Enzyme Nomenclature

Continued from EC 5.4

EC 5.5 and EC 5.99

Sections

EC 5.5 Intramolecular Lyases
EC 5.99 Other Isomerases


EC 5.5 Intramolecular Lyases

Contents

EC 5.5.1.1 muconate cycloisomerase
EC 5.5.1.2 3-carboxy-cis,cis-muconate cycloisomerase
EC 5.5.1.3 tetrahydroxypteridine cycloisomerase
EC 5.5.1.4 inositol-phosphate synthase
EC 5.5.1.5 carboxy-cis,cis-muconate cyclase
EC 5.5.1.6 chalcone isomerase
EC 5.5.1.7 chloromuconate cycloisomerase
EC 5.5.1.8 (+)-bornyl diphosphate synthase
EC 5.5.1.9 cycloeucalenol cycloisomerase
EC 5.5.1.10 α-pinene-oxide decyclase
EC 5.5.1.11 dichloromuconate cycloisomerase
EC 5.5.1.12 copalyl diphosphate synthase
EC 5.5.1.13 ent-copalyl diphosphate synthase
EC 5.5.1.14 syn-copalyl diphosphate synthase
EC 5.5.1.15 terpentedienyl-diphosphate synthase
EC 5.5.1.16 halimadienyl-diphosphate synthase
EC 5.5.1.17 (S)-β-macrocarpene synthase
EC 5.5.1.18 lycopene ε-cyclase
EC 5.5.1.19 lycopene β-cyclase
EC 5.5.1.20 prosolanapyrone-III cycloisomerase
EC 5.5.1.21 deleted
EC 5.5.1.22 (–)-bornyl diphosphate synthase
EC 5.5.1.23 aklanonic acid methyl ester cyclase
EC 5.5.1.24 tocopherol cyclase
EC 5.5.1.25 3,6-anhydro-L-galactonate cycloisomerase
EC 5.5.1.26 nogalonic acid methyl ester cyclase
EC 5.5.1.27 D-galactarolactone cycloisomerase

Entries

EC 5.5.1.1

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; 2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)

Systematic name: 2,5-dihydro-5-oxofuran-2-acetate lyase (ring-opening)

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.

[EC 5.5.1.1 created 1961]

EC 5.5.1.2

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; 2-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)

Systematic name: 2-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (ring-opening)

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.

[EC 5.5.1.2 created 1972]

EC 5.5.1.3

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.

[EC 5.5.1.3 created 1972]

EC 5.5.1.4

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]

[EC 5.5.1.4 created 1972, modified 2001]

EC 5.5.1.5

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; 3-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)

Systematic name: 3-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (ring-opening)

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.

[EC 5.5.1.5 created 1972]

EC 5.5.1.6

Accepted name: chalcone isomerase

Reaction: A chalcone = a flavanone

See diagram for reaction in naringenin or liquiritigenin biosynthesis.

Other name(s): chalcone-flavanone isomerase; flavanone lyase (decyclizing)

Systematic name: flavanone lyase (ring-opening)

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.

[EC 5.5.1.6 created 1972]

EC 5.5.1.7

Accepted name: chloromuconate cycloisomerase

Reaction: (2R)-2-chloro-2,5-dihydro-5-oxofuran-2-acetate = 3-chloro-cis,cis-muconate

For diagram click here.

Glossary: (2R)-2-chloro-2,5-dihydro-5-oxofuran-2-acetate = (+)-4-chloromuconolactone
3-chloro-cis,cis-muconate = (2E,4Z)-3-chlorohexa-2,4-dienedioate

Other name(s): muconate cycloisomerase II; 2-chloro-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing); 2-chloro-2,5-dihydro-5-oxofuran-2-acetate lyase (ring-opening)

Systematic name: (2R)-2-chloro-2,5-dihydro-5-oxofuran-2-acetate lyase (ring-opening)

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]

2. Kaulmann, U., Kaschabek, S.R. and Schlomann, M. Mechanism of chloride elimination from 3-chloro- and 2,4-dichloro-cis,cis-muconate: new insight obtained from analysis of muconate cycloisomerase variant CatB-K169A. J. Bacteriol. 183 (2001) 4551-4561. [PMID: 11443090]

3. Kajander, T., Lehtio, L., Schlomann, M. and Goldman, A. The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function. Protein Sci. 12 (2003) 1855-1864. [PMID: 12930985]

[EC 5.5.1.7 created 1983]

EC 5.5.1.8

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 (ambiguous); bornyl pyrophosphate synthetase (ambiguous); (+)-bornylpyrophosphate cyclase; geranyl-diphosphate cyclase (ambiguous); (+)-bornyl-diphosphate lyase (decyclizing)

Systematic name: (+)-bornyl-diphosphate lyase (ring-opening)

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]

[EC 5.5.1.8 created 1984, modified 2012]

EC 5.5.1.9

Accepted name: cycloeucalenol cycloisomerase

Reaction: cycloeucalenol = obtusifoliol

For diagram click here.

Other name(s): cycloeucalenol—obtusifoliol isomerase; cycloeucalenol lyase (cyclopropane-decyclizing)

Systematic name: cycloeucalenol lyase (cyclopropane-ring opening)

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.

[EC 5.5.1.9 created 1986]

EC 5.5.1.10

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; α-pinene-oxide lyase (decyclizing)

Systematic name: α-pinene-oxide lyase (ring-opening)

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]

[EC 5.5.1.10 created 1990]

EC 5.5.1.11

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.

Other name(s): 2,4-dichloro-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)

Systematic name: 2,4-dichloro-2,5-dihydro-5-oxofuran-2-acetate lyase (ring-opening)

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]

[EC 5.5.1.11 created 1992]

EC 5.5.1.12

Accepted name: copalyl diphosphate synthase

Reaction: geranylgeranyl diphosphate = (+)-copalyl diphosphate

For diagram of reaction click here.

Other name(s): (+)-copalyl-diphosphate lyase (decyclizing)

Systematic name: (+)-copalyl-diphosphate lyase (ring-opening)

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]

[EC 5.5.1.12 created 2002, modified 2012]

EC 5.5.1.13

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; ent-copalyl-diphosphate lyase (decyclizing)

Systematic name: ent-copalyl-diphosphate lyase (ring-opening)

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]

[EC 5.5.1.13 created 2002]

EC 5.5.1.14

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; syn-copalyl diphosphate synthase; 9α-copalyl-diphosphate lyase (decyclizing)

Systematic name: 9α-copalyl-diphosphate lyase (ring-opening)

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]

[EC 5.5.1.14 created 2008]

EC 5.5.1.15

Accepted name: terpentedienyl-diphosphate synthase

Reaction: geranylgeranyl diphosphate = terpentedienyl diphosphate

For diagram of reaction 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, 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]

[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 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); 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, 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]

[EC 5.5.1.16 created 2008, modified 2012]

EC 5.5.1.17

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; (S)-β-macrocarpene lyase (decyclizing)

Systematic name: (S)-β-macrocarpene lyase (ring-opening)

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]

[EC 5.5.1.17 created 2011]

EC 5.5.1.18

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; carotenoid ψ-end group lyase (decyclizing)

Systematic name: carotenoid ψ-end group lyase (ring-opening)

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]

[EC 5.5.1.18 created 2011]

EC 5.5.1.19

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; LCYb; carotenoid β-end group lyase (decyclizing)

Systematic name: carotenoid β-end group lyase (ring-opening)

Comments: The enzyme is a non-redox flavoprotein, containing FADH2 that is used for stabilization of a transition state. Lycopene has a ψ-end group at both ends. When acting on one end, the enzyme forms γ-carotene. When acting on both ends it forms β-carotene. It also acts on neurosporene to give β-zeacarotene.

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]

7. Yu, Q., Schaub, P., Ghisla, S., Al-Babili, S., Krieger-Liszkay, A. and Beyer, P. The lycopene cyclase CrtY from Pantoea ananatis (formerly Erwinia uredovora) catalyzes an FADred-dependent non-redox reaction. J. Biol. Chem. 285 (2010) 12109-12120. [PMID: 20178989]

[EC 5.5.1.19 created 2011]

EC 5.5.1.20

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 5.5.1.20 created 2011]

[EC 5.5.1.21 Deleted entry: 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)]

EC 5.5.1.22

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 (ambiguous); bornyl pyrophosphate synthetase (ambiguous); (–)-bornyl pyrophosphate cyclase; bornyl diphosphate synthase; geranyl-diphosphate cyclase (ambiguous); (–)-bornyl-diphosphate lyase (decyclizing)

Systematic name: (–)-bornyl-diphosphate lyase (ring-opening)

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 5.5.1.22 created 2012]

EC 5.5.1.23

Accepted name: aklanonic acid methyl ester cyclase

Reaction: aklaviketone = methyl aklanonate

For diagram of reaction click here.

Glossary: aklaviketone = methyl (1R,2R)-2-ethyl-2,5,7-trihydroxy-4,6,11-trioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate
methyl aklanonate = methyl [4,5-dihydroxy-9,10-dioxo-3-(3-oxopentanoyl)-9,10-dihydroanthracen-2-yl]acetate

Other name(s): dauD (gene name); aknH (gene name); dnrD (gene name); methyl aklanonate cyclase; methyl aklanonate-aklaviketone isomerase (cyclizing); aklaviketone lyase (decyclizing)

Systematic name: aklaviketone lyase (ring-opening)

Comments: The enzyme is involved in the biosynthesis of aklaviketone, an intermediate in the biosynthetic pathways leading to formation of several anthracycline antibiotics, including aclacinomycin, daunorubicin and doxorubicin.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Dickens, M.L., Ye, J. and Strohl, W.R. Analysis of clustered genes encoding both early and late steps in daunomycin biosynthesis by Streptomyces sp. strain C5. J. Bacteriol. 177 (1995) 536-543. [PMID: 7836284]

2. Kendrew, S.G., Katayama, K., Deutsch, E., Madduri, K. and Hutchinson, C.R. DnrD cyclase involved in the biosynthesis of doxorubicin: purification and characterization of the recombinant enzyme. Biochemistry 38 (1999) 4794-4799. [PMID: 10200167]

3. Kallio, P., Sultana, A., Niemi, J., Mantsala, P. and Schneider, G. Crystal structure of the polyketide cyclase AknH with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity. J. Mol. Biol. 357 (2006) 210-220. [PMID: 16414075]

[EC 5.5.1.23 created 2013, modified 2014]

EC 5.5.1.24

Accepted name: tocopherol cyclase

Reaction: (1) δ-tocopherol = 2-methyl-6-phytylbenzene-1,4-diol
(2) γ-tocopherol = 2,3-dimethyl-6-phytylbenzene-1,4-diol
(3) δ-tocotrienol = 6-geranylgeranyl-2-methylbenzene-1,4-diol
(4) γ-tocotrienol = 6-geranylgeranyl-2,3-dimethylbenzene-1,4-diol

For diagram of tocopherol biosynthesis, click here or tocotrienol biosynthesis click here

Other name(s): VTE1 (gene name); SXD1 (gene name); δ/γ-tocopherol lyase (decyclizing)

Systematic name: δ/γ-tocopherol lyase (ring-opening)

Comments: The enzyme has been described from plants and cyanobacteria. It has similar activity with all four listed benzoquinol substrates. Involved in the biosynthesis of vitamin E tocopherols and tocotrienols.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Porfirova, S., Bergmuller, E., Tropf, S., Lemke, R. and Dormann, P. Isolation of an Arabidopsis mutant lacking vitamin E and identification of a cyclase essential for all tocopherol biosynthesis. Proc. Natl. Acad. Sci. USA 99 (2002) 12495-12500. [PMID: 12213958]

2. Sattler, S.E., Cahoon, E.B., Coughlan, S.J. and DellaPenna, D. Characterization of tocopherol cyclases from higher plants and cyanobacteria. Evolutionary implications for tocopherol synthesis and function. Plant Physiol. 132 (2003) 2184-2195. [PMID: 12913173]

[EC 5.5.1.24 created 2013]

EC 5.5.1.25

Accepted name: 3,6-anhydro-L-galactonate cycloisomerase

Reaction: 3,6-anhydro-L-galactonate = 2-dehydro-3-deoxy-L-galactonate

Other name(s): 3,6-anhydro-α-L-galactonate lyase (ring-opening); 3,6-anhydro-α-L-galactonate cycloisomerase

Systematic name: 3,6-anhydro-L-galactonate lyase (ring-opening)

Comments: The enzyme, characterized from the marine bacteria Vibrio sp. EJY3 and Postechiella marina M091, is involved in a degradation pathway for 3,6-anhydro-α-L-galactopyranose, a major component of the polysaccharides of red macroalgae.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Yun, E.J., Lee, S., Kim, H.T., Pelton, J.G., Kim, S., Ko, H.J., Choi, I.G. and Kim, K.H. The novel catabolic pathway of 3,6-anhydro-L-galactose, the main component of red macroalgae, in a marine bacterium. Environ. Microbiol. 17 (2015) 1677-1688. [PMID: 25156229]

2. Lee, S.B., Cho, S.J., Kim, J.A., Lee, S.Y., Kim, S.M. and Lim, H.S. Metabolic pathway of 3,6-anhydro-L-galactose in agar-degrading microorganisms. Biotechnol. Bioprocess Eng. 19 (2014) 866-878.

[EC 5.5.1.25 created 2014, modified 2015]

EC 5.5.1.26

Accepted name: nogalonic acid methyl ester cyclase

Reaction: nogalaviketone = methyl nogalonate

For diagram of reaction click here.

Glossary: methyl nogalonate = methyl [4,5-dihydroxy-9,10-dioxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate
nogalaviketone = methyl 5,7-dihydroxy-2-methyl-4,6,11-trioxo-3,4,6,11-tetrahydrotetracene-1-carboxylate

Other name(s): methyl nogalonate cyclase; SnoaL (gene name); methyl nogalonate lyase (cyclizing)

Systematic name: nogalaviketone lyase (ring-opening)

Comments: The enzyme, characterized from the bacterium Streptomyces nogalater, is involved in the biosynthesis of the aromatic polyketide nogalamycin.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Sultana, A., Kallio, P., Jansson, A., Wang, J.S., Niemi, J., Mantsala, P. and Schneider, G. Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation. EMBO J. 23 (2004) 1911-1921. [PMID: 15071504]

2. Sultana, A., Kallio, P., Jansson, A., Niemi, J., Mantsala, P. and Schneider, G. Crystallization and preliminary crystallographic data of SnoaL, a polyketide cyclase in nogalamycin biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1118-1120. [PMID: 15159574]

[EC 5.5.1.26 created 2015]

EC 5.5.1.27

Accepted name: D-galactarolactone cycloisomerase

Reaction: (1) D-galactaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate
(2) D-glucaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate

Other name(s): GCI

Systematic name: D-galactaro-1,4-lactone lyase (ring-opening)

Comments: The enzyme, characterized from the bacterium Agrobacterium fabrum strain C58, is involved in degradation of D-galacturonate and D-glucuronate. Activity with D-galactaro-1,4-lactone is 4-fold higher than with D-glucaro-1,4-lactone.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Andberg, M., Maaheimo, H., Boer, H., Penttila, M., Koivula, A. and Richard, P. Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate. J. Biol. Chem. 287 (2012) 17662-17671. [PMID: 22493433]

2. Bouvier, J.T., Groninger-Poe, F.P., Vetting, M., Almo, S.C. and Gerlt, J.A. Galactaro δ-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily. Biochemistry 53 (2014) 614-616. [PMID: 24450804]

[EC 5.5.1.27 created 2015]


EC 5.99 Other Isomerases

Contents

EC 5.99.1.1 thiocyanate isomerase
EC 5.99.1.2 DNA topoisomerase
EC 5.99.1.3 DNA topoisomerase (ATP-hydrolysing)

EC 5.99.1.4 2-hydroxychromene-2-carboxylate isomerase


Entries

EC 5.99.1.1

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.

[EC 5.99.1.1 created 1965]

EC 5.99.1.2

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]

[EC 5.99.1.2 created 1984]

EC 5.99.1.3

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]

[EC 5.99.1.3 created 1984]

EC 5.99.1.4

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]

[EC 5.99.1.4 created 2010]


Continued with EC 6
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