The Enzyme Database

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EC 4.2.3.5     
Accepted name: chorismate synthase
Reaction: 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate
For diagram of shikimate and chorismate biosynthesis, click here and for mechanism of reaction, click here
Other name(s): 5-O-(1-carboxyvinyl)-3-phosphoshikimate phosphate-lyase
Systematic name: 5-O-(1-carboxyvinyl)-3-phosphoshikimate phosphate-lyase (chorismate-forming)
Comments: Requires FMN. The reaction goes via a radical mechanism that involves reduced FMN and its semiquinone (FMNH·). Shikimate is numbered so that the double-bond is between C-1 and C-2, but some earlier papers numbered the ring in the reverse direction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9077-07-0
References:
1.  Gaertner, F.H. and Cole, K.W. Properties of chorismate synthase in Neurospora crassa. J. Biol. Chem. 248 (1973) 4602–4609. [PMID: 4146266]
2.  Morell, H., Clark, M.J., Knowles, P.F. and Sprinson, D.B. The enzymic synthesis of chorismic and prephenic acids from 3-enolpyruvylshikimic acid 5-phosphate. J. Biol. Chem. 242 (1967) 82–90. [PMID: 4289188]
3.  Welch, G.R., Cole, K.W. and Gaertner, F.H. Chorismate synthase of Neurospora crassa: a flavoprotein. Arch. Biochem. Biophys. 165 (1974) 505–518. [DOI] [PMID: 4155270]
4.  Bornemann, S., Lowe, D.J. and Thorneley, R.N. The transient kinetics of Escherichia coli chorismate synthase: substrate consumption, product formation, phosphate dissociation, and characterization of a flavin intermediate. Biochemistry 35 (1996) 9907–9916. [DOI] [PMID: 8703965]
5.  Bornemann, S., Theoclitou, M.E., Brune, M., Webb, M.R., Thorneley, R.N. and Abell, C. A secondary β deuterium kinetic isotope effect in the chorismate synthase reaction. Bioorg. Chem. 28 (2000) 191–204. [DOI] [PMID: 11034781]
6.  Osborne, A., Thorneley, R.N., Abell, C. and Bornemann, S. Studies with substrate and cofactor analogues provide evidence for a radical mechanism in the chorismate synthase reaction. J. Biol. Chem. 275 (2000) 35825–35830. [DOI] [PMID: 10956653]
[EC 4.2.3.5 created 1978 as EC 4.6.1.4, modified 1983, transferred 2000 to EC 4.2.3.5, modified 2002]
 
 
EC 4.2.3.50     
Accepted name: (+)-α-santalene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = (+)-α-santalene + diphosphate
For diagram of santalene and bergamotene biosynthesis, click here
Other name(s): SBS (ambiguous)
Systematic name: (2Z,6Z)-farnesyl diphosphate lyase [cyclizing; (+)-α-santalene-forming]
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2Z,6Z)-farnesyl diphosphate. Following dephosphorylation of (2Z,6Z)-farnesyl diphosphate, the (2Z,6Z)-farnesyl carbocation is converted to either the (6R)- or the (6S)-bisabolyl cations depending on the stereochemistry of the 6,1 closure. The (6R)-bisabolyl cation will then lead to the formation of (+)-α-santalene (EC 4.2.3.50), while the (6S)-bisabolyl cation will give rise to (+)-endo-β-bergamotene (see EC 4.2.3.53) as well as (-)-endo-α-bergamotene (see EC 4.2.3.54). Small amounts of (-)-epi-β-santalene are also formed from the (6R)-bisabolyl cation and small amounts of (-)-exo-α-bergamotene are formed from the (6S)-bisabolyl cation [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301–317. [DOI] [PMID: 19155349]
[EC 4.2.3.50 created 2010]
 
 
EC 4.2.3.51     
Accepted name: β-phellandrene synthase (neryl-diphosphate-cyclizing)
Reaction: neryl diphosphate = β-phellandrene + diphosphate
Other name(s): phellandrene synthase 1; PHS1; monoterpene synthase PHS1
Systematic name: neryl-diphosphate diphosphate-lyase [cyclizing; β-phellandrene-forming]
Comments: The enzyme from Solanum lycopersicum has very poor affinity with geranyl diphosphate as substrate. Catalyses the formation of the acyclic myrcene and ocimene as major products in addition to β-phellandrene [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Schilmiller, A.L., Schauvinhold, I., Larson, M., Xu, R., Charbonneau, A.L., Schmidt, A., Wilkerson, C., Last, R.L. and Pichersky, E. Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate. Proc. Natl. Acad. Sci. USA 106 (2009) 10865–10870. [DOI] [PMID: 19487664]
[EC 4.2.3.51 created 2010]
 
 
EC 4.2.3.52     
Accepted name: (4S)-β-phellandrene synthase (geranyl-diphosphate-cyclizing)
Reaction: geranyl diphosphate = (4S)-β-phellandrene + diphosphate
For diagram of menthane monoterpenoid biosynthesis, click here
Other name(s): phellandrene synthase; (-)-β-phellandrene synthase; (-)-(4S)-β-phellandrene synthase
Systematic name: geranyl-diphosphate diphosphate-lyase [cyclizing; (4S)-β-phellandrene-forming]
Comments: Requires Mn2+. Mg2+ is not effective [1]. Some (-)-α-phellandrene is also formed [3]. The reaction involves a 1,3-hydride shift [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 137010-34-5
References:
1.  Savage, T.J., Hatch, M.W. and Croteau, R. Monoterpene synthases of Pinus contorta and related conifers. A new class of terpenoid cyclase. J. Biol. Chem. 269 (1994) 4012–4020. [PMID: 8307957]
2.  Bohlmann, J., Phillips, M., Ramachandiran, V., Katoh, S. and Croteau, R. cDNA cloning, characterization, and functional expression of four new monoterpene synthase members of the Tpsd gene family from grand fir (Abies grandis). Arch. Biochem. Biophys. 368 (1999) 232–243. [DOI] [PMID: 10441373]
3.  Wagschal, K., Savage, T.J. and Croteau, R. Isotopically sensitive branching as a tool for evaluating multiple product formation by monoterpene cyclases. Tetrahedron 31 (1991) 5933–5944.
4.  LaFever, R.E. and Croteau, R. Hydride shifts in the biosynthesis of the p-menthane monoterpenes α-terpinene, γ-terpinene, and β-phellandrene. Arch. Biochem. Biophys. 301 (1993) 361–366. [DOI] [PMID: 8460944]
[EC 4.2.3.52 created 2010]
 
 
EC 4.2.3.53     
Accepted name: (+)-endo-β-bergamotene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = (+)-endo-β-bergamotene + diphosphate
For diagram of santalene and bergamotene biosynthesis, click here
Other name(s): SBS (ambiguous)
Systematic name: (2Z,6Z)-farnesyl diphosphate lyase (cyclizing; (+)-endo-β-bergamotene-forming)
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2Z,6Z)-farnesyl diphosphate. Following dephosphorylation of (2Z,6Z)-farnesyl diphosphate, the (2Z,6Z)-farnesyl carbocation is converted to either the (6R)- or the (6S)-bisabolyl cations depending on the stereochemistry of the 6,1 closure. The (6R)-bisabolyl cation will then lead to the formation of (+)-α-santalene (see EC 4.2.3.50), while the (6S)-bisabolyl cation will give rise to (-)-endo-α-bergamotene (see EC 4.2.3.54), as well as (+)-endo-β-bergamotene. Small amounts of (-)-epi-β-santalene are also formed from the (6R)-bisabolyl cation and small amounts of (-)-exo-α-bergamotene are formed from the (6S)-bisabolyl cation [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301–317. [DOI] [PMID: 19155349]
[EC 4.2.3.53 created 2010]
 
 
EC 4.2.3.54     
Accepted name: (-)-endo-α-bergamotene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = (-)-endo-α-bergamotene + diphosphate
For diagram of santalene and bergamotene biosynthesis, click here
Other name(s): SBS (ambiguous)
Systematic name: (2Z,6Z)-farnesyl diphosphate lyase [cyclizing; (-)-endo-α-bergamotene-forming]
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2Z,6Z)-farnesyl diphosphate. Following dephosphorylation of (2Z,6Z)-farnesyl diphosphate, the (2Z,6Z)-farnesyl carbocation is converted to either the (6R)- or the (6S)-bisabolyl cations depending on the stereochemistry of the 6,1 closure. The (6R)-bisabolyl cation will then lead to the formation of (+)-α-santalene (see EC 4.2.3.50), while the (6S)-bisabolyl cation will give rise to (+)-endo-β-bergamotene (EC 4.2.3.53) as well as (-)-endo-α-bergamotene. Small amounts of (-)-epi-β-santalene are also formed from the (6R)-bisabolyl cation and small amounts of (-)-exo-α-bergamotene are formed from the (6S)-bisabolyl cation [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301–317. [DOI] [PMID: 19155349]
[EC 4.2.3.54 created 2010]
 
 
EC 4.2.3.55     
Accepted name: (S)-β-bisabolene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (S)-β-bisabolene + diphosphate
For diagram of bisabolene biosynthesis, click here, for diagram of bisabolene biosynthesis, click here and for diagram of bisabolene and macrocarpene biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(S)-β-bisabolene-forming]
Comments: The synthesis of (S)-β-macrocarpene from (2E,6E)-farnesyl diphosphate proceeds in two steps. The first step is the cyclization to (S)-β-bisabolene. The second step is the isomerization to (S)-β-macrocarpene (cf. EC 5.5.1.17, (S)-β-macrocarpene synthase). The enzyme requires Mg2+ or Mn2+ for activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Fujisawa, M., Harada, H., Kenmoku, H., Mizutani, S. and Misawa, N. Cloning and characterization of a novel gene that encodes (S)-β-bisabolene synthase from ginger, Zingiber officinale. Planta 232 (2010) 121–130. [DOI] [PMID: 20229191]
[EC 4.2.3.55 created 2011]
 
 
EC 4.2.3.56     
Accepted name: γ-humulene synthase
Reaction: (2E,6E)-farnesyl diphosphate = γ-humulene + diphosphate
For diagram of humulene-based sequiterpenoid biosynthesis, click here
Other name(s): humulene cyclase
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (γ-humulene-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 110639-19-5
References:
1.  Steele, C.L., Crock, J., Bohlmann, J. and Croteau, R. Sesquiterpene synthases from grand fir (Abies grandis). Comparison of constitutive and wound-induced activities, and cDNA isolation, characterization, and bacterial expression of δ-selinene synthase and γ-humulene synthase. J. Biol. Chem. 273 (1998) 2078–2089. [DOI] [PMID: 9442047]
2.  Little, D.B. and Croteau, R.B. Alteration of product formation by directed mutagenesis and truncation of the multiple-product sesquiterpene synthases δ-selinene synthase and γ-humulene synthase. Arch. Biochem. Biophys. 402 (2002) 120–135. [DOI] [PMID: 12051690]
[EC 4.2.3.56 created 2011]
 
 
EC 4.2.3.57     
Accepted name: (-)-β-caryophyllene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (-)-β-caryophyllene + diphosphate
For diagram of humulene-based sequiterpenoid biosynthesis, click here
Other name(s): β-caryophyllene synthase; (2E,6E)-farnesyl-diphosphate diphosphate-lyase (caryophyllene-forming)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(-)-β-caryophyllene-forming]
Comments: Widely distributed in higher plants, cf. EC 4.2.3.89 (+)-β-caryophyllene synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 110639-18-4
References:
1.  Cai, Y., Jia, J.W., Crock, J., Lin, Z.X., Chen, X.Y. and Croteau, R. A cDNA clone for β-caryophyllene synthase from Artemisia annua. Phytochemistry 61 (2002) 523–529. [DOI] [PMID: 12409018]
[EC 4.2.3.57 created 2011, modified 2011]
 
 
EC 4.2.3.58     
Accepted name: longifolene synthase
Reaction: (2E,6E)-farnesyl diphosphate = longifolene + diphosphate
For diagram of humulene-based sequiterpenoid biosynthesis, click here, and for mechanism, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (longifolene-forming)
Comments: As well as 61% longifolene the enzyme gives 15% of α-longipinene, 6% longicyclene and traces of other sesquiterpenoids.
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 4.2.3.58 created 2011]
 
 
EC 4.2.3.59     
Accepted name: (E)-γ-bisabolene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (E)-γ-bisabolene + diphosphate
For diagram of bisabolene biosynthesis, click here and for diagram of bisabolene biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(E)-γ-bisabolene-forming]
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  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 4.2.3.59 created 2011]
 
 


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