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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.1.267 1-deoxy-D-xylulose-5-phosphate reductoisomerase
EC 1.2.1.74 abieta-7,13-dien-18-al dehydrogenase
EC 1.3.1.83 geranylgeranyl diphosphate reductase
EC 1.14.13.108 abieta-7,13-diene hydroxylase
EC 1.14.13.109 abieta-7,13-dien-18-ol hydroxylase
EC 1.14.13.110 geranylgeraniol 18-hydroxylase
*EC 2.7.1.119 hygromycin-B 7′′-O-kinase
EC 3.1.7.5 geranylgeranyl diphosphate diphosphatase
EC 4.2.3.41 elisabethatriene synthase
EC 4.2.3.42 aphidicolan-16β-ol synthase
EC 4.2.3.43 fusicocca-2,10(14)-diene synthase
EC 4.2.3.44 isopimara-7,15-diene synthase


*EC 1.1.1.267
Accepted name: 1-deoxy-D-xylulose-5-phosphate reductoisomerase
Reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP+ = 1-deoxy-D-xylulose 5-phosphate + NADPH + H+
For diagram of non-mevalonate terpenoid biosynthesis, click here
Other name(s): DXP-reductoisomerase; 1-deoxy-D-xylulose-5-phosphate isomeroreductase; 2-C-methyl-D-erythritol 4-phosphate (MEP) synthase
Systematic name: 2-C-methyl-D-erythritol-4-phosphate:NADP+ oxidoreductase (isomerizing)
Comments: The enzyme requires Mn2+, Co2+ or Mg2+ for activity, with the first being most effective. The enzyme from several eubacteria, including Escherichia coli, forms part of an alternative nonmevalonate pathway for terpenoid biosynthesis (for diagram, click here). The mechanism has been shown to be a retroaldol/aldol reaction [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 210756-42-6
References:
1.  Takahashi, S., Kuzuyama, T., Watanabe, H. and Seto, H.   A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis. Proc. Natl. Acad. Sci. USA 95 (1998) 9879–9884. [PMID: 9707569]
2.  Munos, J.W., Pu, X., Mansoorabadi, S.O., Kim, H.J. and Liu, H.W. A secondary kinetic isotope effect study of the 1-deoxy-D-xylulose-5-phosphate reductoisomerase-catalyzed reaction: evidence for a retroaldol-aldol rearrangement. J. Am. Chem. Soc. 131 (2009) 2048–2049. [PMID: 19159292]
[EC 1.1.1.267 created 2001]
 
 
EC 1.2.1.74
Accepted name: abieta-7,13-dien-18-al dehydrogenase
Reaction: abieta-7,13-dien-18-al + H2O + NAD+ = abieta-7,13-dien-18-oate + NADH + H+
For diagram of abietadiene, abietate, isopimaradiene, labdadienol and sclareol biosynthesis, click here
Glossary: abieta-7,13-dien-18-al = (1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene-1-carbaldehyde
abieta-7,13-dien-18-oate = (1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene-1-carboxylate
Other name(s): abietadienal dehydrogenase (ambiguous)
Systematic name: abieta-7,13-dien-18-al:NAD+ oxidoreductase
Comments: Abietic acid is the principle component of conifer resin. This enzyme catalyses the last step of the pathway of abietic acid biosynthesis in Abies grandis (grand fir). The activity has been demonstrated in cell-free stem extracts of A. grandis, was present in the cytoplasm, and required NAD+ as cofactor [1]. The enzyme is expressed constitutively at a high level, and is not inducible by wounding of the plant tissue [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Funk, C. and Croteau, R. Diterpenoid resin acid biosynthesis in conifers: characterization of two cytochrome P450-dependent monooxygenases and an aldehyde dehydrogenase involved in abietic acid biosynthesis. Arch. Biochem. Biophys. 308 (1994) 258–266. [PMID: 8311462]
2.  Funk, C., Lewinsohn, E., Vogel, B.S., Steele, C.L. and Croteau, R. Regulation of oleoresinosis in grand fir (Abies grandis) (coordinate induction of monoterpene and diterpene cyclases and two cytochrome P450-dependent diterpenoid hydroxylases by stem wounding). Plant Physiol. 106 (1994) 999–1005. [PMID: 12232380]
[EC 1.2.1.74 created 2009, modified 2012]
 
 
EC 1.3.1.83
Accepted name: geranylgeranyl diphosphate reductase
Reaction: phytyl diphosphate + 3 NADP+ = geranylgeranyl diphosphate + 3 NADPH + 3 H+
For diagram of acyclic diterpenoid biosynthesis, click here
Other name(s): geranylgeranyl reductase; CHL P
Systematic name: geranylgeranyl-diphosphate:NADP+ oxidoreductase
Comments: This enzyme also acts on geranylgeranyl-chlorophyll a. The reaction occurs in three steps. Which order the three double bonds are reduced is not known.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Soll, J., Schultz, G., Rudiger, W. and Benz, J. Hydrogenation of geranylgeraniol : two pathways exist in spinach chloroplasts. Plant Physiol. 71 (1983) 849–854. [PMID: 16662918]
2.  Tanaka, R., Oster, U., Kruse, E., Rudiger, W. and Grimm, B. Reduced activity of geranylgeranyl reductase leads to loss of chlorophyll and tocopherol and to partially geranylgeranylated chlorophyll in transgenic tobacco plants expressing antisense RNA for geranylgeranyl reductas. Plant Physiol. 120 (1999) 695–704. [PMID: 10398704]
3.  Keller, Y., Bouvier, F., d'Harlingue, A. and Camara, B. Metabolic compartmentation of plastid prenyllipid biosynthesis—evidence for the involvement of a multifunctional geranylgeranyl reductase. Eur. J. Biochem. 251 (1998) 413–417. [PMID: 9492312]
[EC 1.3.1.83 created 2009]
 
 
EC 1.14.13.108
Accepted name: abieta-7,13-diene hydroxylase
Reaction: abieta-7,13-diene + NADPH + H+ + O2 = abieta-7,13-dien-18-ol + NADP+ + H2O
For diagram of abietadiene, abietate, isopimaradiene, labdadienol and sclareol biosynthesis, click here
Glossary: abieta-7,13-diene = (4aS,4bR,10aS)-7-isopropyl-1,1,4a-trimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene
abieta-7,13-dien-18-ol = ((1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthren-1-yl)methanol
Other name(s): abietadiene hydroxylase (ambiguous)
Systematic name: abieta-7,13-diene,NADPH:oxygen oxidoreductase (18-hydroxylating)
Comments: A heme-thiolate protein (P-450). This enzyme catalyses a step in the pathway of abietic acid biosynthesis. The activity has been demonstrated in cell-free stem extracts of Abies grandis (grand fir) and Pinus contorta (lodgepole pine). The enzyme is localized in the microsomal fraction and requires both oxygen and NADPH. Inhibition by carbon monoxide and several substituted N-heterocyclic inhibitors suggests that the enzyme is a cytochrome P-450-dependent monooxygenase [1]. Activity is induced by wounding of the plant tissue [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Funk, C. and Croteau, R. Diterpenoid resin acid biosynthesis in conifers: characterization of two cytochrome P450-dependent monooxygenases and an aldehyde dehydrogenase involved in abietic acid biosynthesis. Arch. Biochem. Biophys. 308 (1994) 258–266. [PMID: 8311462]
2.  Funk, C., Lewinsohn, E., Vogel, B.S., Steele, C.L. and Croteau, R. Regulation of oleoresinosis in grand fir (Abies grandis) (coordinate induction of monoterpene and diterpene cyclases and two cytochrome P450-dependent diterpenoid hydroxylases by stem wounding). Plant Physiol. 106 (1994) 999–1005. [PMID: 12232380]
[EC 1.14.13.108 created 2009, modified 2012]
 
 
EC 1.14.13.109
Accepted name: abieta-7,13-dien-18-ol hydroxylase
Reaction: abieta-7,13-dien-18-ol + NADPH + H+ + O2 = abieta-7,13-dien-18-al + NADP+ + 2 H2O (overall reaction)
(1a) abieta-7,13-dien-18-ol + NADPH + H+ + O2 = abieta-7,13-dien-18,18-diol + NADP+ + H2O
(1b) abieta-7,13-dien-18,18-diol = abieta-7,13-dien-18-al + H2O (spontaneous)
For diagram of abietadiene, abietate, isopimaradiene, labdadienol and sclareol biosynthesis, click here and for diagram of abietane diterpenoids biosynthesis, click here
Glossary: abieta-7,13-dien-18-ol = ((1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthren-1-yl)methanol
abieta-7,13-dien-18-al = (1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene-1-carbaldehyde
Other name(s): CYP720B1; PtAO; abietadienol hydroxylase (ambiguous)
Systematic name: abieta-7,13-dien-18-ol,NADPH:oxygen oxidoreductase (18-hydroxylating)
Comments: A heme-thiolate protein (P-450). This enzyme catalyses a step in the pathway of abietic acid biosynthesis. The activity has been demonstrated in cell-free stem extracts of Abies grandis (grand fir) and Pinus contorta (lodgepole pine) [1], and the gene encoding the enzyme has been identified in Pinus taeda (loblolly pine) [3]. The recombinant enzyme catalyses the oxidation of multiple diterpene alcohol and aldehydes, including levopimaradienol, isopimara-7,15-dienol, isopimara-7,15-dienal, dehydroabietadienol and dehydroabietadienal. It is not able to oxidize abietadiene.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Funk, C. and Croteau, R. Diterpenoid resin acid biosynthesis in conifers: characterization of two cytochrome P450-dependent monooxygenases and an aldehyde dehydrogenase involved in abietic acid biosynthesis. Arch. Biochem. Biophys. 308 (1994) 258–266. [PMID: 8311462]
2.  Funk, C., Lewinsohn, E., Vogel, B.S., Steele, C.L. and Croteau, R. Regulation of oleoresinosis in grand fir (Abies grandis) (coordinate induction of monoterpene and diterpene cyclases and two cytochrome P450-dependent diterpenoid hydroxylases by stem wounding). Plant Physiol. 106 (1994) 999–1005. [PMID: 12232380]
3.  Ro, D.K., Arimura, G., Lau, S.Y., Piers, E. and Bohlmann, J. Loblolly pine abietadienol/abietadienal oxidase PtAO (CYP720B1) is a multifunctional, multisubstrate cytochrome P450 monooxygenase. Proc. Natl. Acad. Sci. USA 102 (2005) 8060–8065. [PMID: 15911762]
[EC 1.14.13.109 created 2009, modified 2012]
 
 
EC 1.14.13.110
Accepted name: geranylgeraniol 18-hydroxylase
Reaction: geranylgeraniol + NADPH + H+ + O2 = 18-hydroxygeranylgeraniol + NADP+ + H2O
For diagram of acyclic diterpenoid biosynthesis, click here
Glossary: plaunotol = 18-hydroxygeranylgeraniol
Other name(s): GGOH-18-hydroxylase
Systematic name: geranylgeraniol,NADPH:oxygen oxidoreductase (18-hydroxylating)
Comments: A heme-thiolate protein (P-450).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Tansakul, P. and De-Eknamkul, W. Geranylgeraniol-18-hydroxylase: the last enzyme in the plaunotol biosynthetic pathway in Croton sublyratus. Phytochemistry 47 (1998) 1241–1246.
[EC 1.14.13.110 created 2009]
 
 
*EC 2.7.1.119
Accepted name: hygromycin-B 7′′-O-kinase
Reaction: ATP + hygromycin B = ADP + 7′′-O-phosphohygromycin B
For diagram click here
Other name(s): hygromycin B phosphotransferase; hygromycin-B kinase (ambiguous)
Systematic name: ATP:hygromycin-B 7′′-O-phosphotransferase
Comments: Phosphorylates the antibiotics hygromycin B, 1-N-hygromycin B and destomycin, but not hygromycin B2, at the 7′′-hydroxy group in the destomic acid ring.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 88361-67-5
References:
1.  Zalacain, M., Pardo, J.M. and Jiménez, A. Purification and characterization of a hygromycin B phosphotransferase from Streptomyces hygroscopicus. Eur. J. Biochem. 162 (1987) 419–422. [PMID: 3026811]
[EC 2.7.1.119 created 1989, modified 2009, modified 2011]
 
 
EC 3.1.7.5
Accepted name: geranylgeranyl diphosphate diphosphatase
Reaction: geranylgeranyl diphosphate + H2O = geranylgeraniol + diphosphate
For diagram of acyclic diterpenoid biosynthesis, click here
Glossary: plaunotol = 18-hydroxygeranylgeraniol
Other name(s): geranylgeranyl diphosphate phosphatase
Systematic name: geranyl-diphosphate diphosphohydrolase
Comments: Involved in the biosynthesis of plaunotol. There are two isoenzymes with different ion requirements. Neither require Mg2+ but in addition PII is inhibited by Zn2+, Mn2+ and Co2+. It is not known which isoenzyme is involved in plaunotol biosynthesis.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Nualkaew, N., De-Eknamkul, W., Kutchan, T.M. and Zenk, M.H. Membrane-bound geranylgeranyl diphosphate phosphatases: purification and characterization from Croton stellatopilosus leaves. Phytochemistry 67 (2006) 1613–1620. [PMID: 16445953]
[EC 3.1.7.5 created 2009]
 
 
EC 4.2.3.41
Accepted name: elisabethatriene synthase
Reaction: geranylgeranyl diphosphate = elisabethatriene + diphosphate
For diagram of diterpenoid biosynthesis, click here and for reaction mechanism, click here
Other name(s): elisabethatriene cyclase
Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (elisabethatriene-forming)
Comments: Requires Mg2+ or less efficiently Mn2+. The enzyme is also able to use farnesyl diphosphate and geranyl diphosphate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 334022-59-2
References:
1.  Kohl, A.C. and Kerr, R.G. Identification and characterization of the pseudopterosin diterpene cyclase, elisabethatriene synthase, from the marine gorgonian, Pseudopterogorgia elisabethae. Arch. Biochem. Biophys. 424 (2004) 97–104. [PMID: 15019841]
2.  Bruck, T.B. and Kerr, R.G. Purification and kinetic properties of elisabethatriene synthase from the coral Pseudopterogorgia elisabethae. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 143 (2006) 269–278. [PMID: 16423548]
[EC 4.2.3.41 created 2009]
 
 
EC 4.2.3.42
Accepted name: aphidicolan-16β-ol synthase
Reaction: 9α-copalyl diphosphate + H2O = aphidicolan-16β-ol + diphosphate
For diagram of diterpenoid biosynthesis, click here and for reaction mechanism, click here
Other name(s): PbACS
Systematic name: 9α-copalyl-diphosphate diphosphate-lyase (aphidicolan-16β-ol-forming)
Comments: This is a bifunctional enzyme which also has EC 5.5.1.14 syn-copalyl diphosphate synthase activity. Aphidicolan-16β-ol is a precursor of aphidicolin, a specific inhibitor of DNA polymerase α (EC 2.7.7.7).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Oikawa, H., Toyomasu, T., Toshima, H., Ohashi, S., Kawaide, H., Kamiya, Y., Ohtsuka, M., Shinoda, S., Mitsuhashi, W. and Sassa, T. Cloning and functional expression of cDNA encoding aphidicolan-16 β-ol synthase: a key enzyme responsible for formation of an unusual diterpene skeleton in biosynthesis of aphidicolin. J. Am. Chem. Soc. 123 (2001) 5154–5155. [PMID: 11457369]
2.  Toyomasu, T., Nakaminami, K., Toshima, H., Mie, T., Watanabe, K., Ito, H., Matsui, H., Mitsuhashi, W., Sassa, T. and Oikawa, H. Cloning of a gene cluster responsible for the biosynthesis of diterpene aphidicolin, a specific inhibitor of DNA polymerase α. Biosci. Biotechnol. Biochem. 68 (2004) 146–152. [PMID: 14745177]
[EC 4.2.3.42 created 2009]
 
 
EC 4.2.3.43
Accepted name: fusicocca-2,10(14)-diene synthase
Reaction: geranylgeranyl diphosphate = fusicocca-2,10(14)-diene + diphosphate
For diagram of diterpenoid biosynthesis, click here and for reaction mechanism, click here
Other name(s): fusicoccadiene synthase; PaFS; PaDC4
Systematic name: geranylgeranyl diphosphate-lyase (fusicocca-2,10(14)-diene-forming)
Comments: A multifunctional enzyme with EC 2.5.1.29 farnesyltranstransferase activity.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Toyomasu, T., Tsukahara, M., Kaneko, A., Niida, R., Mitsuhashi, W., Dairi, T., Kato, N. and Sassa, T. Fusicoccins are biosynthesized by an unusual chimera diterpene synthase in fungi. Proc. Natl. Acad. Sci. USA 104 (2007) 3084–3088. [PMID: 17360612]
[EC 4.2.3.43 created 2009]
 
 
EC 4.2.3.44
Accepted name: isopimara-7,15-diene synthase
Reaction: (+)-copalyl diphosphate = isopimara-7,15-diene + diphosphate
For diagram of abietadiene, abietate, isopimaradiene, labdadienol and sclareol biosynthesis, click here and for diagram of abietadiene, levopimaradiene and isopimara-7,15-diene biosynthesis, click here
Glossary: isopimara-7,15-diene = 13α-pimara-7,15-diene
Other name(s): PaTPS-Iso; copalyl diphosphate-lyase (isopimara-7,15-diene-forming)
Systematic name: (+)-copalyl diphosphate-lyase (isopimara-7,15-diene-forming)
Comments: The enzyme only gave isopimara-7,15-diene.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Martin, D.M., Faldt, J. and Bohlmann, J. Functional characterization of nine Norway Spruce TPS genes and evolution of gymnosperm terpene synthases of the TPS-d subfamily. Plant Physiol. 135 (2004) 1908–1927. [PMID: 15310829]
[EC 4.2.3.44 created 2009]
 
 


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