The Enzyme Database

Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Richard Cammack, Ron Caspi, Masaaki Kotera, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.


Contents

EC 1.1.1.296 dihydrocarveol dehydrogenase
EC 1.1.1.297 limonene-1,2-diol dehydrogenase
EC 1.2.1.73 sulfoacetaldehyde dehydrogenase
EC 1.3.1.81 (+)-pulegone reductase
EC 1.3.1.82 (-)-isopiperitenone reductase
EC 1.3.99.25 carvone reductase
*EC 1.4.3.4 monoamine oxidase
EC 1.4.3.6 deleted
EC 1.4.3.21 primary-amine oxidase
EC 1.4.3.22 diamine oxidase
EC 1.14.13.104 (+)-menthofuran synthase
EC 1.14.13.105 monocyclic monoterpene ketone monooxygenase
EC 1.14.19.4 acyl-lipid (11-3)-desaturase
EC 2.2.1.9 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
EC 2.4.1.245 α,α-trehalose synthase
EC 2.4.1.246 mannosylfructose-phosphate synthase
EC 2.5.1.64 transferred
*EC 2.7.7.61 citrate lyase holo-[acyl-carrier protein] synthase
EC 2.7.7.66 malonate decarboxylase holo-[acyl-carrier protein] synthase
*EC 2.7.8.25 triphosphoribosyl-dephospho-CoA synthase
EC 3.1.1.83 monoterpene ε-lactone hydrolase
EC 3.1.4.53 3′,5′-cyclic-AMP phosphodiesterase
EC 3.1.7.4 sclareol cyclase
EC 3.1.26.12 ribonuclease E
EC 3.4.11.24 aminopeptidase S
EC 4.1.3.37 transferred
EC 4.2.3.36 terpentetriene synthase
EC 4.2.99.20 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
EC 5.5.1.15 terpentedienyl-diphosphate synthase
EC 5.5.1.16 halimadienyl-diphosphate synthase


EC 1.1.1.296
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, IUBMB, KEGG
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. [PMID: 10832640]
[EC 1.1.1.296 created 2008]
 
 
EC 1.1.1.297
Accepted name: limonene-1,2-diol dehydrogenase
Reaction: menth-8-ene-1,2-diol + NAD+ = 1-hydroxymenth-8-en-2-one + NADH + H+ (general reaction)
(1) (1S,2S,4R)-menth-8-ene-1,2-diol + NAD+ = (1S,4R)-1-hydroxymenth-8-en-2-one + NADH + H+
(2) (1R,2R,4S)-menth-8-ene-1,2-diol + NAD+ = (1R,4S)-1-hydroxymenth-8-en-2-one + NADH + H+
For diagram of limonene catabolism, click here
Glossary: limonene-1,2-diol = menth-8-ene-1,2-diol = 1-methyl-4-(prop-1-en-2-yl)cyclohexane-1,2-diol
Other name(s): NAD+-dependent limonene-1,2-diol dehydrogenase
Systematic name: menth-8-ene-1,2-diol:NAD+ oxidoreductase
Comments: While the enzyme from the Gram-positive bacterium Rhodococcus erythropolis DCL14 can use both (1S,2S,4R)- and (1R,2R,4S)-menth-8-ene-1,2-diol as substrate, activity is higher with (1S,2S,4R)-menth-8-ene-1,2-diol as substrate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
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]
[EC 1.1.1.297 created 2008]
 
 
EC 1.2.1.73
Accepted name: sulfoacetaldehyde dehydrogenase
Reaction: 2-sulfoacetaldehyde + H2O + NAD+ = sulfoacetate + NADH + 2 H+
Glossary: 2-sulfoacetaldehyde = 2-oxoethanesulfonate
taurine = 2-aminoethanesulfonate
Other name(s): SafD
Systematic name: 2-sulfoacetaldehyde:NAD+ oxidoreductase
Comments: This reaction is part of a bacterial pathway that can utilize the amino group of taurine as a sole source of nitrogen for growth. At physiological concentrations, NAD+ cannot be replaced by NADP+. The enzyme is specific for sulfoacetaldehyde, as formaldehyde, acetaldehyde, betaine aldehyde, propanal, glyceraldehyde, phosphonoacetaldehyde, glyoxylate, glycolaldehyde and 2-oxobutyrate are not substrates.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Krejčík, Z., Denger, K., Weinitschke, S., Hollemeyer, K., Pačes, V., Cook, A.M. and Smits, T.H.M. Sulfoacetate released during the assimilation of taurine-nitrogen by Neptuniibacter caesariensis: purification of sulfoacetaldehyde dehydrogenase. Arch. Microbiol. 190 (2008) 159–168. [PMID: 18506422]
[EC 1.2.1.73 created 2008]
 
 
EC 1.3.1.81
Accepted name: (+)-pulegone reductase
Reaction: (1) (-)-menthone + NADP+ = (+)-pulegone + NADPH + H+
(2) (+)-isomenthone + NADP+ = (+)-pulegone + NADPH + H+
Systematic name: (-)-menthone:NADP+ oxidoreductase
Comments: NADH cannot replace NADPH as reductant. The Δ8,9-double bond of (+)-cis-isopulegone and the Δ1,2-double bond of ()-piperitone are not substrates. The enzyme from peppermint (Mentha x piperita) converts (+)-pulegone into both (-)-menthone and (+)-isomenthone at a ratio of 70:30 for native enzyme but it does not catalyse the reverse reaction. This enzyme is a member of the medium-chain dehydrogenase/reductase superfamily.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ringer, K.L., McConkey, M.E., Davis, E.M., Rushing, G.W. and Croteau, R. Monoterpene double-bond reductases of the (-)-menthol biosynthetic pathway: isolation and characterization of cDNAs encoding (-)-isopiperitenone reductase and (+)-pulegone reductase of peppermint. Arch. Biochem. Biophys. 418 (2003) 80–92. [PMID: 13679086]
[EC 1.3.1.81 created 2008]
 
 
EC 1.3.1.82
Accepted name: (-)-isopiperitenone reductase
Reaction: (+)-cis-isopulegone + NADP+ = (-)-isopiperitenone + NADPH + H+
Systematic name: (+)-cis-isopulegone:NADP+ oxidoreductase
Comments: The reaction occurs in the opposite direction to that shown above. The enzyme participates in the menthol-biosynthesis pathway of Mentha plants. (+)-Pulegone, (+)-cis-isopulegone and (-)-menthone are not substrates. The enzyme has a preference for NADPH as the reductant, with NADH being a poor substitute [2]. The enzyme is highly regioselective for the reduction of the endocyclic 1,2-double bond, and is stereoselective, producing only the 1R-configured product. It is a member of the short-chain dehydrogenase/reductase superfamily.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Croteau, R. and Venkatachalam, K.V. Metabolism of monoterpenes: demonstration that (+)-cis-isopulegone, not piperitenone, is the key intermediate in the conversion of (-)-isopiperitenone to (+)-pulegone in peppermint (Mentha piperita). Arch. Biochem. Biophys. 249 (1986) 306–315. [PMID: 3755881]
2.  Ringer, K.L., McConkey, M.E., Davis, E.M., Rushing, G.W. and Croteau, R. Monoterpene double-bond reductases of the (-)-menthol biosynthetic pathway: isolation and characterization of cDNAs encoding (-)-isopiperitenone reductase and (+)-pulegone reductase of peppermint. Arch. Biochem. Biophys. 418 (2003) 80–92. [PMID: 13679086]
[EC 1.3.1.82 created 2008]
 
 
EC 1.3.99.25
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, IUBMB, KEGG
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. [PMID: 10832640]
[EC 1.3.99.25 created 2008]
 
 
*EC 1.4.3.4
Accepted name: monoamine oxidase
Reaction: RCH2NHR′ + H2O + O2 = RCHO + R′NH2 + H2O2
Other name(s): adrenalin oxidase; adrenaline oxidase; amine oxidase (ambiguous); amine oxidase (flavin-containing); amine:oxygen oxidoreductase (deaminating) (flavin-containing); epinephrine oxidase; MAO; MAO A; MAO B; MAO-A; MAO-B; monoamine oxidase A; monoamine oxidase B; monoamine:O2 oxidoreductase (deaminating); polyamine oxidase (ambiguous); serotonin deaminase; spermidine oxidase (ambiguous); spermine oxidase (ambiguous); tyraminase; tyramine oxidase
Systematic name: amine:oxygen oxidoreductase (deaminating)
Comments: A mitochondrial outer-membrane flavoprotein (FAD) that catalyses the oxidative deamination of neurotransmitters and biogenic amines [3]. Acts on primary amines, and also on some secondary and tertiary amines. It differs from EC 1.4.3.21, primary-amine oxidase as it can oxidize secondary and tertiary amines but not methylamine. This enzyme is inhibited by acetylenic compounds such as chlorgyline, 1-deprenyl and pargyline but, unlike EC 1.4.3.21 and EC 1.4.3.22 (diamine oxidase), it is not inhibited by semicarbazide.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, UM-BBD, CAS registry number: 9001-66-5
References:
1.  Blaschko, H. Amine oxidase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 8, Academic Press, New York, 1963, pp. 337–351.
2.  Dostert, P.L., Strolin Benedetti, M. and Tipton, K.F. Interactions of monoamine oxidase with substrates and inhibitors. Med. Res. Rev. 9 (1989) 45–89. [PMID: 2644497]
3.  Edmondson, D.E., Mattevi, A., Binda, C., Li, M. and Hubálek, F. Structure and mechanism of monoamine oxidase. Curr. Med. Chem. 11 (2004) 1983–1993. [PMID: 15279562]
4.  Shih, J.C. and Chen, K. Regulation of MAO-A and MAO-B gene expression. Curr. Med. Chem. 11 (2004) 1995–2005. [PMID: 15279563]
5.  Tipton, K.F., Boyce, S., O'Sullivan, J., Davey, G.P. and Healy, J. Monoamine oxidases: certainties and uncertainties. Curr. Med. Chem. 11 (2004) 1965–1982. [PMID: 15279561]
6.  De Colibus, L., Li, M., Binda, C., Lustig, A., Edmondson, D.E. and Mattevi, A. Three-dimensional structure of human monoamine oxidase A (MAO A): relation to the structures of rat MAO A and human MAO B. Proc. Natl. Acad. Sci. USA 102 (2005) 12684–12689. [PMID: 16129825]
7.  Youdim, M.B., Edmondson, D. and Tipton, K.F. The therapeutic potential of monoamine oxidase inhibitors. Nat. Rev. Neurosci. 7 (2006) 295–309. [PMID: 16552415]
8.  Youdim, M.B. and Bakhle, Y.S. Monoamine oxidase: isoforms and inhibitors in Parkinson′s disease and depressive illness. Br. J. Pharmacol. 147 Suppl. 1 (2006) S287–S296. [PMID: 16402116]
[EC 1.4.3.4 created 1961, modified 1983 (EC 1.4.3.9 created 1972, incorporated 1984), modified 2008]
 
 
EC 1.4.3.6
Deleted entry: amine oxidase (copper-containing). This was classified on the basis of cofactor content rather than reaction catalysed and is now known to contain two distinct enzyme activities. It has been replaced by two enzymes, EC 1.4.3.21 (primary-amine oxidase) and EC 1.4.3.22 (diamine oxidase)
[EC 1.4.3.6 created 1961, modified 1983, modified 1989, deleted 2008]
 
 
EC 1.4.3.21
Accepted name: primary-amine oxidase
Reaction: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2
Other name(s): amine oxidase (ambiguous); amine oxidase (copper-containing); amine oxidase (pyridoxal containing) (incorrect); benzylamine oxidase (incorrect); CAO (ambiguous); copper amine oxidase (ambiguous); Cu-amine oxidase (ambiguous); Cu-containing amine oxidase (ambiguous); diamine oxidase (incorrect); diamino oxhydrase (incorrect); histamine deaminase (ambiguous); histamine oxidase (ambiguous); monoamine oxidase (ambiguous); plasma monoamine oxidase (ambiguous); polyamine oxidase (ambiguous); semicarbazide-sensitive amine oxidase (ambiguous); SSAO (ambiguous)
Systematic name: primary-amine:oxygen oxidoreductase (deaminating)
Comments: A group of enzymes that oxidize primary monoamines but have little or no activity towards diamines, such as histamine, or towards secondary and tertiary amines. They are copper quinoproteins (2,4,5-trihydroxyphenylalanine quinone) and, unlike EC 1.4.3.4, monoamine oxidase, are sensitive to inhibition by carbonyl-group reagents, such as semicarbazide. In some mammalian tissues the enzyme also functions as a vascular-adhesion protein (VAP-1).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Haywood, G.W. and Large, P.J. Microbial oxidation of amines. Distribution, purification and properties of two primary-amine oxidases from the yeast Candida boidinii grown on amines as sole nitrogen source. Biochem. J. 199 (1981) 187–201. [PMID: 7337701]
2.  Tipping, A.J. and McPherson, M.J. Cloning and molecular analysis of the pea seedling copper amine oxidase. J. Biol. Chem. 270 (1995) 16939–16946. [PMID: 7622512]
3.  Lyles, G.A. Mammalian plasma and tissue-bound semicarbazide-sensitive amine oxidases: biochemical, pharmacological and toxicological aspects. Int. J. Biochem. Cell Biol. 28 (1996) 259–274. [PMID: 8920635]
4.  Wilce, M.C., Dooley, D.M., Freeman, H.C., Guss, J.M., Matsunami, H., McIntire, W.S., Ruggiero, C.E., Tanizawa, K. and Yamaguchi, H. Crystal structures of the copper-containing amine oxidase from Arthrobacter globiformis in the holo and apo forms: implications for the biogenesis of topaquinone. Biochemistry 36 (1997) 16116–16133. [PMID: 9405045]
5.  Lee, Y. and Sayre, L.M. Reaffirmation that metabolism of polyamines by bovine plasma amine oxidase occurs strictly at the primary amino termini. J. Biol. Chem. 273 (1998) 19490–19494. [PMID: 9677370]
6.  Houen, G. Mammalian Cu-containing amine oxidases (CAOs): new methods of analysis, structural relationships, and possible functions. APMIS Suppl. 96 (1999) 1–46. [PMID: 10668504]
7.  Andrés, N., Lizcano, J.M., Rodríguez, M.J., Romera, M., Unzeta, M. and Mahy, N. Tissue activity and cellular localization of human semicarbazide-sensitive amine oxidase. J. Histochem. Cytochem. 49 (2001) 209–217. [PMID: 11156689]
8.  Saysell, C.G., Tambyrajah, W.S., Murray, J.M., Wilmot, C.M., Phillips, S.E., McPherson, M.J. and Knowles, P.F. Probing the catalytic mechanism of Escherichia coli amine oxidase using mutational variants and a reversible inhibitor as a substrate analogue. Biochem. J. 365 (2002) 809–816. [PMID: 11985492]
9.  O'Sullivan, J., Unzeta, M., Healy, J., O'Sullivan, M.I., Davey, G. and Tipton, K.F. Semicarbazide-sensitive amine oxidases: enzymes with quite a lot to do. Neurotoxicology 25 (2004) 303–315. [PMID: 14697905]
10.  Airenne, T.T., Nymalm, Y., Kidron, H., Smith, D.J., Pihlavisto, M., Salmi, M., Jalkanen, S., Johnson, M.S. and Salminen, T.A. Crystal structure of the human vascular adhesion protein-1: unique structural features with functional implications. Protein Sci. 14 (2005) 1964–1974. [PMID: 16046623]
[EC 1.4.3.21 created 2007 (EC 1.4.3.6 created 1961, part-incorporated 2008)]
 
 
EC 1.4.3.22
Accepted name: diamine oxidase
Reaction: histamine + H2O + O2 = (imidazol-4-yl)acetaldehyde + NH3 + H2O2
Other name(s): amine oxidase (ambiguous); amine oxidase (copper-containing) (ambiguous); CAO (ambiguous); Cu-containing amine oxidase (ambiguous); copper amine oxidase (ambiguous); diamine oxidase (ambiguous); diamino oxhydrase (ambiguous); histaminase; histamine deaminase (incorrect); semicarbazide-sensitive amine oxidase (incorrect); SSAO (incorrect)
Systematic name: histamine:oxygen oxidoreductase (deaminating)
Comments: A group of enzymes that oxidize diamines, such as histamine, and also some primary monoamines but have little or no activity towards secondary and tertiary amines. They are copper quinoproteins (2,4,5-trihydroxyphenylalanine quinone) and, like EC 1.4.3.21 (primary-amine oxidase) but unlike EC 1.4.3.4 (monoamine oxidase), they are sensitive to inhibition by carbonyl-group reagents, such as semicarbazide.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zeller, E.A. Diamine oxidases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 8, Academic Press, New York, 1963, pp. 313–335.
2.  Crabbe, M.J., Waight, R.D., Bardsley, W.G., Barker, R.W., Kelly, I.D. and Knowles, P.F. Human placental diamine oxidase. Improved purification and characterization of a copper- and manganese-containing amine oxidase with novel substrate specificity. Biochem. J. 155 (1976) 679–687. [PMID: 182134]
3.  Chassande, O., Renard, S., Barbry, P. and Lazdunski, M. The human gene for diamine oxidase, an amiloride binding protein. Molecular cloning, sequencing, and characterization of the promoter. J. Biol. Chem. 269 (1994) 14484–14489. [PMID: 8182053]
4.  Houen, G. Mammalian Cu-containing amine oxidases (CAOs): new methods of analysis, structural relationships, and possible functions. APMIS Suppl. 96 (1999) 1–46. [PMID: 10668504]
5.  Elmore, B.O., Bollinger, J.A. and Dooley, D.M. Human kidney diamine oxidase: heterologous expression, purification, and characterization. J. Biol. Inorg. Chem. 7 (2002) 565–579. [PMID: 12072962]
[EC 1.4.3.22 created 2007 (EC 1.4.3.6 created 1961, part-incorporated 2008)]
 
 
EC 1.14.13.104
Accepted name: (+)-menthofuran synthase
Reaction: (+)-pulegone + NADPH + H+ + O2 = (+)-menthofuran + NADP+ + H2O
For diagram of (-)-carvone, perillyl aldehyde and pulegone biosynthesis, click here and for mechanism of reaction, click here
Other name(s): menthofuran synthase; (+)-pulegone 9-hydroxylase; (+)-MFS; cytochrome P450 menthofuran synthase
Systematic name: (+)-pulegone,NADPH:oxygen oxidoreductase (9-hydroxylating)
Comments: A heme-thiolate protein (P-450). The conversion of substrate into product involves the hydroxylation of the syn-methyl (C9), intramolecular cyclization to the hemiketal and dehydration to the furan [1]. This is the second cytochrome P-450-mediated step of monoterpene metabolism in peppermint, with the other step being catalysed by EC 1.14.13.47, (S)-limonene 3-monooxygenase [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Bertea, C.M., Schalk, M., Karp, F., Maffei, M. and Croteau, R. Demonstration that menthofuran synthase of mint (Mentha) is a cytochrome P450 monooxygenase: cloning, functional expression, and characterization of the responsible gene. Arch. Biochem. Biophys. 390 (2001) 279–286. [PMID: 11396930]
2.  Mahmoud, S.S. and Croteau, R.B. Menthofuran regulates essential oil biosynthesis in peppermint by controlling a downstream monoterpene reductase. Proc. Natl. Acad. Sci. USA 100 (2003) 14481–14486. [PMID: 14623962]
[EC 1.14.13.104 created 2008]
 
 
EC 1.14.13.105
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, IUBMB, KEGG
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. [PMID: 10832640]
[EC 1.14.13.105 created 2008]
 
 
EC 1.14.19.4
Accepted name: acyl-lipid (11-3)-desaturase
Reaction: (1) an (11Z,14Z)-icosa-11,14-dienoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = an (8Z,11Z,14Z)-icosa-8,11,14-trienoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
(2) an (11Z,14Z,17Z)-icosa-11,14,17-trienoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = an (8Z,11Z,14Z,17Z)-icosa-8,11,14,17-tetraenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
Glossary: di-homo-γ-linolenate = (8Z,11Z,14Z)-icosa-8,11,14-trienoate
Other name(s): acyl-lipid 8-desaturase; Δ8 fatty acid desaturase; Δ8-desaturase; Δ8-fatty-acid desaturase; efd1 (gene name); D8Des (gene name); phytosphinganine,hydrogen donor:oxygen Δ8-oxidoreductase (incorrect); SLD
Systematic name: acyl-lipid,ferrocytochrome b5:oxygen oxidoreductase [(11-3),(11-2)-cis-dehydrogenating]
Comments: The enzyme, characterized from the protist Euglena gracilis [1] and the microalga Rebecca salina [2], introduces a cis double bond at the 8-position in 20-carbon fatty acids that are incorporated into a glycerolipid and have an existing Δ11 desaturation. The enzyme is a front-end desaturase, introducing the new double bond between the pre-existing double bond and the carboxyl-end of the fatty acid. It contains a cytochrome b5 domain that acts as the direct electron donor to the active site of the desaturase, and does not require an external cytochrome. Involved in alternative pathways for the biosynthesis of the polyunsaturated fatty acids arachidonate and icosapentaenoate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Wallis, J.G. and Browse, J. The Δ8-desaturase of Euglena gracilis: an alternate pathway for synthesis of 20-carbon polyunsaturated fatty acids. Arch. Biochem. Biophys. 365 (1999) 307–316. [PMID: 10328826]
2.  Zhou, X.R., Robert, S.S., Petrie, J.R., Frampton, D.M., Mansour, M.P., Blackburn, S.I., Nichols, P.D., Green, A.G. and Singh, S.P. Isolation and characterization of genes from the marine microalga Pavlova salina encoding three front-end desaturases involved in docosahexaenoic acid biosynthesis. Phytochemistry 68 (2007) 785–796. [PMID: 17291553]
[EC 1.14.19.4 created 2008, modified 2015]
 
 
EC 2.2.1.9
Accepted name: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
Reaction: isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2
Other name(s): SEPHCHC synthase; MenD
Systematic name: isochorismate:2-oxoglutarate 4-oxopentanoatetransferase (decarboxylating)
Comments: Requires Mg2+ for maximal activity. 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 products of the reaction were (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate (SHCHC), pyruvate and CO2 but it is now known that two separate enzymes are involved: this enzyme and EC 4.2.99.20, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. Under basic conditions, the product can spontaneously lose pyruvate to form SHCHC.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 1112282-73-1
References:
1.  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. [PMID: 17760421]
[EC 2.2.1.9 created 2008 (EC 2.5.1.64 created 2003, part-incorporated 2008)]
 
 
EC 2.4.1.245
Accepted name: α,α-trehalose synthase
Reaction: NDP-α-D-glucose + D-glucose = α,α-trehalose + NDP
Glossary: NDP = a nucleoside diphosphate
Other name(s): trehalose synthase; trehalose synthetase; UDP-glucose:glucose 1-glucosyltransferase; TreT; PhGT; ADP-glucose:D-glucose 1-α-D-glucosyltransferase
Systematic name: NDP-α-D-glucose:D-glucose 1-α-D-glucosyltransferase
Comments: Requires Mg2+ for maximal activity [1]. The enzyme-catalysed reaction is reversible [1]. In the reverse direction to that shown above, the enzyme is specific for α,α-trehalose as substrate, as it cannot use α- or β-paranitrophenyl glucosides, maltose, sucrose, lactose or cellobiose [1]. While the enzymes from the thermophilic bacterium Rubrobacter xylanophilus and the hyperthermophilic archaeon Pyrococcus horikoshii can use ADP-, UDP- and GDP-α-D-glucose to the same extent [2,3], that from the hyperthermophilic archaeon Thermococcus litoralis has a marked preference for ADP-α-D-glucose [1] and that from the hyperthermophilic archaeon Thermoproteus tenax has a marked preference for UDP-α-D-glucose [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Qu, Q., Lee, S.J. and Boos, W. TreT, a novel trehalose glycosyltransferring synthase of the hyperthermophilic archaeon Thermococcus litoralis. J. Biol. Chem. 279 (2004) 47890–47897. [PMID: 15364950]
2.  Ryu, S.I., Park, C.S., Cha, J., Woo, E.J. and Lee, S.B. A novel trehalose-synthesizing glycosyltransferase from Pyrococcus horikoshii: molecular cloning and characterization. Biochem. Biophys. Res. Commun. 329 (2005) 429–436. [PMID: 15737605]
3.  Nobre, A., Alarico, S., Fernandes, C., Empadinhas, N. and da Costa, M.S. A unique combination of genetic systems for the synthesis of trehalose in Rubrobacter xylanophilus: properties of a rare actinobacterial TreT. J. Bacteriol. 190 (2008) 7939–7946. [PMID: 18835983]
4.  Kouril, T., Zaparty, M., Marrero, J., Brinkmann, H. and Siebers, B. A novel trehalose synthesizing pathway in the hyperthermophilic Crenarchaeon Thermoproteus tenax: the unidirectional TreT pathway. Arch. Microbiol. 190 (2008) 355–369. [PMID: 18483808]
[EC 2.4.1.245 created 2008, modified 2013]
 
 
EC 2.4.1.246
Accepted name: mannosylfructose-phosphate synthase
Reaction: GDP-mannose + D-fructose 6-phosphate = GDP + β-D-fructofuranosyl-α-D-mannopyranoside 6F-phosphate
Glossary: mannosylfructose = β-D-fructofuranosyl-α-D-mannopyranoside
Other name(s): mannosylfructose-6-phosphate synthase; MFPS
Systematic name: GDP-mannose:D-fructose-6-phosphate 2-α-D-mannosyltransferase
Comments: This enzyme, from the soil proteobacterium and plant pathogen Agrobacterium tumefaciens strain C58, requires Mg2+ or Mn2+ for activity. GDP-mannose can be replaced by ADP-mannose but with a concomitant decrease in activity. The product of this reaction is dephosphorylated by EC 3.1.3.79 (mannosylfructose-phosphate phosphatase) to form the non-reducing disaccharide mannosylfructose, which is the major endogenous osmolyte produced by several α-proteobacteria in response to osmotic stress. The F in the product name is used to indicate that the fructose residue of sucrose carries the substituent.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 92480-04-1 (not distinguished from EC 2.4.1.167)
References:
1.  Torres, L.L. and Salerno, G.L. A metabolic pathway leading to mannosylfructose biosynthesis in Agrobacterium tumefaciens uncovers a family of mannosyltransferases. Proc. Natl. Acad. Sci. USA 104 (2007) 14318–14323. [PMID: 17728402]
[EC 2.4.1.246 created 2008]
 
 
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 2.7.7.61
Accepted name: citrate lyase holo-[acyl-carrier protein] synthase
Reaction: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA + apo-[citrate (pro-3S)-lyase] = diphosphate + holo-[citrate (pro-3S)-lyase]
For diagram of reaction, click here
Other name(s): 2′-(5′′-phosphoribosyl)-3′-dephospho-CoA transferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase; CitX; holo-ACP synthase (ambiguous); 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase adenylyltransferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA transferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate-lyase adenylyltransferase; holo-citrate lyase synthase (incorrect); 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate-lyase 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Systematic name: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-[citrate (pro-3S)-lyase] 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Comments: The γ-subunit of EC 4.1.3.6, citrate (pro-3S) lyase, serves as an acyl-carrier protein (ACP) and contains the prosthetic group 2′-(5-triphosphoribosyl)-3′-dephospho-CoA [1,3]. Synthesis and attachment of the prosthetic group requires the concerted action of this enzyme and EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase [1]. In the enzyme from Escherichia coli, the prosthetic group is attached to serine-14 of the ACP via a phosphodiester bond.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 312492-44-7
References:
1.  Schneider, K., Dimroth, P. and Bott, M. Biosynthesis of the prosthetic group of citrate lyase. Biochemistry 39 (2000) 9438–9450. [PMID: 10924139]
2.  Schneider, K., Dimroth, P. and Bott, M. Identification of triphosphoribosyl-dephospho-CoA as precursor of the citrate lyase prosthetic group. FEBS Lett. 483 (2000) 165–168. [PMID: 11042274]
3.  Schneider, K., Kästner, C.N., Meyer, M., Wessel, M., Dimroth, P. and Bott, M. Identification of a gene cluster in Klebsiella pneumoniae which includes citX, a gene required for biosynthesis of the citrate lyase prosthetic group. J. Bacteriol. 184 (2002) 2439–2446. [PMID: 11948157]
[EC 2.7.7.61 created 2002, modified 2008]
 
 
EC 2.7.7.66
Accepted name: malonate decarboxylase holo-[acyl-carrier protein] synthase
Reaction: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA + malonate decarboxylase apo-[acyl-carrier protein] = malonate decarboxylase holo-[acyl-carrier protein] + diphosphate
For diagram of reaction, click here
Other name(s): holo ACP synthase (ambiguous); 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo ACP 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA transferase; MdcG; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-malonate-decarboxylase adenylyltransferase; holo-malonate-decarboxylase synthase (incorrect)
Systematic name: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-malonate-decarboxylase 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Comments: The δ subunit of malonate decarboxylase serves as an an acyl-carrier protein (ACP) and contains the prosthetic group 2-(5-triphosphoribosyl)-3-dephospho-CoA. Two reactions are involved in the production of the holo-ACP form of this enzyme. The first reaction is catalysed by EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase. The resulting prosthetic group is then attached to the ACP subunit via a phosphodiester linkage to a serine residue, thus forming the holo form of the enzyme, in a manner analogous to that of EC 2.7.7.61, citrate lyase holo-[acyl-carrier protein] synthase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hoenke, S., Wild, M.R. and Dimroth, P. Biosynthesis of triphosphoribosyl-dephospho-coenzyme A, the precursor of the prosthetic group of malonate decarboxylase. Biochemistry 39 (2000) 13223–13232. [PMID: 11052675]
2.  Hoenke, S., Schmid, M. and Dimroth, P. Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases. Biochemistry 39 (2000) 13233–13240. [PMID: 11052676]
[EC 2.7.7.66 created 2008]
 
 
*EC 2.7.8.25
Transferred entry: triphosphoribosyl-dephospho-CoA synthase. Now EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase
[EC 2.7.8.25 created 2002, modified 2008, deleted 2013]
 
 
EC 3.1.1.83
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, IUBMB, KEGG
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. [PMID: 11157238]
[EC 3.1.1.83 created 2008]
 
 
EC 3.1.4.53
Accepted name: 3′,5′-cyclic-AMP phosphodiesterase
Reaction: adenosine 3′,5′-cyclic phosphate + H2O = AMP
Glossary: AMP = adenosine 5′-phosphate
Other name(s): cAMP-specific phosphodiesterase; cAMP-specific PDE; PDE1; PDE2A; PDE2B; PDE4; PDE7; PDE8; PDEB1; PDEB2
Systematic name: 3′,5′-cyclic-AMP 5′-nucleotidohydrolase
Comments: Requires Mg2+ or Mn2+ for activity [2]. This enzyme is specific for 3′,5′-cAMP and does not hydrolyse other nucleoside 3′,5′-cyclic phosphates such as cGMP (cf. EC 3.1.4.17, 3,5-cyclic-nucleotide phosphodiesterase and EC 3.1.4.35, 3,5-cyclic-GMP phosphodiesterase). It is involved in modulation of the levels of cAMP, which is a mediator in the processes of cell transformation and proliferation [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Alonso, G.D., Schoijet, A.C., Torres, H.N. and Flawiá, M.M. TcPDE4, a novel membrane-associated cAMP-specific phosphodiesterase from Trypanosoma cruzi. Mol. Biochem. Parasitol. 145 (2006) 40–49. [PMID: 16225937]
2.  Bader, S., Kortholt, A., Snippe, H. and Van Haastert, P.J. DdPDE4, a novel cAMP-specific phosphodiesterase at the surface of Dictyostelium cells. J. Biol. Chem. 281 (2006) 20018–20026. [PMID: 16644729]
3.  Rascón, A., Soderling, S.H., Schaefer, J.B. and Beavo, J.A. Cloning and characterization of a cAMP-specific phosphodiesterase (TbPDE2B) from Trypanosoma brucei. Proc. Natl. Acad. Sci. USA 99 (2002) 4714–4719. [PMID: 11930017]
4.  Johner, A., Kunz, S., Linder, M., Shakur, Y. and Seebeck, T. Cyclic nucleotide specific phosphodiesterases of Leishmania major. BMC Microbiol. 6:25 (2006). [PMID: 16522215]
5.  Lugnier, C., Keravis, T., Le Bec, A., Pauvert, O., Proteau, S. and Rousseau, E. Characterization of cyclic nucleotide phosphodiesterase isoforms associated to isolated cardiac nuclei. Biochim. Biophys. Acta 1472 (1999) 431–446. [PMID: 10564757]
6.  Imamura, R., Yamanaka, K., Ogura, T., Hiraga, S., Fujita, N., Ishihama, A. and Niki, H. Identification of the cpdA gene encoding cyclic 3′,5′-adenosine monophosphate phosphodiesterase in Escherichia coli. J. Biol. Chem. 271 (1996) 25423–25429. [PMID: 8810311]
[EC 3.1.4.53 created 2008, modified 2011]
 
 
EC 3.1.7.4
Deleted entry: Now recognized as two enzymes EC 4.2.1.133, copal-8-ol diphosphate synthase and EC 4.2.3.141 sclareol synthase
[EC 3.1.7.4 created 2008, deleted 2013]
 
 
EC 3.1.26.12
Accepted name: ribonuclease E
Reaction: Endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions
Other name(s): endoribonuclease E; RNase E; Rne protein
Comments: RNase E is a bacterial ribonuclease that plays a role in the processing of ribosomal RNA (9S to 5S rRNA), the chemical degradation of bulk cellular RNA, the decay of specific regulatory, messenger and structural RNAs and the control of plasmid DNA replication [1]. The enzyme binds to monophosphorylated 5′ ends of substrates but exhibits sequential cleavages in the 3′ to 5′ direction [1]. 2′-O-Methyl nucleotide substitutions at RNase E binding sites do not prevent binding but do prevent cleavage of non-modified target sequences 5′ to that locus [1]. In Escherichia coli, the enzyme is found in the RNA degradosome. The C-terminal half of the protein contains binding sites for the three other major degradosomal components, the DEAD-box RNA helicase Rh1B, enolase (EC 4.1.1.11) and polynucleotide phosphorylase (EC 2.7.7.8).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 76106-82-6
References:
1.  Feng, Y., Vickers, T.A. and Cohen, S.N. The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection. Proc. Natl. Acad. Sci. USA 99 (2002) 14746–14751. [PMID: 12417756]
2.  Ehretsmann, C.P., Carpousis, A.J. and Krisch, H.M. Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site. Genes Dev. 6 (1992) 149–159. [PMID: 1730408]
3.  Cormack, R.S., Genereaux, J.L. and Mackie, G.A. RNase E activity is conferred by a single polypeptide: overexpression, purification, and properties of the ams/rne/hmp1 gene product. Proc. Natl. Acad. Sci. USA 90 (1993) 9006–9010. [PMID: 8415644]
4.  Vanzo, N.F., Li, Y.S., Py, B., Blum, E., Higgins, C.F., Raynal, L.C., Krisch, H.M. and Carpousis, A.J. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 12 (1998) 2770–2781. [PMID: 9732274]
5.  Steege, D.A. Emerging features of mRNA decay in bacteria. RNA 6 (2000) 1079–1090. [PMID: 10943888]
6.  Callaghan, A.J., Grossmann, J.G., Redko, Y.U., Ilag, L.L., Moncrieffe, M.C., Symmons, M.F., Robinson, C.V., McDowall, K.J. and Luisi, B.F. Quaternary structure and catalytic activity of the Escherichia coli ribonuclease E amino-terminal catalytic domain. Biochemistry 42 (2003) 13848–13855. [PMID: 14636052]
[EC 3.1.26.12 created 2008]
 
 
EC 3.4.11.24
Accepted name: aminopeptidase S
Reaction: Release of an N-terminal amino acid with a preference for large hydrophobic amino-terminus residues
Other name(s): Mername-AA022 peptidase; SGAP; aminopeptidase (Streptomyces griseus); Streptomyces griseus aminopeptidase; S. griseus AP; double-zinc aminopeptidase
Comments: Aminopeptidases are associated with many biological functions, including protein maturation, protein degradation, cell-cycle control and hormone-level regulation [3,4]. This enzyme contains two zinc molecules in its active site and is activated by Ca2+ [4]. In the presence of Ca2+, the best substrates are Leu-Phe, Leu-Ser, Leu-pNA (aminoacyl-p-nitroanilide), Phe-Phe-Phe and Phe-Phe [3]. Peptides with proline in the P1′ position are not substrates [3]. Belongs in peptidase family M28.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Spungin, A. and Blumberg, S. Streptomyces griseus aminopeptidase is a calcium-activated zinc metalloprotein. Purification and properties of the enzyme. Eur. J. Biochem. 183 (1989) 471–477. [PMID: 2503378]
2.  Ben-Meir, D., Spungin, A., Ashkenazi, R. and Blumberg, S. Specificity of Streptomyces griseus aminopeptidase and modulation of activity by divalent metal ion binding and substitution. Eur. J. Biochem. 212 (1993) 107–112. [PMID: 8444149]
3.  Arima, J., Uesugi, Y., Iwabuchi, M. and Hatanaka, T. Study on peptide hydrolysis by aminopeptidases from Streptomyces griseus, Streptomyces septatus and Aeromonas proteolytica. Appl. Microbiol. Biotechnol. 70 (2006) 541–547. [PMID: 16080009]
4.  Fundoiano-Hershcovitz, Y., Rabinovitch, L., Langut, Y., Reiland, V., Shoham, G. and Shoham, Y. Identification of the catalytic residues in the double-zinc aminopeptidase from Streptomyces griseus. FEBS Lett. 571 (2004) 192–196. [PMID: 15280041]
5.  Gilboa, R., Greenblatt, H.M., Perach, M., Spungin-Bialik, A., Lessel, U., Wohlfahrt, G., Schomburg, D., Blumberg, S. and Shoham, G. Interactions of Streptomyces griseus aminopeptidase with a methionine product analogue: a structural study at 1.53 Å resolution. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 551–558. [PMID: 10771423]
[EC 3.4.11.24 created 2008]
 
 
EC 4.1.3.37
Transferred entry: 1-deoxy-D-xylulose 5-phosphate synthase. Now EC 2.2.1.7, 1-deoxy-D-xylulose 5-phosphate synthase
[EC 4.1.3.37 created 2001, deleted 2002]
 
 
EC 4.2.3.36
Accepted name: terpentetriene synthase
Reaction: terpentedienyl diphosphate = terpentetriene + diphosphate
For diagram of diterpenoid biosynthesis, click here
Other name(s): Cyc2
Systematic name: terpentedienyl-diphosphate diphosphate-lyase (terpentetriene-forming)
Comments: Requires Mg2+ for maximal activity but can use Mn2+, Fe2+ or Co2+ to a lesser extent [2]. Following on from EC 5.5.1.15, terpentedienyl-diphosphate synthase, this enzyme completes the transformation of geranylgeranyl diphosphate (GGDP) into terpentetriene, which is a precursor of the diterpenoid antibiotic terpentecin. Farnesyl diphosphate can also act as a substrate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Dairi, T., Hamano, Y., Kuzuyama, T., Itoh, N., Furihata, K. and Seto, H. Eubacterial diterpene cyclase genes essential for production of the isoprenoid antibiotic terpentecin. J. Bacteriol. 183 (2001) 6085–6094. [PMID: 11567009]
2.  Hamano, Y., Kuzuyama, T., Itoh, N., Furihata, K., Seto, H. and Dairi, T. Functional analysis of eubacterial diterpene cyclases responsible for biosynthesis of a diterpene antibiotic, terpentecin. J. Biol. Chem. 277 (2002) 37098–37104. [PMID: 12138123]
3.  Eguchi, T., Dekishima, Y., Hamano, Y., Dairi, T., Seto, H. and Kakinuma, K. A new approach for the investigation of isoprenoid biosynthesis featuring pathway switching, deuterium hyperlabeling, and 1H NMR spectroscopy. The reaction mechanism of a novel streptomyces diterpene cyclase. J. Org. Chem. 68 (2003) 5433–5438. [PMID: 12839434]
[EC 4.2.3.36 created 2008]
 
 
EC 4.2.99.20
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, IUBMB, KEGG, 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. [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. [PMID: 17760421]
[EC 4.2.99.20 created 2008 (EC 2.5.1.64 created 2003, part-incorporated 2008)]
 
 
EC 5.5.1.15
Accepted name: terpentedienyl-diphosphate synthase
Reaction: geranylgeranyl diphosphate = terpentedienyl diphosphate
For diagram of diterpenoid biosynthesis, click here
Other name(s): terpentedienol diphosphate synthase; Cyc1; clerodadienyl diphosphate synthase; terpentedienyl-diphosphate lyase (decyclizing)
Systematic name: terpentedienyl-diphosphate lyase (ring-opening)
Comments: Requires Mg2+. Contains a DXDD motif, which is a characteristic of diterpene cylases whose reactions are initiated by protonation at the 14,15-double bond of geranylgeranyl diphosphate (GGDP) [2]. The triggering proton is lost at the end of the cyclization reaction [3]. The product of the reaction, terpentedienyl diphosphate, is the substrate for EC 4.2.3.36, terpentetriene synthase and is a precursor of the diterpenoid antibiotic terpentecin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Dairi, T., Hamano, Y., Kuzuyama, T., Itoh, N., Furihata, K. and Seto, H. Eubacterial diterpene cyclase genes essential for production of the isoprenoid antibiotic terpentecin. J. Bacteriol. 183 (2001) 6085–6094. [PMID: 11567009]
2.  Hamano, Y., Kuzuyama, T., Itoh, N., Furihata, K., Seto, H. and Dairi, T. Functional analysis of eubacterial diterpene cyclases responsible for biosynthesis of a diterpene antibiotic, terpentecin. J. Biol. Chem. 277 (2002) 37098–37104. [PMID: 12138123]
3.  Eguchi, T., Dekishima, Y., Hamano, Y., Dairi, T., Seto, H. and Kakinuma, K. A new approach for the investigation of isoprenoid biosynthesis featuring pathway switching, deuterium hyperlabeling, and 1H NMR spectroscopy. The reaction mechanism of a novel streptomyces diterpene cyclase. J. Org. Chem. 68 (2003) 5433–5438. [PMID: 12839434]
[EC 5.5.1.15 created 2008]
 
 
EC 5.5.1.16
Accepted name: halimadienyl-diphosphate synthase
Reaction: geranylgeranyl diphosphate = tuberculosinyl diphosphate
For diagram of diterpenoid biosynthesis, click here
Glossary: tuberculosinyl diphosphate = halima-5,13-dien-15-yl diphosphate
Other name(s): Rv3377c; halimadienyl diphosphate synthase; tuberculosinol diphosphate synthase; halima-5(6),13-dien-15-yl-diphosphate lyase (cyclizing); halima-5,13-dien-15-yl-diphosphate lyase (decyclizing)
Systematic name: halima-5,13-dien-15-yl-diphosphate lyase (ring-opening)
Comments: Requires Mg2+ for activity. This enzyme is found in pathogenic prokaryotes such as Mycobacterium tuberculosis but not in non-pathogens such as Mycobacterium smegmatis so may play a role in pathogenicity. The product of the reaction is subsequently dephosphorylated yielding tuberculosinol (halima-5,13-dien-15-ol).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Nakano, C., Okamura, T., Sato, T., Dairi, T. and Hoshino, T. Mycobacterium tuberculosis H37Rv3377c encodes the diterpene cyclase for producing the halimane skeleton. Chem. Commun. (Camb.) (2005) 1016–1018. [PMID: 15719101]
[EC 5.5.1.16 created 2008, modified 2012]
 
 


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