The Enzyme Database

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EC 4.2.3.4     
Accepted name: 3-dehydroquinate synthase
Reaction: 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate = 3-dehydroquinate + phosphate
For diagram of shikimate and chorismate biosynthesis, click here and for mechanism of reaction, click here
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram). The use of the term ’5-dehydroquinate’ for this compound is based on an earlier system of numbering.
Other name(s): 5-dehydroquinate synthase; 5-dehydroquinic acid synthetase; dehydroquinate synthase; 3-dehydroquinate synthetase; 3-deoxy-arabino-heptulosonate-7-phosphate phosphate-lyase (cyclizing); 3-deoxy-arabino-heptulonate-7-phosphate phosphate-lyase (cyclizing); 3-deoxy-arabino-heptulonate-7-phosphate phosphate-lyase (cyclizing; 3-dehydroquinate-forming)
Systematic name: 3-deoxy-D-arabino-hept-2-ulosonate-7-phosphate phosphate-lyase (cyclizing; 3-dehydroquinate-forming)
Comments: Requires Co2+ and bound NAD+. The hydrogen atoms on C-7 of the substrate are retained on C-2 of the product.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37211-77-1
References:
1.  Rotenberg, S.L. and Sprinson, D.B. Mechanism and stereochemistry of 5-dehydroquinate synthetase. Proc. Natl. Acad. Sci. USA 67 (1970) 1669–1672. [DOI] [PMID: 5275368]
2.  Srinivasan, P.R., Rothschild, J. and Sprinson, D.B. The enzymic conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate to 5-dehydroquinate. J. Biol. Chem. 238 (1963) 3176–3182. [PMID: 14085358]
3.  Bender, S.L., Mehdi, S. and Knowles, J.R. Dehydroquinate synthase: the role of divalent metal cations and of nicotinamide adenine dinucleotide in catalysis. Biochemistry 28 (1989) 7555–7560. [PMID: 2514789]
4.  Carpenter, E.P., Hawkins, A.R., Frost, J.W. and Brown, K.A. Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis. Nature 394 (1998) 299–302. [DOI] [PMID: 9685163]
[EC 4.2.3.4 created 1978 as EC 4.6.1.3, transferred 2000 to EC 4.2.3.4, modified 2002]
 
 
EC 4.2.3.40     
Accepted name: (Z)-γ-bisabolene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (Z)-γ-bisabolene + diphosphate
For diagram of bisabolene-derived sesquiterpenoid biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(Z)-γ-bisabolene-forming]
Comments: This sesquiterpenoid enzyme is constitutively expressed in the root, hydathodes and stigma of the plant Arabidopsis thaliana. If the leaves of the plant are wounded, e.g. by cutting, the enzyme is also induced close to the wound site. The sesquiterpenoids (E)-nerolidol and α-bisabolol are also produced by this enzyme as minor products.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ro, D.K., Ehlting, J., Keeling, C.I., Lin, R., Mattheus, N. and Bohlmann, J. Microarray expression profiling and functional characterization of AtTPS genes: duplicated Arabidopsis thaliana sesquiterpene synthase genes At4g13280 and At4g13300 encode root-specific and wound-inducible (Z)-γ-bisabolene synthases. Arch. Biochem. Biophys. 448 (2006) 104–116. [DOI] [PMID: 16297850]
[EC 4.2.3.40 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, KEGG, MetaCyc, 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. [DOI] [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. [DOI] [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, KEGG, MetaCyc
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. [DOI] [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, KEGG, MetaCyc
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. [DOI] [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, KEGG, MetaCyc
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. [DOI] [PMID: 15310829]
[EC 4.2.3.44 created 2009]
 
 
EC 4.2.3.45     
Accepted name: phyllocladan-16α-ol synthase
Reaction: (+)-copalyl diphosphate + H2O = phyllocladan-16α-ol + diphosphate
For diagram of abietadiene, aphidicolanol, sclareol and terpentetriene biosynthesis, click here and for mechanism of reaction, click here
Other name(s): PaDC1
Systematic name: (+)-copalyl-diphosphate diphosphate-lyase (phyllocladan-16α-ol-forming)
Comments: The adjacent gene PaDC2 codes EC 5.5.1.12 copalyl diphosphate synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Toyomasu, T., Niida, R., Kenmoku, H., Kanno, Y., Miura, S., Nakano, C., Shiono, Y., Mitsuhashi, W., Toshima, H., Oikawa, H., Hoshino, T., Dairi, T., Kato, N. and Sassa, T. Identification of diterpene biosynthetic gene clusters and functional analysis of labdane-related diterpene cyclases in Phomopsis amygdali. Biosci. Biotechnol. Biochem. 72 (2008) 1038–1047. [DOI] [PMID: 18391465]
[EC 4.2.3.45 created 2009]
 
 
EC 4.2.3.46     
Accepted name: α-farnesene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (3E,6E)-α-farnesene + diphosphate
For diagram of acyclic sesquiterpenoid biosynthesis, click here
Other name(s): (E,E)-α-farnesene synthase; AFS1; MdAFS1
Systematic name: (2E,6E)-farnesyl-diphosphate lyase [(3E,6E)-α-farnesene-forming]
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pechous, S.W. and Whitaker, B.D. Cloning and functional expression of an (E,E)-α-farnesene synthase cDNA from peel tissue of apple fruit. Planta 219 (2004) 84–94. [DOI] [PMID: 14740213]
2.  Green, S., Squire, C.J., Nieuwenhuizen, N.J., Baker, E.N. and Laing, W. Defining the potassium binding region in an apple terpene synthase. J. Biol. Chem. 284 (2009) 8661–8669. [DOI] [PMID: 19181671]
3.  Nieuwenhuizen, N.J., Wang, M.Y., Matich, A.J., Green, S.A., Chen, X., Yauk, Y.K., Beuning, L.L., Nagegowda, D.A., Dudareva, N. and Atkinson, R.G. Two terpene synthases are responsible for the major sesquiterpenes emitted from the flowers of kiwifruit (Actinidia deliciosa). J. Exp. Bot. 60 (2009) 3203–3219. [DOI] [PMID: 19516075]
[EC 4.2.3.46 created 2010]
 
 
EC 4.2.3.47     
Accepted name: β-farnesene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (E)-β-farnesene + diphosphate
For diagram of acyclic sesquiterpenoid biosynthesis, click here
Other name(s): farnesene synthase; terpene synthase 10; terpene synthase 10-B73; TPS10
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(E)-β-farnesene-forming]
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zhao, B., Lei, L., Vassylyev, D.G., Lin, X., Cane, D.E., Kelly, S.L., Yuan, H., Lamb, D.C. and Waterman, M.R. Crystal structure of albaflavenone monooxygenase containing a moonlighting terpene synthase active site. J. Biol. Chem. 284 (2009) 36711–36719. [DOI] [PMID: 19858213]
2.  Picaud, S., Brodelius, M. and Brodelius, P.E. Expression, purification and characterization of recombinant (E)-β-farnesene synthase from Artemisia annua. Phytochemistry 66 (2005) 961–967. [DOI] [PMID: 15896363]
3.  Kollner, T.G., Gershenzon, J. and Degenhardt, J. Molecular and biochemical evolution of maize terpene synthase 10, an enzyme of indirect defense. Phytochemistry 70 (2009) 1139–1145. [DOI] [PMID: 19646721]
4.  Schnee, C., Kollner, T.G., Held, M., Turlings, T.C., Gershenzon, J. and Degenhardt, J. The products of a single maize sesquiterpene synthase form a volatile defense signal that attracts natural enemies of maize herbivores. Proc. Natl. Acad. Sci. USA 103 (2006) 1129–1134. [DOI] [PMID: 16418295]
5.  Maruyama, T., Ito, M. and Honda, G. Molecular cloning, functional expression and characterization of (E)-β farnesene synthase from Citrus junos. Biol. Pharm. Bull. 24 (2001) 1171–1175. [PMID: 11642326]
6.  Crock, J., Wildung, M. and Croteau, R. Isolation and bacterial expression of a sesquiterpene synthase cDNA clone from peppermint (Mentha × piperita, L.) that produces the aphid alarm pheromone (E)-β-farnesene. Proc. Natl. Acad. Sci. USA 94 (1997) 12833–12838. [DOI] [PMID: 9371761]
7.  Schnee, C., Kollner, T.G., Gershenzon, J. and Degenhardt, J. The maize gene terpene synthase 1 encodes a sesquiterpene synthase catalyzing the formation of (E)-β-farnesene, (E)-nerolidol, and (E,E)-farnesol after herbivore damage. Plant Physiol. 130 (2002) 2049–2060. [DOI] [PMID: 12481088]
8.  Huber, D.P.W., Philippe, R.N., Godard, K.-A., Sturrock, R.N. and Bohlmann, J. Characterization of four terpene synthase cDNAs from methyl jasmonate-induced Douglas-fir, Pseudotsuga menziesii. Phytochemistry 66 (2005) 1427–1439. [DOI] [PMID: 15921711]
[EC 4.2.3.47 created 2010]
 
 
EC 4.2.3.48     
Accepted name: (3S,6E)-nerolidol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (3S,6E)-nerolidol + diphosphate
For diagram of acyclic sesquiterpenoid biosynthesis, click here
Glossary: (3S,6E)-nerolidol = (3R,6E)-3,7,11-trimethyldodeca-1,6,10-trien-3-ol
Other name(s): (E)-nerolidol synthase; nerolidol synthase; (3S)-(E)-nerolidol synthase; FaNES1
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(3S,6E)-nerolidol-forming]
Comments: The enzyme catalyses a step in the formation of (3E)-4,8-dimethylnona-1,3,7-triene, a key signal molecule in induced plant defense mediated by the attraction of enemies of herbivores [2]. Nerolidol is a naturally occurring sesquiterpene found in the essential oils of many types of plants.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Aharoni, A., Giri, A.P., Verstappen, F.W., Bertea, C.M., Sevenier, R., Sun, Z., Jongsma, M.A., Schwab, W. and Bouwmeester, H.J. Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species. Plant Cell 16 (2004) 3110–3131. [DOI] [PMID: 15522848]
2.  Bouwmeester, H.J., Verstappen, F.W., Posthumus, M.A. and Dicke, M. Spider mite-induced (3S)-(E)-nerolidol synthase activity in cucumber and lima bean. The first dedicated step in acyclic C11-homoterpene biosynthesis. Plant Physiol. 121 (1999) 173–180. [PMID: 10482672]
3.  Degenhardt, J. and Gershenzon, J. Demonstration and characterization of (E)-nerolidol synthase from maize: a herbivore-inducible terpene synthase participating in (3E)-4,8-dimethyl-1,3,7-nonatriene biosynthesis. Planta 210 (2000) 815–822. [DOI] [PMID: 10805454]
4.  Arimura, G., Garms, S., Maffei, M., Bossi, S., Schulze, B., Leitner, M., Mithofer, A. and Boland, W. Herbivore-induced terpenoid emission in Medicago truncatula: concerted action of jasmonate, ethylene and calcium signaling. Planta 227 (2008) 453–464. [DOI] [PMID: 17924138]
[EC 4.2.3.48 created 2010]
 
 
EC 4.2.3.49     
Accepted name: (3R,6E)-nerolidol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (3R,6E)-nerolidol + diphosphate
For diagram of acyclic sesquiterpenoid biosynthesis, click here
Other name(s): terpene synthase 1
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(3R,6E)-nerolidol-forming]
Comments: The enzyme catalyses a step in the formation of (3E)-4,8-dimethylnona-1,3,7-triene, a key signal molecule in induced plant defense mediated by the attraction of enemies of herbivores [1]. Nerolidol is a naturally occurring sesquiterpene found in the essential oils of many types of plants.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Schnee, C., Kollner, T.G., Gershenzon, J. and Degenhardt, J. The maize gene terpene synthase 1 encodes a sesquiterpene synthase catalyzing the formation of (E)-β-farnesene, (E)-nerolidol, and (E,E)-farnesol after herbivore damage. Plant Physiol. 130 (2002) 2049–2060. [DOI] [PMID: 12481088]
[EC 4.2.3.49 created 2010]
 
 


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