Continued from EC 5.4
EC 5.5 Intramolecular Lyases
EC 5.99 Other Isomerases
Accepted name: muconate cycloisomerase
Reaction: 2,5-dihydro-5-oxofuran-2-acetate = cis,cis-hexadienedioate
For diagram click here (another example).
Glossary: muconolactone = (2,5-dihydro-5-oxofuran-2-yl)acetate
cis,cis-hexadienedioate = (2Z,4Z)-hexa-2,4-dienedioate = cis,cis-muconate
Other name(s): muconate cycloisomerase I; cis,cis-muconate-lactonizing enzyme; cis,cis-muconate cycloisomerase; muconate lactonizing enzyme; 4-carboxymethyl-4-hydroxyisocrotonolactone lyase (decyclizing); CatB; MCI
Systematic name: 2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)
Comments: Requires Mn2+. Also acts (in the reverse reaction) on 3-methyl-cis,cis-hexadienedioate and, very slowly, on cis,trans-hexadienedioate. Not identical with EC 5.5.1.7 (chloromuconate cycloisomerase) or EC 5.5.1.11 (dichloromuconate cycloisomerase).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 9023-72-7
References:
1. Ornston, L.N. The conversion of catechol and protocatechuate to β-ketoadipate by Pseudomonas putida. 3. Enzymes of the catechol pathway. J. Biol. Chem. 241 (1966) 3795-3799. [PMID: 5330966]
2. Ornston, L.N. Conversion of catechol and protocatechuate to β-ketoadipate (Pseudomonas putida). Methods Enzymol. 17A (1970) 529-549.
3. Sistrom, W.R. and Stanier, R.Y. The mechanism of formation of β-ketoadipic acid by bacteria. J. Biol. Chem. 210 (1954) 821-836.
Accepted name: 3-carboxy-cis,cis-muconate cycloisomerase
Reaction: 2-carboxy-2,5-dihydro-5-oxofuran-2-acetate = cis,cis-butadiene-1,2,4-tricarboxylate
For diagram click here (another example).
Other name(s): β-carboxymuconate lactonizing enzyme; 3-carboxymuconolactone hydrolase
Systematic name: 2-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9075-77-8
References:
1. Ornston, L.N. The conversion of catechol and protocatechuate to β-ketoadipate by Pseudomonas putida. II. Enzymes of the protocatechuate pathway. J. Biol. Chem. 241 (1966) 3787-3794. [PMID: 5916392]
2. Ornston, L.N. Conversion of catechol and protocatechuate to β-ketoadipate (Pseudomonas putida). Methods Enzymol. 17A (1970) 529-549.
Accepted name: tetrahydroxypteridine cycloisomerase
Reaction: tetrahydroxypteridine = xanthine-8-carboxylate
Systematic name: tetrahydroxypteridine lyase (isomerizing)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 37318-54-0
References:
1. McNutt, W.S. and Damle, S.P. Tetraoxypteridine isomerase. J. Biol. Chem. 239 (1964) 4272-4279.
Accepted name: inositol-3-phosphate synthase
Reaction: D-glucose 6-phosphate = 1D-myo-inositol 3-phosphate
EC 5.5.1.4 inositol-3-phosphate synthase (mechanism)
Other name(s): myo-inositol-1-phosphate synthase; D-glucose 6-phosphate cycloaldolase; inositol 1-phosphate synthatase; glucose 6-phosphate cyclase; inositol 1-phosphate synthetase; glucose-6-phosphate inositol monophosphate cycloaldolase; glucocycloaldolase; 1L-myo-inositol-1-phosphate lyase (isomerizing)
Systematic name: 1D-myo-inositol-3-phosphate lyase (isomerizing)
Comments: Requires NAD+, which dehydrogenates the -CHOH- group to -CO- at C-5 of the glucose 6-phosphate, making C-6 into an active methylene, able to condense with the -CHO at C-1. Finally, the enzyme-bound NADH reconverts C-5 into the -CHOH- form.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9032-95-5
References:
1. Eisenberg, F., Jr. D-Myoinositol 1-phosphate as product of cyclization of glucose 6-phosphate and substrate for a specific phosphatase in rat testis. J. Biol. Chem. 242 (1967) 1375-1382. [PMID: 4290245]
2. Sherman, W.R., Stewart, M.A. and Zinbo, M. Mass spectrometric study on the mechanism of D-glucose 6-phosphate-L-myo-inositol 1-phosphate cyclase. J. Biol. Chem. 244 (1969) 5703-5708. [PMID: 4310603]
3. Barnett, J.E.G. and Corina, D.L. The mechanism of glucose 6-phosphate-D-myo-inositol 1-phosphate cyclase of rat testis. The involvement of hydrogen atoms. Biochem. J. 108 (1968) 125-129. [PMID: 4297937]
4. Barnett, J.E.G., Rasheed, A. and Corina, D.L. Partial reactions of glucose 6-phosphate-1L-myo-inositol 1-phosphate cyclase. Biochem. J. 131 (1973) 21-30. [PMID: 4352864]
Accepted name: carboxy-cis,cis-muconate cyclase
Reaction: 3-carboxy-2,5-dihydro-5-oxofuran-2-acetate = 3-carboxy-cis,cis-muconate
For diagram click here.
Other name(s): 3-carboxymuconate cyclase
Systematic name: 3-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37318-55-1
References:
1. Gross, S.R., Gafford, R.D. and Tatum, E.L. The metabolism of protocatechuic acid by Neurospora. J. Biol. Chem. 219 (1956) 781-796.
Accepted name: chalcone isomerase
Reaction: A chalcone = a flavanone
See diagram for reaction in naringenin or liquiritigenin biosynthesis.
Other name(s): chalcone-flavanone isomerase
Systematic name: flavanone lyase (decyclizing)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9073-57-8
References:
1. Moustafa, E. and Wong, E. Purification and properties of chalcone-flavanone isomerase from soya bean seed. Phytochemistry 6 (1967) 625-632.
Accepted name: chloromuconate cycloisomerase
Reaction: 2-chloro-2,5-dihydro-5-oxofuran-2-acetate = 3-chloro-cis,cis-muconate
For diagram click here.
Glossary: muconolactone = (2,5-dihydro-5-oxofuran-2-yl)acetate
3-chloro-cis,cis-muconate = (2E,4Z)-3-chlorohexa-2,4-dienedioate
Other name(s): muconate cycloisomerase II
Systematic name: 2-chloro-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)
Comments: Requires Mn2+. The product of cycloisomerization of 3-chloro-cis,cis-muconate spontaneously eliminates chloride to produce cis-4-carboxymethylenebut-2-en-4-olide. Also acts (in the reverse direction) on 2-chloro-cis,cis-muconate. Not identical with EC 5.5.1.1 (muconate cycloisomerase) or EC 5.5.1.11 (dichloromuconate cycloisomerase).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 95990-33-3
References:
1. Schmidt, E. and Knackmuss, H.-J. Chemical structure and biodegradability of halogenated aromatic compounds. Conversion of chlorinated muconic acids into maleoylacetic acid. Biochem. J. 192 (1980) 339-347. [PMID: 7305906]
Accepted name: (+)-bornyl diphosphate synthase
Reaction: geranyl diphosphate = (+)-bornyl diphosphate
For diagram of reaction click here and mechanism click here.
Glossary: (+)-bornyl diphosphate = (1R,2S,4R)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl diphosphate
Other name(s): bornyl pyrophosphate synthase; bornyl pyrophosphate synthetase; (+)-bornylpyrophosphate cyclase; geranyl-diphosphate cyclase (ambiguous)
Systematic name: (+)-bornyl-diphosphate lyase (decyclizing)
Comments: Requires Mg2+. The enzyme from Salvia officinalis (sage) can also use (3R)-linalyl diphosphate or more slowly neryl diphosphate in vitro [3]. The reaction proceeds via isomeration of geranyl diphosphate to (3R)-linalyl diphosphate. The oxygen and phosphorus originally linked to C-1 of geranyl diphosphate end up linked to C-2 of (+)-bornyl diphosphate [3]. cf. EC 5.5.1.22 [(–)-bornyl diphosphate synthase].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 72668-91-8
References:
1. Croteau, R. and Karp, F. Biosynthesis of monoterpenes: preliminary characterization of bornyl pyrophosphate synthetase from sage (Salvia officinalis) and demonstration that geranyl pyrophosphate is the preferred substrate for cyclization. Arch. Biochem. Biophys. 198 (1979) 512-522. [PMID: 42356]
2. Croteau, R., Gershenzon, J., Wheeler, C.J. and Satterwhite, D.M. Biosynthesis of monoterpenes: stereochemistry of the coupled isomerization and cyclization of geranyl pyrophosphate to camphane and isocamphane monoterpenes. Arch. Biochem. Biophys. 277 (1990) 374-381. [PMID: 2178556]
3. Croteau, R., Satterwhite, D.M., Cane, D.E. and Chang, C.C. Biosynthesis of monoterpenes. Enantioselectivity in the enzymatic cyclization of (+)- and (–)-linalyl pyrophosphate to (+)- and (–)-bornyl pyrophosphate. J. Biol. Chem. 261 (1986) 13438-13445. [PMID: 3759972]
4. Croteau, R., Felton, N.M. and Wheeler, C.J. Stereochemistry at C-1 of geranyl pyrophosphate and neryl pyrophosphate in the cyclization to (+)- and (–)-bornyl pyrophosphate. J. Biol. Chem. 260 (1985) 5956-5962. [PMID: 3997807]
5. Croteau, R.B., Shaskus, J.J., Renstrom, B., Felton, N.M., Cane, D.E., Saito, A. and Chang, C. Mechanism of the pyrophosphate migration in the enzymatic cyclization of geranyl and linalyl pyrophosphates to (+)- and (–)-bornyl pyrophosphates. Biochemistry 24 (1985) 7077-7085. [PMID: 4084562]
6. McGeady, P. and Croteau, R. Isolation and characterization of an active-site peptide from a monoterpene cyclase labeled with a mechanism-based inhibitor. Arch. Biochem. Biophys. 317 (1995) 149-155. [PMID: 7872777]
7. Wise, M.L., Savage, T.J., Katahira, E. and Croteau, R. Monoterpene synthases from common sage (Salvia officinalis). cDNA isolation, characterization, and functional expression of (+)-sabinene synthase, 1,8-cineole synthase, and (+)-bornyl diphosphate synthase. J. Biol. Chem. 273 (1998) 14891-14899. [PMID: 9614092]
8. Whittington, D.A., Wise, M.L., Urbansky, M., Coates, R.M., Croteau, R.B. and Christianson, D.W. Bornyl diphosphate synthase: structure and strategy for carbocation manipulation by a terpenoid cyclase. Proc. Natl. Acad. Sci. USA 99 (2002) 15375-15380. [PMID: 12432096]
9. Peters, R.J. and Croteau, R.B. Alternative termination chemistries utilized by monoterpene cyclases: chimeric analysis of bornyl diphosphate, 1,8-cineole, and sabinene synthases. Arch. Biochem. Biophys. 417 (2003) 203-211. [PMID: 12941302]
Accepted name: cycloeucalenol cycloisomerase
Reaction: cycloeucalenol = obtusifoliol
For diagram click here.
Other name(s): cycloeucalenol—obtusifoliol isomerase
Systematic name: cycloeucalenol lyase (cyclopropane-decyclizing)
Comments: Opens the cyclopropane ring of a number of related 4α-methyl-9β-19-cyclosterols, but not those with a 4β-methyl group, with formation of an 8(9) double bond. Involved in the synthesis of plant sterols.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 60496-19-7
References:
1. Heintz, R. and Benveniste, P. Plant sterol metabolism. Enzymatic cleavage of the 9β,19β-cyclopropane ring of cyclopropyl sterols in bramble tissue cultures. J. Biol. Chem. 249 (1974) 4267-4274. [PMID: 4369016]
2. Rahier, A., Schmitt, P. and Benveniste, P. 7-oxo-24ξ(28)-dihydrocycloeucalenol, a potent inhibitor of plant sterol biosynthesis. Phytochemistry 21 (1982) 1969-1974.
Accepted name: α-pinene-oxide decyclase
Reaction: α-pinene oxide = (Z)-2-methyl-5-isopropylhexa-2,5-dienal
Other name(s): α-pinene oxide lyase
Systematic name: α-pinene-oxide lyase (decyclizing)
Comments: Both rings of pinene are cleaved in the reaction.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD , CAS registry number: 112692-50-9
References:
1. Griffiths, E.T., Harries, P.C., Jeffcoat, R. and Trudgill, P.W. Purification and properties of α-pinene oxide lyase from Nocardia sp. strain P18.3. J. Bacteriol. 169 (1987) 4980-4983. [PMID: 3667522]
Accepted name: dichloromuconate cycloisomerase
Reaction: 2,4-dichloro-2,5-dihydro-5-oxofuran-2-acetate = 2,4-dichloro-cis,cis-muconate
For diagram click here.
Systematic name: 2,4-dichloro-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)
Comments: Requires Mn2+. The product of cycloisomerization of dichloro-cis,cis-muconate spontaneously eliminates chloride to produce cis-4-carboxymethylene-3-chlorobut-2-en-4-olide. Also acts, in the reverse direction, on cis,cis-muconate and its monochloro-derivatives, but with lower affinity. Not identical with EC 5.5.1.1 (muconate cycloisomerase) or EC 5.5.1.7 (chloromuconate cycloisomerase).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number: 126904-95-8
References:
1. Kuhm, A.E., Schlömann, M., Knackmuss, H.-J. and Pieper, D.H. Purification and characterization of dichloromuconate cycloisomerase from Alcaligenes eutrophus JMP 134. Biochem. J. 266 (1990) 877-883. [PMID: 2327971]
Accepted name: copalyl diphosphate synthase
Reaction: geranylgeranyl diphosphate = (+)-copalyl diphosphate
For diagram of reaction click here.
Systematic name: (+)-copalyl-diphosphate lyase (decyclizing)
Comments: In some plants, such as Salvia miltiorrhiza, this enzyme is monofunctional. In other plants this activity is often a part of a bifunctional enzyme. For example, in Selaginella moellendorffii this activity is catalysed by a bifunctional enzyme that also catalyses EC 4.2.3.131, miltiradiene synthase, while in the tree Abies grandis (grand fir) it is catalysed by a bifunctional enzyme that also catalyses EC 4.2.3.18, abietadiene synthase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 157972-08-2
References:
1. Peters, R.J., Ravn, M.M., Coates, R.M. and Croteau, R.B. Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites. J. Am. Chem. Soc. 123 (2001) 8974-8978. [PMID: 11552804]
2. Sugai, Y., Ueno, Y., Hayashi, K., Oogami, S., Toyomasu, T., Matsumoto, S., Natsume, M., Nozaki, H. and Kawaide, H. Enzymatic 13C labeling and multidimensional NMR analysis of miltiradiene synthesized by bifunctional diterpene cyclase in Selaginella moellendorffii. J. Biol. Chem. 286 (2011) 42840-42847. [PMID: 22027823]
3. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement. Proc. Natl. Acad. Sci. USA 99 (2002) 580-584. [PMID: 11805316]
4. Ravn, M.M., Peters, R.J., Coates, R.M. and Croteau, R. Mechanism of abietadiene synthase catalysis: stereochemistry and stabilization of the cryptic pimarenyl carbocation intermediates. J. Am. Chem. Soc. 124 (2002) 6998-7006. [PMID: 12059223]
5. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate. Biochemistry 41 (2002) 1836-1842. [PMID: 11827528]
Accepted name: ent-copalyl diphosphate synthase
Reaction: geranylgeranyl diphosphate = ent-copalyl diphosphate
For diagram of reaction, click here.
Other name(s): ent-kaurene synthase A; ent-kaurene synthetase A; ent-CDP synthase
Systematic name: ent-copalyl-diphosphate lyase (decyclizing)
Comments: Part of a bifunctional enzyme involved in the biosynthesis of kaurene. See also EC 4.2.3.19 (ent-kaurene synthase)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9055-64-5
References:
1. Fall, R.R., West, C.A. Purification and properties of kaurene synthetase from Fusarium moniliforme. J. Biol. Chem. 246 (1971) 6913-6928. [PMID: 4331199]
2. Sun, T.P. and Kamiya, Y. The Arabidopsis GA1 locus encodes the cyclase ent-kaurene synthetase A of gibberellin biosynthesis. Plant Cell 6 (1994) 1509-1518. [PMID: 7994182]
3. Kawaide, H., Imai, R., Sassa, T. and Kamiya, Y. Ent-kaurene synthase from the fungus Phaeosphaeria sp. L487. cDNA isolation, characterization, and bacterial expression of a bifunctional diterpene cyclase in fungal gibberellin biosynthesis. J. Biol. Chem. 272 (1997) 21706-21712. [PMID: 9268298]
4. Toyomasu, T., Kawaide, H., Ishizaki, A., Shinoda, S., Otsuka, M., Mitsuhashi, W. and Sassa, T. Cloning of a full-length cDNA encoding ent-kaurene synthase from Gibberella fujikuroi: functional analysis of a bifunctional diterpene cyclase. Biosci. Biotechnol. Biochem. 64 (2000) 660-664. [PMID: 10803977]
Accepted name: syn-copalyl diphosphate synthase
Reaction: geranylgeranyl diphosphate = 9α-copalyl diphosphate
For diagram of reaction, click here
Glossary: syn-copalyl diphosphate = 9α-copalyl diphosphate
Other name(s): OsCyc1; OsCPSsyn; syn-CPP synthase
Systematic name: 9α-copalyl-diphosphate lyase (decyclizing)
Comments: Requires a divalent metal ion, preferably Mg2+, for activity. This class II terpene synthase produces syn-copalyl diphosphate, a precursor of several rice phytoalexins, including oryzalexin S and momilactones A and B. Phytoalexins are diterpenoid secondary metabolites that are involved in the defense mechanism of the plant, and are produced in response to pathogen attack through the perception of elicitor signal molecules such as chitin oligosaccharide, or after exposure to UV irradiation. The enzyme is constitutively expressed in the roots of plants where one of its products, momilactone B, acts as an allelochemical (a molecule released into the environment to suppress the growth of neighbouring plants). In other tissues the enzyme is upregulated by conditions that stimulate the biosynthesis of phytoalexins.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Otomo, K., Kenmoku, H., Oikawa, H., Konig, W.A., Toshima, H., Mitsuhashi, W., Yamane, H., Sassa, T. and Toyomasu, T. Biological functions of ent- and syn-copalyl diphosphate synthases in rice: key enzymes for the branch point of gibberellin and phytoalexin biosynthesis. Plant J. 39 (2004) 886-893. [PMID: 15341631]
2. Xu, M., Hillwig, M.L., Prisic, S., Coates, R.M. and Peters, R.J. Functional identification of rice syn-copalyl diphosphate synthase and its role in initiating biosynthesis of diterpenoid phytoalexin/allelopathic natural products. Plant J. 39 (2004) 309-318. [PMID: 15255861]
Accepted name: terpentedienyl-diphosphate synthase
Reaction: geranylgeranyl diphosphate = terpentedienyl diphosphate
For diagram of reaction click here and mechanism click here.
Other name(s): terpentedienol diphosphate synthase; Cyc1; clerodadienyl diphosphate synthase
Systematic name: terpentedienyl-diphosphate lyase (decyclizing)
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, KEGG, Metacyc, CAS registry number:
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]
Accepted name: halimadienyl-diphosphate synthase
Reaction: geranylgeranyl diphosphate = tuberculosinyl diphosphate
For diagram of rection 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)
Systematic name: halima-5,13-dien-15-yl-diphosphate lyase (decyclizing)
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, KEGG, Metacyc, CAS registry number:
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]
Accepted name: (S)-β-macrocarpene synthase
Reaction: (S)-β-bisabolene = (S)-β-macrocarpene
For diagram of reaction click here and mechanism click here.
Other name(s): TPS6; TPS11
Systematic name: (S)-β-macrocarpene lyase (decyclizing)
Comment: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 (cf. EC 4.2.3.55, (S)-β-bisabolene synthase). The second step is the isomerization to (S)-β-macrocarpene. Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Kollner, T.G., Schnee, C., Li, S., Svatos, A., Schneider, B., Gershenzon, J. and Degenhardt, J. Protonation of a neutral (S)-β-bisabolene intermediate is involved in (S)-β-macrocarpene formation by the maize sesquiterpene synthases TPS6 and TPS11. J. Biol. Chem. 283 (2008) 20779-20788. [PMID: 18524777]
Accepted name: lycopene ε-cyclase
Reaction: carotenoid ψ-end group = carotenoid ε-end group
For diagram of reaction click here and mechanism click here.
Other name(s): CrtL-e; LCYe
Systematic name: carotenoid ψ-end group lyase (decyclizing)
Comments: The carotenoid lycopene has the ψ-end group at both ends. When acting on one end, this enzyme forms δ-carotene. When acting on both ends, it forms ε-carotene.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Cunningham, F.X., Jr. and Gantt, E. One ring or two? Determination of ring number in carotenoids by lycopene ε-cyclases. Proc. Natl. Acad. Sci. USA 98 (2001) 2905-2910. [PMID: 11226339]
2. Stickforth, P., Steiger, S., Hess, W.R. and Sandmann, G. A novel type of lycopene ε-cyclase in the marine cyanobacterium Prochlorococcus marinus MED4. Arch. Microbiol. 179 (2003) 409-415. [PMID: 12712234]
Accepted name: lycopene β-cyclase
Reaction: carotenoid ψ-end group = carotenoid β-end group
For diagram of reaction click here, and here click here, and mechanism click here.
Other name(s): CrtL; CrtL-b; CrtY
Systematic name: carotenoid β-end group lyase (decyclizing)
Comments: Requires NAD(P)H. Lycopene has a ψ-end group at both ends. When acting on one end, this enzyme forms γ-carotene. When acting on both ends it forms β-carotene. It also acts on neurosporene to give β-zeacarotene. The hydrogen introduced at C-2 originates from water, not from NAD(P)H.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Cunningham, F.X., Jr., Chamovitz, D., Misawa, N., Gantt, E. and Hirschberg, J. Cloning and functional expression in Escherichia coli of a cyanobacterial gene for lycopene cyclase, the enzyme that catalyzes the biosynthesis of β-carotene. FEBS Lett. 328 (1993) 130-138. [PMID: 8344419]
2. Cunningham, F.X., Jr., Sun, Z., Chamovitz, D., Hirschberg, J. and Gantt, E. Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942. Plant Cell 6 (1994) 1107-1121. [PMID: 7919981]
3. Hugueney, P., Badillo, A., Chen, H.C., Klein, A., Hirschberg, J., Camara, B. and Kuntz, M. Metabolism of cyclic carotenoids: a model for the alteration of this biosynthetic pathway in Capsicum annuum chromoplasts. Plant J. 8 (1995) 417-424. [PMID: 7550379]
4. Pecker, I., Gabbay, R., Cunningham, F.X., Jr. and Hirschberg, J. Cloning and characterization of the cDNA for lycopene β-cyclase from tomato reveals decrease in its expression during fruit ripening. Plant Mol. Biol. 30 (1996) 807-819. [PMID: 8624411]
5. Hornero-Mendez, D. and Britton, G. Involvement of NADPH in the cyclization reaction of carotenoid biosynthesis. FEBS Lett. 515 (2002) 133-136. [PMID: 11943208]
6. Maresca, J.A., Graham, J.E., Wu, M., Eisen, J.A. and Bryant, D.A. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc. Natl. Acad. Sci. USA 104 (2007) 11784-11789. [PMID: 17606904]
Accepted name: prosolanapyrone-III cycloisomerase
Reaction: prosolanapyrone III = (–)-solanapyrone A
For diagram of reaction click here
Glossary: prosolanapyrone III = 4-methoxy-2-oxo-6-(1E,7E,9E)-undeca-1,7,9-trien-1-yl-2H-pyran-3-carboxaldehyde
(–)-solanapyrone A = 4-methoxy-6-((1R,2S,4aR,8aR)-2-methyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl)-2-oxo-2H-pyran-3-carboxaldehyde
Other name(s): Sol5 (ambiguous); SPS (ambiguos); solanapyrone synthase (bifunctional enzyme: prosolanapyrone II oxidase/prosolanapyrone III cyclosiomerase)
Systematic name: prosolanapyrone-III:(–)-solanapyrone A isomerase
Comments: The enzyme is involved in the biosynthesis of the phytotoxin solanapyrone in some fungi. The bifunctional enzyme catalyses the oxidation of prosolanapyrone II and the subsequent Diels Alder cycloisomerization of the product prosolanapyrone III to (–)-solanapyrone A (cf. EC 1.1.3.42, prosolanapyrone II oxidase).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Kasahara, K., Miyamoto, T., Fujimoto, T., Oguri, H., Tokiwano, T., Oikawa, H., Ebizuka, Y. and Fujii, I. Solanapyrone synthase, a possible Diels-Alderase and iterative type I polyketide synthase encoded in a biosynthetic gene cluster from Alternaria solani. Chembiochem. 11 (2010) 1245-1252. [PMID: 20486243]
2. Katayama, K., Kobayashi, T., Oikawa, H., Honma, M. and Ichihara, A. Enzymatic activity and partial purification of solanapyrone synthase: first enzyme catalyzing Diels-Alder reaction. Biochim. Biophys. Acta 1384 (1998) 387-395. [PMID: 9659400]
3. Katayama, K., Kobayashi, T., Chijimatsu, M., Ichihara, A. and Oikawa, H. Purification and N-terminal amino acid sequence of solanapyrone synthase, a natural Diels-Alderase from Alternaria solani. Biosci. Biotechnol. Biochem. 72 (2008) 604-607. [PMID: 18256508]
[EC 5.5.1.21 copal-8-ol diphosphate synthase. This enzyme was discovered at the public-review stage to have been misclassified and so was withdrawn. See EC 4.2.1.133, copal-8-ol diphosphate hydratase. (EC 5.5.1.21 created 2012, deleted 2012)]
Accepted name: (–)-bornyl diphosphate synthase
Reaction: geranyl diphosphate = (–)-bornyl diphosphate
For diagram of reaction click here.
Glossary: (–)-bornyl diphosphate = (2R,4S)-1,7,7-trimethylbicyclo[2.2.1]hept-2-yl diphosphate
Other name(s): bornyl pyrophosphate synthase; bornyl pyrophosphate synthetase; (–)-bornyl pyrophosphate cyclase; bornyl diphosphate synthase; geranyl-diphosphate cyclase (ambiguous)
Systematic name: (–)-bornyl-diphosphate lyase (decyclizing)
Comments: Requires Mg2+. The enzyme from Tanacetum vulgare (tansey) can also use (3S)-linalyl diphosphate or more slowly neryl diphosphate in vitro. The reaction proceeds via isomeration of geranyl diphosphate to (3S)-linalyl diphosphate [3]. The oxygen and phosphorus originally linked to C-1 of geranyl diphosphate end up linked to C-2 of (–)-bornyl diphosphate [4]. cf. EC 5.5.1.8 (+)-bornyl diphosphate synthase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Croteau, R., Gershenzon, J., Wheeler, C.J. and Satterwhite, D.M. Biosynthesis of monoterpenes: stereochemistry of the coupled isomerization and cyclization of geranyl pyrophosphate to camphane and isocamphane monoterpenes. Arch. Biochem. Biophys. 277 (1990) 374-381. [PMID: 2178556]
2. Croteau, R. and Shaskus, J. Biosynthesis of monoterpenes: demonstration of a geranyl pyrophosphate:(–)-bornyl pyrophosphate cyclase in soluble enzyme preparations from tansy (Tanacetum vulgare). Arch. Biochem. Biophys. 236 (1985) 535-543. [PMID: 3970524]
3. Croteau, R., Felton, N.M. and Wheeler, C.J. Stereochemistry at C-1 of geranyl pyrophosphate and neryl pyrophosphate in the cyclization to (+)- and (–)-bornyl pyrophosphate. J. Biol. Chem. 260 (1985) 5956-5962. [PMID: 3997807]
4. Croteau, R.B., Shaskus, J.J., Renstrom, B., Felton, N.M., Cane, D.E., Saito, A. and Chang, C. Mechanism of the pyrophosphate migration in the enzymatic cyclization of geranyl and linalyl pyrophosphates to (+)- and (–)-bornyl pyrophosphates. Biochemistry 24 (1985) 7077-7085. [PMID: 4084562]
5. Adam, K.P. and Croteau, R. Monoterpene biosynthesis in the liverwort Conocephalum conicum: demonstration of sabinene synthase and bornyl diphosphate synthase. Phytochemistry 49 (1998) 475-480. [PMID: 9747540]
EC 5.99.1.4 2-hydroxychromene-2-carboxylate isomerase
Accepted name: thiocyanate isomerase
Reaction: benzyl isothiocyanate = benzyl thiocyanate
Other name(s): isothiocyanate isomerase
Systematic name: benzyl-thiocyanate isomerase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-71-6
References:
1. Virtanen, A.I. On enzymic and chemical reactions in crushed plants. Arch. Biochem. Biophys. Suppl. 1 (1962) 200-208.
Accepted name: DNA topoisomerase
Reaction: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Other name(s): type I DNA topoisomerase; untwisting enzyme; relaxing enzyme; nicking-closing enzyme; swivelase; ω-protein; deoxyribonucleate topoisomerase; topoisomerase; type I DNA topoisomerase
Systematic name: DNA topoisomerase
Comments: These enzymes bring about the conversion of one topological isomer of DNA into another, e.g., the relaxation of superhelical turns in DNA, the interconversion of simple and knotted rings of single-stranded DNA, and the intertwisting of single-stranded rings of complementary sequences, cf. EC 5.99.1.3 DNA topoisomerase (ATP-hydrolysing).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 80449-01-0
References:
1. Gellert, M. DNA topoisomerases. Annu. Rev. Biochem. 50 (1981) 879-910. [PMID: 6267993]
Accepted name: DNA topoisomerase (ATP-hydrolysing)
Reaction: ATP-dependent breakage, passage and rejoining of double-stranded DNA
Other name(s): type II DNA topoisomerase; DNA-gyrase; deoxyribonucleate topoisomerase; deoxyribonucleic topoisomerase; topoisomerase; DNA topoisomerase II;
Systematic name: DNA topoisomerase (ATP-hydrolysing)
Comments: The enzyme can introduce negative superhelical turns into double-stranded circular DNA. One unit has nicking-closing activity, and another catalyses super-twisting and hydrolysis of ATP (cf. EC 5.99.1.2 DNA topoisomerase).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 142805-56-9
References:
1. Gellert, M. DNA topoisomerases. Annu. Rev. Biochem. 50 (1981) 879-910. [PMID: 6267993]
Accepted name: 2-hydroxychromene-2-carboxylate isomerase
Reaction: 2-hydroxy-2H-chromene-2-carboxylate = (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate
For diagram of reaction, click here
Other name(s): HCCA isomerase; 2HC2CA isomerase; 2-hydroxychromene-2-carboxylic acid isomerase
Systematic name: 2-hydroxy-2H-chromene-2-carboxylate—(3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate isomerase
Comments: This enzyme is involved in naphthalene degradation.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number:
References:
1. Ohmoto, T., Kinoshita, T., Moriyoshi, K., Sakai, K., Hamada, N. and Ohe, T. Purification and some properties of 2-hydroxychromene-2-carboxylate isomerase from naphthalenesulfonate-assimilating Pseudomonas sp. TA-2. J. Biochem. 124 (1998) 591-597. [PMID: 9722670]
2. Keck, A., Conradt, D., Mahler, A., Stolz, A., Mattes, R. and Klein, J. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152 (2006) 1929-1940. [PMID: 16804169]
3. Eaton, R.W. Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J. Bacteriol. 176 (1994) 7757-7762. [PMID: 8002605]
4. Thompson, L.C., Ladner, J.E., Codreanu, S.G., Harp, J., Gilliland, G.L. and Armstrong, R.N. 2-Hydroxychromene-2-carboxylic acid isomerase: a kappa class glutathione transferase from Pseudomonas putida. Biochemistry 46 (2007) 6710-6722. [PMID: 17508726]