in the opposite direction [1-3]. It accepts the enol-form of 4-oxalomesaconate, 2-hydroxy-4-carboxy-hexa-2,4-dienedioate [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 85204-95-1
References:
1.  Maruyama, K. Enzymes responsible for degradation of 4-oxalmesaconic acid in Pseudomonas ochraceae. J. Biochem. 93 (1983) 567–574. [PMID: 6841354]
2.  Maruyama, K. Purification and properties of γ-oxalomesaconate hydratase from Pseudomonas ochraceae grown with phthalate. Biochem. Biophys. Res. Commun. 128 (1985) 271–277. [DOI] [PMID: 3985968]
3.  Hara, H., Masai, E., Katayama, Y. and Fukuda, M. The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6. J. Bacteriol. 182 (2000) 6950–6957. [DOI] [PMID: 11092855]
4.  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 4.2.1.83 created 1986, modified 2011]
 
 
EC 1.1.1.296     Relevance: 86.8%
Accepted name: dihydrocarveol dehydrogenase
Reaction: menth-8-en-2-ol + NAD+ = menth-8-en-2-one + NADH + H+
For diagram of (–)-carvone catabolism, click here
Glossary: (+)-dihydrocarveol = (1S,2S,4S)-menth-8-en-2-ol
(+)-isodihydrocarveol = (1S,2S,4R)-menth-8-en-2-ol
(+)-neoisodihydrocarveol = (1S,2R,4R)-menth-8-en-2-ol
(–)-dihydrocarvone = (1S,4S)-menth-8-en-2-one
(+)-isodihydrocarvone = (1S,4R)-menth-8-en-2-one
Other name(s): carveol dehydrogenase (ambiguous)
Systematic name: menth-8-en-2-ol:NAD+ oxidoreductase
Comments: This enzyme from the Gram-positive bacterium Rhodococcus erythropolis DCL14 forms part of the carveol and dihydrocarveol degradation pathway. The enzyme accepts all eight stereoisomers of menth-8-en-2-ol as substrate, although some isomers are converted faster than others. The preferred substrates are (+)-neoisodihydrocarveol, (+)-isodihydrocarveol, (+)-dihydrocarveol and (–)-isodihydrocarveol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  van der Werf, M.J. and Boot, A.M. Metabolism of carveol and dihydrocarveol in Rhodococcus erythropolis DCL14. Microbiology 146 (2000) 1129–1141. [DOI] [PMID: 10832640]
[EC 1.1.1.296 created 2008]
 
 
EC 1.23.1.3     Relevance: 84%
Accepted name: (–)-pinoresinol reductase
Reaction: (–)-lariciresinol + NADP+ = (–)-pinoresinol + NADPH + H+
For diagram of (–)-lariciresinol biosynthesis, click here
Glossary: (–)-lariciresinol = 4-[(2R,3S,4S)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-(hydroxymethyl)oxolan-2-yl]-2-methoxyphenol
(–)-pinoresinol = (1R,3aS,4R,6aS)-4,4′-(tetrahydro-1H,3H-furo[3,4-c]furan-1,4-diyl)bis(2-methoxyphenol)
Other name(s): pinoresinol/lariciresinol reductase; pinoresinol-lariciresinol reductases; (–)-pinoresinol-(–)-lariciresinol reductase; PLR
Systematic name: (–)-lariciresinol:NADP+ oxidoreductase
Comments: The reaction is catalysed in vivo in the opposite direction to that shown. A multifunctional enzyme that usually further reduces the product to (+)-secoisolariciresinol [EC 1.23.1.4, (–)-lariciresinol reductase]. Isolated from the plants Thuja plicata (western red cedar) [1], Linum perenne (perennial flax) [2] and Arabidopsis thaliana (thale cress) [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Fujita, M., Gang, D.R., Davin, L.B. and Lewis, N.G. Recombinant pinoresinol-lariciresinol reductases from western red cedar (Thuja plicata) catalyze opposite enantiospecific conversions. J. Biol. Chem. 274 (1999) 618–627. [DOI] [PMID: 9872995]
2.  Hemmati, S., Schmidt, T.J. and Fuss, E. (+)-Pinoresinol/(-)-lariciresinol reductase from Linum perenne Himmelszelt involved in the biosynthesis of justicidin B. FEBS Lett. 581 (2007) 603–610. [DOI] [PMID: 17257599]
3.  Nakatsubo, T., Mizutani, M., Suzuki, S., Hattori, T. and Umezawa, T. Characterization of Arabidopsis thaliana pinoresinol reductase, a new type of enzyme involved in lignan biosynthesis. J. Biol. Chem. 283 (2008) 15550–15557. [DOI] [PMID: 18347017]
[EC 1.23.1.3 created 2013]
 
 
EC 1.14.13.47      
Transferred entry: (S)-limonene 3-monooxygenase. Now EC 1.14.14.99, (S)-limonene 3-monooxygenase
[EC 1.14.13.47 created 1992, modified 2003, deleted 2018]
 
 
EC 3.1.1.83     Relevance: 82.2%
Accepted name: monoterpene ε-lactone hydrolase
Reaction: (1) isoprop(en)ylmethyloxepan-2-one + H2O = 6-hydroxyisoprop(en)ylmethylhexanoate (general reaction)
(2) 4-isopropenyl-7-methyloxepan-2-one + H2O = 6-hydroxy-3-isopropenylheptanoate
(3) 7-isopropyl-4-methyloxepan-2-one + H2O = 6-hydroxy-3,7-dimethyloctanoate
For diagram of (–)-carvone catabolism, click here and for diagram of menthol biosynthesis, click here
Other name(s): MLH
Systematic name: isoprop(en)ylmethyloxepan-2-one lactonohydrolase
Comments: The enzyme catalyses the ring opening of ε-lactones which are formed during degradation of dihydrocarveol by the Gram-positive bacterium Rhodococcus erythropolis DCL14. The enzyme also acts on ethyl caproate, indicating that it is an esterase with a preference for lactones (internal cyclic esters). The enzyme is not stereoselective.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  van der Vlugt-Bergmans , C.J. and van der Werf , M.J. Genetic and biochemical characterization of a novel monoterpene ε-lactone hydrolase from Rhodococcus erythropolis DCL14. Appl. Environ. Microbiol. 67 (2001) 733–741. [DOI] [PMID: 11157238]
[EC 3.1.1.83 created 2008]
 
 
EC 1.14.13.48      
Transferred entry: (S)-limonene 6-monooxygenase. Now classified as EC 1.14.14.51, (S)-limonene 6-monooxygenase
[EC 1.14.13.48 created 1992, modified 2003, deleted 2017]
 
 
EC 2.5.1.64      
Transferred entry: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. The reaction that was attributed to this enzyme is now known to be catalysed by two separate enzymes: EC 2.2.1.9 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase) and EC 4.2.99.20 (2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase)
[EC 2.5.1.64 created 2003, deleted 2008]
 
 
EC 1.14.13.49      
Transferred entry: (S)-limonene 7-monooxygenase. Now classified as EC 1.14.14.52, (S)-limonene 7-monooxygenase
[EC 1.14.13.49 created 1992, modified 2003, deleted 2017]
 
 
EC 2.9.1.3     Relevance: 77%
Accepted name: tRNA 2-selenouridine synthase
Reaction: selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O = 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate (overall reaction)
(1a) geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA = 5-methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA + diphosphate
(1b) selenophosphate + 5-methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA = 5-methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol
(1c) 5-methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA + H2O = 5-methylaminomethyl-2-selenouridine34 in tRNA + phosphate
Other name(s): selU (gene name); mnmH (gene name); ybbB (gene name); sufY (gene name)
Systematic name: geranyl diphosphate/selenophosphate:tRNA 5-methylaminomethyl-2-thiouridine34 geranyl/selenophosphatetransferase
Comments: This bacterial enzyme converts 5-methylaminomethyl-2-uridine and 5-carboxymethylaminomethyl-2-uridine to the respective selenouridine forms in a two-step process that involves geranylation and subsequent phosphoselenation of the resulting geranylated intermediates. The resultant seleno-phosphorylated uridine intermediates further react with a water molecule to release a phosphate anion and 2-selenouridine tRNA. The enzyme contains a rhodanese domain.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bartos, P., Maciaszek, A., Rosinska, A., Sochacka, E. and Nawrot, B. Transformation of a wobble 2-thiouridine to 2-selenouridine via S-geranyl-2-thiouridine as a possible cellular pathway. Bioorg. Chem. 56 (2014) 49–53. [PMID: 24971911]
2.  Jager, G., Chen, P. and Bjork, G.R. Transfer RNA bound to mnmh protein is enriched with geranylated tRNA—a possible intermediate in its selenation. PLoS One 11:e0153488 (2016). [PMID: 27073879]
3.  Sierant, M., Leszczynska, G., Sadowska, K., Komar, P., Radzikowska-Cieciura, E., Sochacka, E. and Nawrot, B. Escherichia coli tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to Se2U-RNA via S-geranylated-intermediate. FEBS Lett. 592 (2018) 2248–2258. [PMID: 29862510]
[EC 2.9.1.3 created 2020]
 
 
EC 1.3.1.19     Relevance: 70.3%
Accepted name: cis-1,2-dihydrobenzene-1,2-diol dehydrogenase
Reaction: cis-1,2-dihydrobenzene-1,2-diol + NAD+ = catechol + NADH + H+
Other name(s): cis-benzene glycol dehydrogenase; cis-1,2-dihydrocyclohexa-3,5-diene (nicotinamide adenine dinucleotide) oxidoreductase;
Systematic name: cis-1,2-dihydrobenzene-1,2-diol:NAD+ oxidoreductase
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 51923-03-6
References:
1.  Axcell, B.C. and Geary, P.J. The metabolism of benzene by bacteria. Purification and some properties of the enzyme cis-1,2-dihydroxycyclohexa-3,5-diene (nicotinamide adenine dinucleotide) oxidoreductase (cis-benzene glycol dehydrogenase). Biochem. J. 136 (1973) 927–934. [PMID: 4362337]
2.  Gibson, D.T., Koch, J.R. and Kallio, R.E. Oxidative degradation of aromatic hydrocarbons by microorganisms. I. Enzymatic formation of catechol from benzene. Biochemistry 7 (1968) 2653–2662. [PMID: 4298226]
[EC 1.3.1.19 created 1972]
 
 
EC 1.14.13.147      
Transferred entry: taxoid 7β-hydroxylase. Now EC 1.14.14.182, taxoid 7β-hydroxylase
[EC 1.14.13.147 created 2012, deleted 2022]
 
 
EC 1.14.13.105     Relevance: 69.5%
Accepted name: monocyclic monoterpene ketone monooxygenase
Reaction: (1) (–)-menthone + NADPH + H+ + O2 = (4R,7S)-7-isopropyl-4-methyloxepan-2-one + NADP+ + H2O
(2) dihydrocarvone + NADPH + H+ + O2 = 4-isopropenyl-7-methyloxepan-2-one + NADP+ + H2O
(3) (iso)-dihydrocarvone + NADPH + H+ + O2 = 6-isopropenyl-3-methyloxepan-2-one + NADP+ + H2O
(4a) 1-hydroxymenth-8-en-2-one + NADPH + H+ + O2 = 7-hydroxy-4-isopropenyl-7-methyloxepan-2-one + NADP+ + H2O
(4b) 7-hydroxy-4-isopropenyl-7-methyloxepan-2-one = 3-isopropenyl-6-oxoheptanoate (spontaneous)
For diagram of (–)-carvone catabolism, click here, for diagram of limonene catabolism, click here and for diagram of menthol biosynthesis, click here
Other name(s): 1-hydroxy-2-oxolimonene 1,2-monooxygenase; dihydrocarvone 1,2-monooxygenase; MMKMO
Systematic name: (–)-menthone,NADPH:oxygen oxidoreductase
Comments: A flavoprotein (FAD). This Baeyer-Villiger monooxygenase enzyme from the Gram-positive bacterium Rhodococcus erythropolis DCL14 has wide substrate specificity, catalysing the lactonization of a large number of monocyclic monoterpene ketones and substituted cyclohexanones [2]. Both (1R,4S)- and (1S,4R)-1-hydroxymenth-8-en-2-one are metabolized, with the lactone product spontaneously rearranging to form 3-isopropenyl-6-oxoheptanoate [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  van der Werf, M.J., Swarts, H.J. and de Bont, J.A. Rhodococcus erythropolis DCL14 contains a novel degradation pathway for limonene. Appl. Environ. Microbiol. 65 (1999) 2092–2102. [PMID: 10224006]
2.  Van Der Werf, M.J. Purification and characterization of a Baeyer-Villiger mono-oxygenase from Rhodococcus erythropolis DCL14 involved in three different monocyclic monoterpene degradation pathways. Biochem. J. 347 (2000) 693–701. [PMID: 10769172]
3.  van der Werf, M.J. and Boot, A.M. Metabolism of carveol and dihydrocarveol in Rhodococcus erythropolis DCL14. Microbiology 146 (2000) 1129–1141. [DOI] [PMID: 10832640]
[EC 1.14.13.105 created 2008]
 
 
EC 1.14.99.24     Relevance: 69.4%
Accepted name: steroid 9α-monooxygenase
Reaction: pregna-4,9(11)-diene-3,20-dione + reduced acceptor + O2 = 9,11α-epoxypregn-4-ene-3,20-dione + acceptor + H2O
Other name(s): steroid 9α-hydroxylase
Systematic name: steroid,hydrogen-donor:oxygen oxidoreductase (9-epoxidizing)
Comments: An enzyme system involving a flavoprotein (FMN) and two iron-sulfur proteins.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 82869-33-8
References:
1.  Strijewski, A. The steroid-9α-hydroxylation system from Nocardia species. Eur. J. Biochem. 128 (1982) 125–135. [DOI] [PMID: 7173200]
[EC 1.14.99.24 created 1986]
 
 
EC 1.14.12.15     Relevance: 67.8%
Accepted name: terephthalate 1,2-dioxygenase
Reaction: terephthalate + NADH + H+ + O2 = (1R,6S)-dihydroxycyclohexa-2,4-diene-1,4-dicarboxylate + NAD+
For diagram of reaction, click here
Other name(s): benzene-1,4-dicarboxylate 1,2-dioxygenase; 1,4-dicarboxybenzoate 1,2-dioxygenase
Systematic name: benzene-1,4-dicarboxylate,NADH:oxygen oxidoreductase (1,2-hydroxylating)
Comments: Has been shown to contain a Rieske [2Fe-2S] cluster
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 162032-76-0
References:
1.  Schläfli, H.R., Weiss, M.A., Leisinger, T. and Cook, A.M. Terephthalate 1,2-dioxygenase system from Comamonas testosteroni T-2; purification and some properties of the oxygenase component. J. Bacteriol. 176 (1994) 6644–6652. [DOI] [PMID: 7961417]
[EC 1.14.12.15 created 1999]
 
 
EC 1.14.12.7     Relevance: 67.3%
Accepted name: phthalate 4,5-dioxygenase
Reaction: phthalate + NADH + H+ + O2 = cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,2-dicarboxylate + NAD+
For diagram of reaction, click here
Other name(s): PDO ; phthalate dioxygenase
Systematic name: phthalate,NADH:oxygen oxidoreductase (4,5-hydroxylating)
Comments: A system, containing a reductase which is an iron-sulfur flavoprotein (FMN), an iron-sulfur oxygenase, and no independent ferredoxin. Requires Fe2+.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 63626-44-8
References:
1.  Batie, C.J., LaHaie, E. and Ballou, D.P. Purification and characterization of phthalate oxygenase and phthalate oxygenase reductase from Pseudomonas cepacia. J. Biol. Chem. 262 (1987) 1510–1518. [PMID: 3805038]
[EC 1.14.12.7 created 1990]
 
 
EC 5.3.3.10     Relevance: 67%
Accepted name: 5-carboxymethyl-2-hydroxymuconate Δ-isomerase
Reaction: 5-carboxymethyl-2-hydroxymuconate = (3E,5R)-5-carboxy-2-oxohept-3-enedioate
Glossary: 5-carboxymethyl-2-hydroxymuconate = (2E,4Z)-5-hydroxypenta-2,4-diene-1,2,5-tricarboxylate
Other name(s): CHM isomerase; 5-carboxymethyl-2-hydroxymuconic acid isomerase
Systematic name: 5-carboxymethyl-2-hydroxymuconate Δ2,Δ4-2-oxo,Δ3-isomerase
Comments: Part of the homoprotocatechuate degradation pathway in Escherichia coli C.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 79079-05-3
References:
1.  Garrido-Pertierra, A. and Cooper, R.A. Identification and purification of distinct isomerase and decarboxylase enzymes involved in the 4-hydroxyphenylacetate pathway of Escherichia coli. Eur. J. Biochem. 117 (1981) 581–584. [DOI] [PMID: 7026235]
2.  Johnson, W.H., Jr., Hajipour, G. and Whitman, C.P. Stereochemical studies of 5-(carboxymethyl)-2-hydroxymuconate isomerase and 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dioate decarboxylase from Escherichia coli C: mechanistic and evolutionary implications. J. Am. Chem. Soc. 117 (1995) 8719–8726.
[EC 5.3.3.10 created 1984]
 
 
EC 1.14.12.3     Relevance: 66.8%
Accepted name: benzene 1,2-dioxygenase
Reaction: benzene + NADH + H+ + O2 = cis-cyclohexa-3,5-diene-1,2-diol + NAD+
For diagram of reaction, click here
Other name(s): benzene hydroxylase; benzene dioxygenase
Systematic name: benzene,NADH:oxygen oxidoreductase (1,2-hydroxylating)
Comments: A system, containing a reductase which is an iron-sulfur flavoprotein (FAD), an iron-sulfur oxygenase and ferredoxin. Requires Fe2+.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-66-5
References:
1.  Gibson, D.T., Koch, J.R. and Kallio, R.E. Oxidative degradation of aromatic hydrocarbons by microorganisms. I. Enzymatic formation of catechol from benzene. Biochemistry 7 (1968) 2653–2662. [PMID: 4298226]
[EC 1.14.12.3 created 1972]
 
 
EC 4.2.3.142     Relevance: 66.7%
Accepted name: 7-epizingiberene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = 7-epizingiberene + diphosphate
Glossary: 7-epizingiberene = (5R)-2-methyl-5-[(2R)-6-methylhept-5-en-2-yl]cyclohexa-1,3-diene
Other name(s): ShZIS (gene name)
Systematic name: (2Z,6Z)-farnesyl-diphosphate lyase (cyclizing; 7-epizingiberene-forming)
Comments: Isolated from the plant Solanum habrochaites. 7-Epizingiberene is a whitefly repellant.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bleeker, P.M., Mirabella, R., Diergaarde, P.J., Vandoorn, A., Tissier, A., Kant, M.R., Prins, M., de Vos, M., Haring, M.A. and Schuurink, R.C. Improved herbivore resistance in cultivated tomato with the sesquiterpene biosynthetic pathway from a wild relative. Proc. Natl. Acad. Sci. USA 109 (2012) 20124–20129. [DOI] [PMID: 23169639]
[EC 4.2.3.142 created 2013]
 
 
EC 5.4.99.66     Relevance: 66.1%
Accepted name: α-onocerin synthase
Reaction: pre-α-onocerin = α-onocerin
For diagram of α-onocerin biosynthesis, click here
Glossary: α-onocerin = 8,14-secogammacera-8(26),14(27)-diene-3β,21α-diol
pre-α-onocerin = (21S)-21,22-epoxypolypoda-8(26)-13,17-trien-3β-ol
Other name(s): LCD
Systematic name: pre-α-onocerin mutase (cyclizing, α-onocerin-forming)
Comments: Isolated from the plant Lycopodium clavatum.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Araki, T., Saga, Y., Marugami, M., Otaka, J., Araya, H., Saito, K., Yamazaki, M., Suzuki, H. and Kushiro, T. Onocerin biosynthesis requires two highly dedicated triterpene cyclases in a fern Lycopodium clavatum. ChemBioChem 17 (2016) 288–290. [DOI] [PMID: 26663356]
[EC 5.4.99.66 created 2017]
 
 
EC 1.14.12.11     Relevance: 65.2%
Accepted name: toluene dioxygenase
Reaction: toluene + NADH + H+ + O2 = (1S,2R)-3-methylcyclohexa-3,5-diene-1,2-diol + NAD+
For diagram of reaction, click here
Other name(s): toluene 2,3-dioxygenase
Systematic name: toluene,NADH:oxygen oxidoreductase (1,2-hydroxylating)
Comments: A system, containing a reductase which is an iron-sulfur flavoprotein (FAD), an iron-sulfur oxygenase, and a ferredoxin. Some other aromatic compounds, including ethylbenzene, 4-xylene and some halogenated toluenes, are converted into the corresponding cis-dihydrodiols.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 120038-36-0
References:
1.  Renganathan, V. Possible involvement of toluene-2,3-dioxygenase in defluorination of 3-fluoro-substituted benzenes by toluene-degrading Pseudomonas sp. strain T-12. Appl. Exp. Microbiol. 55 (1989) 330–334. [PMID: 16347845]
2.  Subramanian, V., Liu, T.-N., Yeh, W.K. and Gibson, D.T. Toluene dioxygenase: purification of an iron-sulfur protein by affinity chromatography. Biochem. Biophys. Res. Commun. 91 (1979) 1131–1139. [DOI] [PMID: 526270]
[EC 1.14.12.11 created 1992]
 
 
EC 4.2.3.77     Relevance: 65%
Accepted name: (+)-germacrene D synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-germacrene D + diphosphate
For diagram of germacrene sesquiterpenoid biosynthesis, click here
Glossary: (+)-germacrene D = (1E,6E,8R)-1-methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-D-forming]
Comments: Requires Mg2+, Mn2+, Ni2+ or Co2+. The formation of (+)-germacrene D involves a 1,2-hydride shift whereas for (-)-germacrene D there is a 1,3-hydride shift (see EC 4.2.3.75).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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 4.2.1.124     Relevance: 65%
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: BRENDA, EXPASY, KEGG, MetaCyc
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]
 
 
EC 4.2.3.75     Relevance: 63.9%
Accepted name: (-)-germacrene D synthase
Reaction: (2E,6E)-farnesyl diphosphate = (-)-germacrene D + diphosphate
For diagram of gurjunene, patchoulol and selinene biosynthesis, click here
Glossary: (-)-germacrene D = (1E,6E,8S)-1-methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(-)-germacrene-D-forming]
Comments: In Solidago canadensis the biosynthesis results in the pro-R hydrogen at C-1 of the farnesy diphosphate ending up at C-11 of the (-)-germacrene D [1]. With Streptomyces coelicolor the pro-S hydrogen at C-1 ends up at C-11 of the (-)-germacrene D [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Schmidt, C.O., Bouwmeester, H.J., Franke, S. and König, W.A. Mechanisms of the biosynthesis of sesquiterpene enantiomers (+)- and (-)-germacrene D in Solidago canadensis. Chirality 11 (1999) 353–362.
2.  He, X. and Cane, D.E. Mechanism and stereochemistry of the germacradienol/germacrene D synthase of Streptomyces coelicolor A3(2). J. Am. Chem. Soc. 126 (2004) 2678–2679. [DOI] [PMID: 14995166]
3.  Lucker, J., Bowen, P. and Bohlmann, J. Vitis vinifera terpenoid cyclases: functional identification of two sesquiterpene synthase cDNAs encoding (+)-valencene synthase and (-)-germacrene D synthase and expression of mono- and sesquiterpene synthases in grapevine flowers and berries. Phytochemistry 65 (2004) 2649–2659. [DOI] [PMID: 15464152]
4.  Prosser, I., Altug, I.G., Phillips, A.L., Konig, W.A., Bouwmeester, H.J. and Beale, M.H. Enantiospecific (+)- and (-)-germacrene D synthases, cloned from goldenrod, reveal a functionally active variant of the universal isoprenoid-biosynthesis aspartate-rich motif. Arch. Biochem. Biophys. 432 (2004) 136–144. [DOI] [PMID: 15542052]
[EC 4.2.3.75 created 2011]
 
 
EC 4.2.3.15     Relevance: 63.9%
Accepted name: myrcene synthase
Reaction: geranyl diphosphate = myrcene + diphosphate
For diagram of monoterpenoid biosynthesis, click here
Glossary: myrcene = 7-methyl-3-methyleneocta-1,6-diene and is a monoterpenoid
Systematic name: geranyl-diphosphate diphosphate-lyase (myrcene-forming)
Comments: A recombinant enzyme (also known as a monoterpene synthase or cyclase) from the grand fir (Abies grandis) requires Mn2+ and K+ for activity. Mg2+ is essentially ineffective as the divalent metal ion cofactor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 197462-59-2
References:
1.  Bohlmann, J., Steele, C.L. and Croteau, R. Monoterpene synthases from grand fir (Abies grandis). cDNA isolation, characterization, and functional expression of myrcene synthase, (-)-(4S)-limonene synthase, and (-)-(1S,5S)-pinene synthase. J. Biol. Chem. 272 (1997) 21784–21792. [DOI] [PMID: 9268308]
[EC 4.2.3.15 created 2000 as EC 4.1.99.9, transferred 2000 to EC 4.2.3.15]
 
 
EC 3.3.2.1     Relevance: 63.9%
Accepted name: isochorismatase
Reaction: isochorismate + H2O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
For diagram of shikimate and chorismate biosynthesis, click here
Glossary: isochorismate = (5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylate
Other name(s): 2,3-dihydro-2,3-dihydroxybenzoate synthase; 2,3-dihydroxy-2,3-dihydrobenzoate synthase; 2,3-dihydroxy-2,3-dihydrobenzoic synthase
Systematic name: isochorismate pyruvate-hydrolase
Comments: The enzyme is involved in the biosynthesis of several siderophores, such as 2,3-dihydroxybenzoylglycine, enterobactin, bacillibactin, and vibriobactin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37288-64-5
References:
1.  Young, I.G. and Gibson, F. Regulation of the enzymes involved in the biosynthesis of 2,3-dihydroxybenzoic acid in Aerobacter aerogenes and Escherichia coli. Biochim. Biophys. Acta 177 (1969) 401–411. [DOI] [PMID: 4306838]
[EC 3.3.2.1 created 1972]
 
 
EC 3.1.1.57     Relevance: 63.5%
Accepted name: 2-pyrone-4,6-dicarboxylate lactonase
Reaction: 2-oxo-2H-pyran-4,6-dicarboxylate + H2O = (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
For diagram of the protocatechuate 3,4-cleavage pathway, click here
Other name(s): 2-pyrone-4,6-dicarboxylate hydrolase; 2-pyrone-4,6-dicarboxylate lactonohydrolase
Systematic name: 2-oxo-2H-pyran-4,6-dicarboxylate lactonohydrolase
Comments: The product is most likely the keto-form of 4-oxalomesaconate (as shown in the reaction) [1,2]. It can be converted to the enol-form, 4-hydroxybuta-1,3-diene-1,2,4-trioate, either spontaneously or by EC 5.3.2.8, 4-oxalomesaconate tautomerase [3].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 84177-55-9
References:
1.  Kersten, P.J., Dagley, S., Whittaker, J.W., Arciero, D.M. and Lipscomb, J.D. 2-Pyrone-4,6-dicarboxylic acid, a catabolite of gallic acids in Pseudomonas species. J. Bacteriol. 152 (1982) 1154–1162. [PMID: 7142106]
2.  Maruyama, K. Purification and properties of 2-pyrone-4,6-dicarboxylate hydrolase. J. Biochem. (Tokyo) 93 (1983) 557–565. [PMID: 6841353]
3.  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 3.1.1.57 created 1986, modified 2010]
 
 
EC 1.3.8.10     Relevance: 62.9%
Accepted name: cyclohex-1-ene-1-carbonyl-CoA dehydrogenase
Reaction: cyclohex-1-ene-1-carbonyl-CoA + electron-transfer flavoprotein = cyclohex-1,5-diene-1-carbonyl-CoA + reduced electron-transfer flavoprotein
Systematic name: cyclohex-1-ene-1-carbonyl-CoA:electron transfer flavoprotein oxidoreductase
Comments: Contains FAD. The enzyme, characterized from the strict anaerobic bacterium Syntrophus aciditrophicus, is involved in production of cyclohexane-1-carboxylate, a byproduct produced by that organism during fermentation of benzoate and crotonate to acetate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kung, J.W., Seifert, J., von Bergen, M. and Boll, M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J. Bacteriol. 195 (2013) 3193–3200. [DOI] [PMID: 23667239]
[EC 1.3.8.10 created 2013]
 
 
EC 2.3.1.166     Relevance: 62.1%
Accepted name: 2α-hydroxytaxane 2-O-benzoyltransferase
Reaction: benzoyl-CoA + 10-deacetyl-2-debenzoylbaccatin III = CoA + 10-deacetylbaccatin III
For diagram of taxol biosynthesis, click here
Other name(s): benzoyl-CoA:taxane 2α-O-benzoyltransferase
Systematic name: benzoyl-CoA:taxan-2α-ol O-benzoyltransferase
Comments: The enzyme was studied using the semisynthetic substrate 2-debenzoyl-7,13-diacetylbaccatin III. It will not acylate the hydroxy group at 1β, 7β, 10β or 13α of 10-deacetyl baccatin III, or at 2α or 5α of taxa-4(20),11-diene-2α,5α-diol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 329318-50-5
References:
1.  Walker, K. and Croteau, R. Taxol biosynthesis: molecular cloning of a benzoyl-CoA:taxane 2α-O-benzoyltransferase cDNA from taxus and functional expression in Escherichia coli. Proc. Natl. Acad. Sci. USA 97 (2000) 13591. [DOI] [PMID: 11095755]
[EC 2.3.1.166 created 2002]
 
 
EC 1.14.12.25     Relevance: 61.9%
Accepted name: p-cumate 2,3-dioxygenase
Reaction: p-cumate + NADH + H+ + O2 = (2R,3S)-2,3-dihydroxy-2,3-dihydro-p-cumate + NAD+
For diagram of EC 1.14.12, click here
Glossary: p-cumate = 4-isopropylbenzoate
(2R,3S)-2,3-dihydroxy-2,3-dihydro-p-cumate = (5S,6R)-5,6-dihydroxy-4-isopropylcyclohexa-1,3-diene-1-carboxylate
Systematic name: 4-isopropylbenzoate:oxygen 2,3-oxidoreductase
Comments: The enzyme, characterized from several Pseudomonas strains, is involved in the degradation of p-cymene and p-cumate. It comprises four components: a ferredoxin, a ferredoxin reductase, and two subunits of a catalytic component. The enzyme can also act on indole, transforming it to the water-insoluble blue dye indigo.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  DeFrank, J.J. and Ribbons, D.W. p-cymene pathway in Pseudomonas putida: initial reactions. J. Bacteriol. 129 (1977) 1356–1364. [PMID: 845117]
2.  Wigmore, G.J. and Ribbons, D.W. p-Cymene pathway in Pseudomonas putida: selective enrichment of defective mutants by using halogenated substrate analogs. J. Bacteriol. 143 (1980) 816–824. [PMID: 7204334]
3.  Eaton, R.W. and Chapman, P.J. Formation of indigo and related compounds from indolecarboxylic acids by aromatic acid-degrading bacteria: chromogenic reactions for cloning genes encoding dioxygenases that act on aromatic acids. J. Bacteriol. 177 (1995) 6983–6988. [DOI] [PMID: 7592495]
4.  Eaton, R.W. p-Cumate catabolic pathway in Pseudomonas putida Fl: cloning and characterization of DNA carrying the cmt operon. J. Bacteriol. 178 (1996) 1351–1362. [DOI] [PMID: 8631713]
[EC 1.14.12.25 created 2016]
 
 
EC 1.14.12.26     Relevance: 61.9%
Accepted name: chlorobenzene dioxygenase
Reaction: chlorobenzene + NADH + H+ + O2 = (1R,2R)-3-chlorocyclohexa-3,5-diene-1,2-diol + NAD+
For diagram of chlorobenzene catabolism, click here and for diagram of EC 1.14.12, click here
Other name(s): TecA
Systematic name: chlorobenzene,NADH:oxygen oxidoreductase (1,2-hydroxylating)
Comments: This bacterial enzyme is a class IIB dioxygenase, comprising three components - a heterodimeric terminal dioxygenase, a ferredoxin protein, and a ferredoxin reductase. The enzyme acts on a range of aromatic compounds, including mono-, di-, tri-, and tetra-chlorinated benzenes and toluenes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Spiess, E., Sommer, C. and Gorisch, H. Degradation of 1,4-dichlorobenzene by Xanthobacter flavus 14p1. Appl. Environ. Microbiol. 61 (1995) 3884–3888. [PMID: 8526500]
2.  Sommer, C. and Gorisch, H. Enzymology of the degradation of (di)chlorobenzenes by Xanthobacter flavus 14p1. Arch. Microbiol. 167 (1997) 384–391. [PMID: 9148781]
3.  Beil, S., Happe, B., Timmis, K.N. and Pieper, D.H. Genetic and biochemical characterization of the broad spectrum chlorobenzene dioxygenase from Burkholderia sp. strain PS12 - dechlorination of 1,2,4,5-tetrachlorobenzene. Eur. J. Biochem. 247 (1997) 190–199. [PMID: 9249026]
4.  Beil, S., Mason, J.R., Timmis, K.N. and Pieper, D.H. Identification of chlorobenzene dioxygenase sequence elements involved in dechlorination of 1,2,4,5-tetrachlorobenzene. J. Bacteriol. 180 (1998) 5520–5528. [PMID: 9791099]
[EC 1.14.12.26 created 2018]
 
 
EC 4.2.3.143     Relevance: 61.8%
Accepted name: kunzeaol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = kunzeaol + diphosphate
For diagram of germacrene sesquiterpenoid biosynthesis, click here
Glossary: kunzeaol = 6β-hydroxygermacra-1(10),4-diene = (1R,2E,6E,10R)-3,7-dimethyl-10-isopropylcyclodeca-2,6-dienol
Other name(s): TgTPS2 (gene name)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (kunzeaol-forming)
Comments: Isolated from the root of the plant Thapsia garganica. The enzyme also produces germacrene D, bicyclogermacrene and traces of other sesquiterpenoids. See EC 4.2.3.77, (+)-germacrene D synthase and EC 4.2.3.100, bicyclogermacrene synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pickel, B., Drew, D.P., Manczak, T., Weitzel, C., Simonsen, H.T. and Ro, D.K. Identification and characterization of a kunzeaol synthase from Thapsia garganica: implications for the biosynthesis of the pharmaceutical thapsigargin. Biochem. J. 448 (2012) 261–271. [DOI] [PMID: 22938155]
[EC 4.2.3.143 created 2013]
 
 
EC 4.2.3.27     Relevance: 61.6%
Accepted name: isoprene synthase
Reaction: prenyl diphosphate = isoprene + diphosphate
For diagram of isoprene biosynthesis and metabolism, click here
Glossary: isoprene = 2-methylbuta-1,3-diene
Other name(s): ISPC; ISPS; dimethylallyl-diphosphate diphosphate-lyase (isoprene-forming)
Systematic name: prenyl-diphosphate diphosphate-lyase (isoprene-forming)
Comments: Requires Mg2+ or Mn2+ for activity. This enzyme is located in the chloroplast of isoprene-emitting plants, such as poplar and aspen, and may be activitated by light-dependent changes in chloroplast pH and Mg2+ concentration [2,8].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 139172-14-8
References:
1.  Silver, G.M. and Fall, R. Enzymatic synthesis of isoprene from dimethylallyl diphosphate in aspen leaf extracts. Plant Physiol. 97 (1991) 1588–1591. [PMID: 16668590]
2.  Silver, G.M. and Fall, R. Characterization of aspen isoprene synthase, an enzyme responsible for leaf isoprene emission to the atmosphere. J. Biol. Chem. 270 (1995) 13010–13016. [DOI] [PMID: 7768893]
3.  Wildermuth, M.C. and Fall, R. Light-dependent isoprene emission (characterization of a thylakoid-bound isoprene synthase in Salix discolor chloroplasts). Plant Physiol. 112 (1996) 171–182. [PMID: 12226383]
4.  Schnitzler, J.P., Arenz, R., Steinbrecher, R. and Lehming, A. Characterization of an isoprene synthase from leaves of Quercus petraea. Bot. Acta 109 (1996) 216–221.
5.  Miller, B., Oschinski, C. and Zimmer, W. First isolation of an isoprene synthase gene from poplar and successful expression of the gene in Escherichia coli. Planta 213 (2001) 483–487. [PMID: 11506373]
6.  Sivy, T.L., Shirk, M.C. and Fall, R. Isoprene synthase activity parallels fluctuations of isoprene release during growth of Bacillus subtilis. Biochem. Biophys. Res. Commun. 294 (2002) 71–75. [DOI] [PMID: 12054742]
7.  Sasaki, K., Ohara, K. and Yazaki, K. Gene expression and characterization of isoprene synthase from Populus alba. FEBS Lett. 579 (2005) 2514–2518. [DOI] [PMID: 15848197]
8.  Schnitzler, J.-P., Zimmer, I., Bachl, A., Arend, M., Fromm, J. and Fischbach, R.J. Biochemical properties of isoprene synthase in poplar (Populus x canescens). Planta 222 (2005) 777–786. [DOI] [PMID: 16052321]
[EC 4.2.3.27 created 2007]
 
 


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