The Enzyme Database

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EC 1.3.7.10      
Transferred entry: pentalenolactone synthase. Now EC 1.14.19.8, pentalenolactone synthase
[EC 1.3.7.10 created 2012, deleted 2013]
 
 
EC 1.14.11.36     
Accepted name: pentalenolactone F synthase
Reaction: pentalenolactone D + 2 2-oxoglutarate + 2 O2 = pentalenolactone F + 2 succinate + 2 CO2 + H2O (overall reaction)
(1a) pentalenolactone D + 2-oxoglutarate + O2 = pentalenolactone E + succinate + CO2 + H2O
(1b) pentalenolactone E + 2-oxoglutarate + O2 = pentalenolactone F + succinate + CO2
For diagram of pentalenolactone biosynthesis, click here
Glossary: pentalenolactone D = (1S,4aR,6aS,9aR)-1,8,8-trimethyl-2-oxo-1,2,4,4a,6a,7,8,9-octahydropentaleno[1,6a-c]pyran-5-carboxylate
pentalenolactone E = (4aR,6aS,9aR)-8,8-dimethyl-1-methylene-2-oxo-1,2,4,4a,6a,7,8,9-octahydropentaleno[1,6a-c]pyran-5-carboxylate
pentalenolactone F = (1′R,4′aR,6′aS,9′aR)-8′,8′-dimethyl-2′-oxo-4′,4′a,6′a,8′,9′-hexahydrospiro[oxirane-2,1′-pentaleno[1,6a-c]pyran]-5′-carboxylic acid
Other name(s): penD (gene name); pntD (gene name); ptlD (gene name)
Systematic name: pentalenolactone-D,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires iron(II) and ascorbate. Isolated from the bacteria Streptomyces exfoliatus, Streptomyces arenae and Streptomyces avermitilis. Part of the pentalenolactone biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Seo, M.J., Zhu, D., Endo, S., Ikeda, H. and Cane, D.E. Genome mining in Streptomyces. Elucidation of the role of Baeyer-Villiger monooxygenases and non-heme iron-dependent dehydrogenase/oxygenases in the final steps of the biosynthesis of pentalenolactone and neopentalenolactone. Biochemistry 50 (2011) 1739–1754. [DOI] [PMID: 21250661]
[EC 1.14.11.36 created 2012]
 
 
EC 1.14.11.81     
Accepted name: (–)-cyclopenine synthase
Reaction: (1) cyclopeptine + 2-oxoglutarate + O2 = dehydrocyclopeptine + succinate + CO2 + H2O
(2) dehydrocyclopeptine + 2-oxoglutarate + O2 = (–)-cyclopenine + succinate + CO2
For diagram of cyclopeptine, cyclopenine and viridicatin biosynthesis, click here
Glossary: cyclopeptine = (3S)-3-benzyl-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
(–)-cyclopenine = (3S,3′R)-4-methyl-3′-phenyl-1H-spiro[1,4-benzodiazepine-3,2′-oxirane]-2,5-dione
Other name(s): asqJ (gene name)
Systematic name: cyclopeptine,2-oxoglutarate:oxygen oxidoreductase ((–)-cyclopenine-forming)
Comments: This fungal enzyme is involved in the biosynthesis of quinolone compounds. it catalyses two oxidation reactions: the first reaction results in a desaturation; the second reaction is a monooxygenation of the double bond, forming an epoxide. The enzyme is also active with 4′-methoxycyclopeptine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Nover, L. and Luckner, M. Mixed functional oxygenations during the biosynthesis of cyclopenin and cyclopenol, benzodiazepine alkaloids of Penicillium cyclopium westling. Incorporation of molecular oxygen and NIH-shift. FEBS Lett. 3 (1969) 292–296. [DOI] [PMID: 11947032]
2.  Ishikawa, N., Tanaka, H., Koyama, F., Noguchi, H., Wang, C.C., Hotta, K. and Watanabe, K. Non-heme dioxygenase catalyzes atypical oxidations of 6,7-bicyclic systems to form the 6,6-quinolone core of viridicatin-type fungal alkaloids. Angew. Chem. Int. Ed. Engl. 53 (2014) 12880–12884. [DOI] [PMID: 25251934]
3.  Brauer, A., Beck, P., Hintermann, L. and Groll, M. Structure of the dioxygenase AsqJ: Mechanistic insights into a one-pot multistep quinolone antibiotic biosynthesis. Angew. Chem. Int. Ed. Engl. 55 (2016) 422–426. [DOI] [PMID: 26553478]
4.  Chang, W.C., Li, J., Lee, J.L., Cronican, A.A. and Guo, Y. Mechanistic investigation of a non-heme iron enzyme catalyzed epoxidation in (–)-4′-methoxycyclopenin biosynthesis. J. Am. Chem. Soc. 138 (2016) 10390–10393. [DOI] [PMID: 27442345]
5.  Song, X., Lu, J. and Lai, W. Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations. Phys Chem Chem Phys 19 (2017) 20188–20197. [DOI] [PMID: 28726913]
6.  Liao, H.J., Li, J., Huang, J.L., Davidson, M., Kurnikov, I., Lin, T.S., Lee, J.L., Kurnikova, M., Guo, Y., Chan, N.L. and Chang, W.C. Insights into the desaturation of cyclopeptin and its C3 epimer catalyzed by a non-heme iron enzyme: structural characterization and mechanism elucidation. Angew. Chem. Int. Ed. Engl. 57 (2018) 1831–1835. [DOI] [PMID: 29314482]
7.  Mader, S.L., Brauer, A., Groll, M. and Kaila, V.RI. Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ. Nat. Commun. 9:1168 (2018). [DOI] [PMID: 29563492]
8.  Wojdyla, Z. and Borowski, T. On how the binding cavity of AsqJ dioxygenase controls the desaturation reaction regioselectivity: a QM/MM study. J. Biol. Inorg. Chem. 23 (2018) 795–808. [DOI] [PMID: 29876666]
9.  Li, J., Liao, H.J., Tang, Y., Huang, J.L., Cha, L., Lin, T.S., Lee, J.L., Kurnikov, I.V., Kurnikova, M.G., Chang, W.C., Chan, N.L. and Guo, Y. Epoxidation catalyzed by the nonheme iron(II)- and 2-oxoglutarate-dependent oxygenase, AsqJ: mechanistic elucidation of oxygen atom transfer by a ferryl intermediate. J. Am. Chem. Soc. 142 (2020) 6268–6284. [DOI] [PMID: 32131594]
10.  Tang, H., Tang, Y., Kurnikov, I.V., Liao, H.J., Chan, N.L., Kurnikova, M.G., Guo, Y. and Chang, W.C. Harnessing the substrate promiscuity of dioxygenase AsqJ and developing efficient chemoenzymatic synthesis for quinolones. ACS Catal. 11 (2021) 7186–7192. [DOI] [PMID: 35721870]
[EC 1.14.11.81 created 2022]
 
 
EC 1.14.14.11     
Accepted name: styrene monooxygenase
Reaction: styrene + FADH2 + O2 = (S)-2-phenyloxirane + FAD + H2O
Other name(s): StyA; SMO; NSMOA
Systematic name: styrene,FADH2:oxygen oxidoreductase
Comments: The enzyme catalyses the first step in the aerobic styrene degradation pathway. It forms a two-component system with a reductase (StyB) that utilizes NADH to reduce flavin-adenine dinucleotide, which is then transferred to the oxygenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Otto, K., Hofstetter, K., Rothlisberger, M., Witholt, B. and Schmid, A. Biochemical characterization of StyAB from Pseudomonas sp. strain VLB120 as a two-component flavin-diffusible monooxygenase. J. Bacteriol. 186 (2004) 5292–5302. [DOI] [PMID: 15292130]
2.  Tischler, D., Kermer, R., Groning, J.A., Kaschabek, S.R., van Berkel, W.J. and Schlomann, M. StyA1 and StyA2B from Rhodococcus opacus 1CP: a multifunctional styrene monooxygenase system. J. Bacteriol. 192 (2010) 5220–5227. [DOI] [PMID: 20675468]
[EC 1.14.14.11 created 2011]
 
 
EC 1.14.19.8     
Accepted name: pentalenolactone synthase
Reaction: pentalenolactone F + O2 + 2 reduced ferredoxin + 2 H+ = pentalenolactone + 2 oxidized ferredoxin + 2 H2O
For diagram of pentalenolactone biosynthesis, click here
Glossary: pentalenolactone F = (1R,4aR,6aS,9aR)-8,8-dimethyl-2-oxo-4,4a,6a,8,9-hexahydrospiro[oxirane-2,1-pentaleno[1,6a-c]pyran]-5-carboxylic acid
pentalenolactone = (1R,4aR,6aR,7S,9aS)-7,8-dimethyl-2-oxo-4,4a,6a,7-tetrahydrospiro[oxirane-2,1-pentaleno[1,6a-c]pyran]-5-carboxylic acid
Other name(s): penM (gene name); pntM (gene name)
Systematic name: pentalenolactone-reduced-ferredoxin:oxygen oxidoreductase (pentalenolactone-forming)
Comments: A heme-thiolate protein (P-450). Isolated from the bacteria Streptomyces exfoliatus and Streptomyces arenae.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Zhu, D., Seo, M.J., Ikeda, H. and Cane, D.E. Genome mining in streptomyces. Discovery of an unprecedented P450-catalyzed oxidative rearrangement that is the final step in the biosynthesis of pentalenolactone. J. Am. Chem. Soc. 133 (2011) 2128–2131. [DOI] [PMID: 21284395]
[EC 1.14.19.8 created 2012 as EC 1.3.7.10, transferred 2013 to EC 1.14.19.8]
 
 
EC 3.3.2.9     
Accepted name: microsomal epoxide hydrolase
Reaction: (1) cis-stilbene oxide + H2O = (1R,2R)-1,2-diphenylethane-1,2-diol
(2) 1-(4-methoxyphenyl)-N-methyl-N-[(3-methyloxetan-3-yl)methyl]methanamine + H2O = 2-({[(4-methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol
Glossary: oxirane = ethylene oxide = a 3-membered oxygen-containing ring
oxetane = 1,3-propylene oxide = a 4-membered oxygen-containing ring
Other name(s): microsomal oxirane/oxetane hydrolase; epoxide hydratase (ambiguous); microsomal epoxide hydratase (ambiguous); epoxide hydrase; microsomal epoxide hydrase; arene-oxide hydratase (ambiguous); benzo[a]pyrene-4,5-oxide hydratase; benzo(a)pyrene-4,5-epoxide hydratase; aryl epoxide hydrase (ambiguous); cis-epoxide hydrolase; mEH; EPHX1 (gene name)
Systematic name: cis-stilbene-oxide hydrolase
Comments: This is a key hepatic enzyme that catalyses the hydrolytic ring opening of oxiranes (epoxides) and oxetanes to give the corresponding diols. The enzyme is involved in the metabolism of numerous substrates including the stereoselective hydrolytic ring opening of 7-oxabicyclo[4.1.0]hepta-2,4-dienes (arene oxides) to the corresponding trans-dihydrodiols. The reaction proceeds via a triad mechanism and involves the formation of an hydroxyalkyl-enzyme intermediate. Five epoxide-hydrolase enzymes have been identified in vertebrates to date: EC 3.3.2.6 (leukotriene-A4 hydrolase), EC 3.3.2.7 (hepoxilin-epoxide hydrolase), EC 3.3.2.9 (microsomal epoxide hydrolase), EC 3.3.2.10 (soluble epoxide hydrolase) and EC 3.3.2.11 (cholesterol-5,6-oxide hydrolase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Oesch, F. and Daly, J. Solubilization, purification, and properties of a hepatic epoxide hydrase. Biochim. Biophys. Acta 227 (1971) 692–697. [DOI] [PMID: 4998715]
2.  Jakoby, W.B. and Fjellstedt, T.A. Epoxidases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 199–212.
3.  Oesch, F. Mammalian epoxide hydrases: inducible enzymes catalysing the inactivation of carcinogenic and cytotoxic metabolites derived from aromatic and olefinic compounds. Xenobiotica 3 (1973) 305–340. [DOI] [PMID: 4584115]
4.  Oesch, F. Purification and specificity of a human microsomal epoxide hydratase. Biochem. J. 139 (1974) 77–88. [PMID: 4463951]
5.  Lu, A.Y., Ryan, D., Jerina, D.M., Daly, J.W. and Levin, W. Liver microsomal expoxide hydrase. Solubilization, purification, and characterization. J. Biol. Chem. 250 (1975) 8283–8288. [PMID: 240858]
6.  Bellucci, G., Chiappe, C. and Ingrosso, G. Kinetics and stereochemistry of the microsomal epoxide hydrolase-catalyzed hydrolysis of cis-stilbene oxides. Chirality 6 (1994) 577–582. [DOI] [PMID: 7986671]
7.  Fretland, A.J. and Omiecinski, C.J. Epoxide hydrolases: biochemistry and molecular biology. Chem. Biol. Interact. 129 (2000) 41–59. [DOI] [PMID: 11154734]
8.  Morisseau, C. and Hammock, B.D. Epoxide hydrolases: mechanisms, inhibitor designs, and biological roles. Annu. Rev. Pharmacol. Toxicol. 45 (2005) 311–333. [DOI] [PMID: 15822179]
9.  Newman, J.W., Morisseau, C. and Hammock, B.D. Epoxide hydrolases: their roles and interactions with lipid metabolism. Prog. Lipid Res. 44 (2005) 1–51. [DOI] [PMID: 15748653]
10.  Toselli, F., Fredenwall, M., Svensson, P., Li, X.Q., Johansson, A., Weidolf, L. and Hayes, M.A. Oxetane substrates of human microsomal epoxide hydrolase. Drug Metab. Dispos. 45 (2017) 966–973. [DOI] [PMID: 28600384]
[EC 3.3.2.9 created 2006 (EC 3.3.2.3 created 1978, modified 1999, part incorporated 2006), modified 2017]
 
 
EC 4.1.99.27     
Accepted name: cyclopenase
Reaction: (–)-cyclopenine = viridicatin + methyl isocyanate
For diagram of cyclopeptine, cyclopenine and viridicatin biosynthesis, click here
Glossary: (–)-cyclopenine = (3S,3′R)-4-methyl-3′-phenyl-1H-spiro[1,4-benzodiazepine-3,2′-oxirane]-2,5-dione
viridicatin = 3-hydroxy-4-phenyl-1H-quinolin-2-one
Other name(s): asqI (gene name)
Systematic name: (–)-cyclopenine methyl-isocyanate lyase (viridicatin-forming)
Comments: This fungal enzyme catalyses a key reaction in the biosynthesis of quinolone compounds, converting the benzodiazepine structure into a quinolone structure. The enzyme is also active with (–)-4′-methoxycyclopenine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kishimoto, S., Hara, K., Hashimoto, H., Hirayama, Y., Champagne, P.A., Houk, K.N., Tang, Y. and Watanabe, K. Enzymatic one-step ring contraction for quinolone biosynthesis. Nat. Commun. 9:2826 (2018). [DOI] [PMID: 30026518]
[EC 4.1.99.27 created 2022]
 
 


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