Enzyme Nomenclature

Continued from EC 5.3.1 and EC 5.3.2

EC 5.3.3 to EC 5.3.99

Sections

EC 5.3.3 Transposing C=C Bonds
EC 5.3.4 Transposing S-S Bonds
EC 5.3.99 Other Intramolecular Oxidoreductases


EC 5.3.3 Transposing C=C Bonds

Contents

EC 5.3.3.1 steroid Δ-isomerase
EC 5.3.3.2 isopentenyl-diphosphate Δ-isomerase
EC 5.3.3.3 vinylacetyl-CoA Δ-isomerase
EC 5.3.3.4 muconolactone Δ-isomerase
EC 5.3.3.5 cholestenol Δ-isomerase
EC 5.3.3.6 methylitaconate Δ-isomerase
EC 5.3.3.7 aconitate Δ-isomerase
EC 5.3.3.8 dodecenoyl-CoA Δ-isomerase
EC 5.3.3.9 prostaglandin-A1 Δ-isomerase
EC 5.3.3.10 5-carboxymethyl-2-hydroxymuconate Δ-isomerase
EC 5.3.3.11 isopiperitenone Δ-isomerase
EC 5.3.3.12 L-dopachrome isomerase
EC 5.3.3.13 polyenoic fatty acid isomerase
EC 5.3.3.14 trans-2-decenoyl-[acyl-carrier protein] isomerase
EC 5.3.3.15 now EC 5.3.2.7
EC 5.3.3.16 now EC 5.3.2.8
EC 5.3.3.17 trans-2,3-dihydro-3-hydroxyanthranilate isomerase
EC 5.3.3.18 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
EC 5.3.3.19 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase
EC 5.3.3.20 2-hydroxyisobutanoyl-CoA mutase


Entries

EC 5.3.3.1

Accepted name: steroid Δ-isomerase

Reaction: A 3-oxo-Δ5-steroid = a 3-oxo-Δ4-steroid

For diagram click here.

Other name(s): hydroxysteroid isomerase; steroid isomerase; Δ5-ketosteroid isomerase; Δ5(or Δ4)-3-keto steroid isomerase; Δ5-steroid isomerase; 3-oxosteroid isomerase; Δ5-3-keto steroid isomerase; Δ5-3-oxosteroid isomerase

Systematic name: 3-oxosteroid Δ54-isomerase

Comments: This activity is catalysed by several distinct enzymes (cf. EC 1.1.3.6, cholesterol oxidase and EC 1.1.1.145, 3-hydroxy-5-steroid dehydrogenase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9031-36-1

References:

1. Ewald, W., Werbein, H. and Chaikoff, I.L. Evidence for the presence of 17-hydroxypregnenedione isomerase in beef adrenal cortex. Biochim. Biophys. Acta 111 (1965) 306-312. [PMID: 5867327]

2. Kawahara, F.S. and Talalay, P. Crystalline Δ5-3-ketosteroid isomerase. J. Biol. Chem. 235 (1960) PC1-PC2.

3. Talalay, P. and Wang, V.S. Enzymic isomerization of Δ5-3-ketosteroids. Biochim. Biophys. Acta 18 (1955) 300-301.

[EC 5.3.3.1 created 1961]

EC 5.3.3.2

Accepted name: isopentenyl-diphosphate Δ-isomerase

Reaction: isopentenyl diphosphate = dimethylallyl diphosphate

For reaction pathway click here.

Other name(s): isopentenylpyrophosphate Δ-isomerase; methylbutenylpyrophosphate isomerase; isopentenylpyrophosphate isomerase

Systematic name: isopentenyl-diphosphate Δ32-isomerase

Comments: The enzyme from Streptomyces sp. strain CL190 requires FMN and NAD(P)H as cofactors. Activity is reduced if FMN is replaced by FAD, but the enzyme becomes inactive when NAD(P)H is replaced by NAD+ or NADP+. That enzyme also requires Mg2+, Mn2+ or Ca2+ for activity.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9033-27-6

References:

1. Kaneda, K., Kuzuyama, T., Takagi, M., Hayakawa, Y. and Seto, H. An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. strain CL190. Proc. Natl. Acad. Sci. USA 98 (2001) 932-937. [PMID: 11158573]

2. Bishop, J.M. Cellular oncogenes and retroviruses. Annu. Rev. Biochem. 52 (1983) 301-354. [PMID: 6351725]

3. Agranoff, B.W., Eggerer, H., Henning, U. and Lynen, F. Biosynthesis of terpenes. VII. Isopentenyl pyrophosphate isomerase. J. Biol. Chem. 235 (1960) 326-332.

[EC 5.3.3.2 created 1961, modified 2002]

EC 5.3.3.3

Accepted name: vinylacetyl-CoA Δ-isomerase

Reaction: vinylacetyl-CoA = (E)-but-2-enoyl-CoA

Glossary: (E)-but-2-enoyl-CoA = crotonyl-CoA

Other name(s): vinylacetyl coenzyme A Δ-isomerase; vinylacetyl coenzyme A isomerase; Δ3-cis-Δ2-trans-enoyl-CoA isomerase

Systematic name: vinylacetyl-CoA Δ32-isomerase

Comments: Also acts on 3-methyl-vinylacetyl-CoA.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-73-8

References:

1. Lynen, F., Knappe, J., Lorch, E., Jütting, G. and Ringelmann, E. Die biochemische Funktion des Biotins. Angew. Chem. 71 (1959) 481-486.

2. Rilling, H.C. and Coon, M.J. The enzymatic isomerization of α-methylvinylacetyl coenzyme A and the specificity of a bacterial α-methylcrotonyl coenzyme A carboxylase. J. Biol. Chem. 235 (1960) 3087-3092.

[EC 5.3.3.3 created 1961]

EC 5.3.3.4

Accepted name: muconolactone Δ-isomerase

Reaction: (S)-5-oxo-2,5-dihydrofuran-2-acetate = 5-oxo-4,5-dihydrofuran-2-acetate

For diagram click here.

Other name(s): muconolactone isomerase

Systematic name: 5-oxo-4,5-dihydrofuran-2-acetate Δ32-isomerase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37318-46-0

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.

[EC 5.3.3.4 created 1961 as EC 3.1.1.16, part transferred 1972 to EC 5.3.3.4 rest to EC 5.3.3.4]

EC 5.3.3.5

Accepted name: cholestenol Δ-isomerase

Reaction: 5α-cholest-7-en-3β-ol = 5α-cholest-8-en-3β-ol

For diagram click here.

Systematic name: Δ7-cholestenol Δ78-isomerase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 52410-46-5

References:

1. Wilton, D.C., Rahimtula, A.D. and Akhtar, M. The reversibility of the Δ8-cholestenol-Δ7-cholestenol isomerase reaction in cholesterol biosynthesis. Biochem. J. 114 (1969) 71-73. [PMID: 5810070]

[EC 5.3.3.5 created 1972]

EC 5.3.3.6

Accepted name: methylitaconate Δ-isomerase

Reaction: methylitaconate = 2,3-dimethylmaleate

For diagram click here.

Other name(s): methylitaconate isomerase

Systematic name: methylitaconate Δ23-isomerase

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9059-08-9

References:

1. Kung, H.-F. and Stadtman, T.C. Nicotinic acid metabolism. VI. Purification and properties of α-methyleneglutarate mutase (B12-dependent) and methylitaconate isomerase. J. Biol. Chem. 246 (1971) 3378-3388. [PMID: 5574401]

[EC 5.3.3.6 created 1972]

EC 5.3.3.7

Accepted name: aconitate Δ-isomerase

Reaction: trans-aconitate = cis-aconitate

Glossary: cis-aconitate = (Z)-prop-1-ene-1,2,3-tricarboxylate
trans-aconitate = (E)-prop-1-ene-1,2,3-tricarboxylate

Other name(s): aconitate isomerase

Systematic name: aconitate Δ23-isomerase

Comments: cis-Aconitate is used to designate the isomer (Z)-prop-1-ene-1,2,3-tricarboxylate. This isomerization could take place either in a direct cis-trans interconversion or by an allylic rearrangement; the enzyme has been shown to catalyse the latter change.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37318-48-2

References:

1. Klinman, J.P. and Rose, I.A. Purification and kinetic properties of aconitate isomerase from Pseudomonas putida. Biochemistry 10 (1971) 2253-2259.

2. Klinman, J.P. and Rose, I.A. Mechanism of the aconitate isomerase reaction. Biochemistry 10 (1971) 2259-2266.

[EC 5.3.3.7 created 1972]

EC 5.3.3.8

Accepted name: dodecenoyl-CoA isomerase

Reaction: (3Z)-dodec-3-enoyl-CoA = (2E)-dodec-2-enoyl-CoA

For diagram of reaction click here.

Other name(s): dodecenoyl-CoA Δ-isomerase; Δ3-cis-Δ2-trans-enoyl-CoA isomerase; acetylene-allene isomerase; dodecenoyl-CoA Δ-isomerase; dodecenoyl-CoA Δ3-cis-Δ2-trans-isomerase

Systematic name: dodecenoyl-CoA (3Z)-(2E)-isomerase

Comments: Also catalyses the interconversion of 3-acetylenic fatty acyl thioesters and (+)-2,3-dienoyl fatty acyl thioesters, with fatty acid chain lengths C6 to C12.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 62213-29-0

References:

1. Miesowicz, F.M. and Bloch, K. Purification of hog liver isomerase. Mechanism of isomerization of 3-alkenyl and 3-alkynyl thioesters. J. Biol. Chem. 254 (1979) 5868-5877. [PMID: 376522]

2. Stoffel, W., Ditzer, R. and Caesar, H. Der Stoffwechsel der ungesättigten Fettsäuren. III. Zur β-Oxydation der Mono- und Polyenfettsäuren. Der Mechanismus der enzymatischen Reaktionen an Δ3cis-Enoyl-CoA-Verbindungen. Hoppe-Seyler's Z. Physiol. Chem. 339 (1964) 167-181. [PMID: 5830064]

3. Stoffel, W. and Ecker, W. Δ3-cis,-Δ2-trans-Enoyl-CoA isomerase from rat liver mitochondria. Methods Enzymol. 14 (1979) 99-105.

4. Stoffel, W. and Grol, M. Purification and properties of 3-cis-2-trans-enoyl-CoA isomerase (dodecenoyl-CoA Δ-isomerase) from rat liver mitochondria. Hoppe-Seyler's Z. Physiol. Chem. 359 (1978) 1777-1782. [PMID: 738702]

[EC 5.3.3.8 created 1978, modified 1980]

EC 5.3.3.9

Accepted name: prostaglandin-A1 Δ-isomerase

Reaction: (13E)-(15S)-15-hydroxy-9-oxoprosta-10,13-dienoate = (13E)-(15S)-15-hydroxy-9-oxoprosta-11,13-dienoate

Other name(s): prostaglandin A isomerase

Systematic name: (13E)-(15S)-15-hydroxy-9-oxoprosta-10,13-dienoate Δ1011-isomerase

Comments: Interconverts prostaglandin A1 and prostaglandin C1.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9055-01-0

References:

1. Polet, H. and Levine, L. Metabolism of prostaglandins E, A, and C in serum. J. Biol. Chem. 250 (1975) 351-357. [PMID: 234423]

[EC 5.3.3.9 created 1978]

EC 5.3.3.10

Accepted name: 5-carboxymethyl-2-hydroxymuconate Δ-isomerase

Reaction: 5-carboxymethyl-2-hydroxymuconate = (3E,5R)-5-carboxy-2-oxohept-3-enedioate

Glossary: 5-carboxymethyl-2-hydroxymuconate = (2E,4Z)-5-hydroxypenta-2,4-diene-1,2,5-tricarboxylate

Other name(s): CHM isomerase; 5-carboxymethyl-2-hydroxymuconic acid isomerase

Systematic name: 5-carboxymethyl-2-hydroxymuconate Δ24-2-oxo,Δ3-isomerase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 79079-05-3

References:

1. Garrido-Pertierra, A. and Cooper, R.A. Identification and purification of distinct isomerase and decarboxylase enzymes involved in the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli. Eur. J. Biochem. 117 (1981) 581-584. [PMID: 7026235]

[EC 5.3.3.10 created 1984]

EC 5.3.3.11

Accepted name: isopiperitenone Δ-isomerase

Reaction: isopiperitenone = piperitenone

Systematic name: isopiperitenone Δ84-isomerase

Comments: Involved in the biosynthesis of menthol and related monoterpenes in peppermint (Mentha piperita) leaves.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 96595-07-2

References:

1. Kjonaas, R.B., Venkatachalam, K.V. and Croteau, R. Metabolism of monoterpenes: oxidation of isopiperitenol to isopiperitenone, and subsequent isomerization to piperitenone by soluble enzyme preparations from peppermint (Mentha piperita) leaves. Arch. Biochem. Biophys. 238 (1985) 49-60. [PMID: 3885858]

[EC 5.3.3.11 created 1989]

EC 5.3.3.12

Accepted name: L-dopachrome isomerase

Reaction: L-dopachrome = 5,6-dihydroxyindole-2-carboxylate

For diagram click here.

Glossary: L-dopachrome = (2S)-5,6-dioxo-2,3,5,6-tetrahydro-1H-indole-2-carboxylate

Other name(s): dopachrome tautomerase; tyrosinase-related protein 2; TRP-1; TRP2; TRP-2; tyrosinase-related protein-2; dopachrome Δ72-isomerase; dopachrome Δ-isomerase; dopachrome conversion factor; dopachrome isomerase; dopachrome oxidoreductase; dopachrome-rearranging enzyme; DCF; DCT; dopachrome keto-enol isomerase; L-dopachrome-methyl ester tautomerase

Systematic name: L-dopachrome keto-enol isomerase

Comments: A zinc enzyme. Stereospecific for L-dopachrome. Dopachrome methyl ester is a substrate, but dopaminochrome (2,3-dihydroindole-5,6-quinone) is not (see also EC 4.1.1.84, D-dopachrome decarboxylase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 130122-81-5

References:

1. Solano, F., Jiménez-Cervantes, C., Martinez-Liarte, J.H., Garcia-Borrón and J.C., Lozano, J.A. Molecular mechanism for catalysis by a new zinc enzyme, dopachrome tautomerase. Biochem. J. 313 (1996) 447-453. [PMID: 8573077]

2. Pawelek, J.M. Dopachrome conversion factor functions as an isomerase. Biochem. Biophys. Res. Commun. 166 (1990) 1328-1333. [PMID: 2106316]

3. Pennock, J.L., Behnke, J.M., Bickle, Q.D., Devaney, E., Grencis, R.K., Isaac, R.E., Joshua. G.W., Selkirk. M.E., Zhang. Y. and Meyer, D.J. Rapid purification and characterization of L-dopachrome-methyl ester tautomerase (macrophage-migration-inhibitory factor) from Trichinella spiralis, Trichuris muris and Brugia pahangi. Biochem. J. 335 (1998) 495-498. [PMID: 9794786]

[EC 5.3.3.12 created 1992, modified 1999, modified 2005]

EC 5.3.3.13

Accepted name: polyenoic fatty acid isomerase

Reaction: (5Z,8Z,11Z,14Z,17Z)-icosapentaenoate = (5Z,7E,9E,14Z,17Z)-icosapentaenoate

For diagram click here.

Other name(s): PFI; eicosapentaenoate cis-Δ5,8,11,14,17-eicosapentaenoate cis-Δ5-trans-Δ7,9-cis-Δ14,17 isomerase; (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate Δ8,117,8-isomerase (incorrect); (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate Δ8,117,9-isomerase (trans-double-bond-forming)

Systematic name: (5Z,8Z,11Z,14Z,17Z)-icosapentaenoate Δ8,117,9-isomerase (trans-double-bond-forming)

Comments: The enzyme from the red alga Ptilota filicina catalyses the isomerization of skip dienes (methylene-interrupted double bonds) in a broad range of fatty acids and fatty-acid analogues, such as arachidonate and γ-linolenate, to yield a conjugated triene.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 159002-84-3

References:

1. Wise, M.L., Hamberg, M. and Gerwick, W.H. Biosynthesis of conjugated fatty acids by a novel isomerase from the red marine alga Ptilota filicina. Biochemistry 33 (1994) 15223-15232. [PMID: 7803384]

2. Wise, M.L., Soderstrom, K., Murray, T.F. and Gerwick, W.H. Synthesis and cannabinoid receptor binding activity of conjugated triene anandamide, a novel eicosanoid. Experientia 52 (1996) 88-92. [PMID: 8575565]

3. Wise, M.L., Rossi, J. and Gerwick, W.H. Binding site characterization of polyenoic fatty-acid isomerase from the marine alga Ptilota filicina. Biochemistry 36 (1997) 2985-2992. [PMID: 9062129]

4. Zheng, W., Wise, M.L., Wyrick, A., Metz, J.G., Yuan, L. and Gerwick, W.H.Polyenoic fatty-acid isomerase from the marine red alga Ptilota filicina: protein characterization and functional expression of the cloned cDNA. Arch. Biochem. Biophys. 401 (2002) 11-20. [PMID: 12054482]

[EC 5.3.3.13 created 2004]

EC 5.3.3.14

Accepted name: trans-2-decenoyl-[acyl-carrier protein] isomerase

Reaction: trans-dec-2-enoyl-[acyl-carrier protein] = cis-dec-3-enoyl-[acyl-carrier protein]

Other name(s): β-hydroxydecanoyl thioester dehydrase; trans-2-cis-3-decenoyl-ACP isomerase; trans-2,cis-3-decenoyl-ACP isomerase; trans-2-decenoyl-ACP isomerase; FabM

Systematic name: decenoyl-[acyl-carrier protein] Δ2-trans-Δ3-cis-isomerase

Comments: While the enzyme from Escherichia coli is highly specific for the 10-carbon enoyl-ACP, the enzyme from Streptococcus pneumoniae can also use the 12-carbon enoyl-ACP as substrate in vitro but not 14- or 16-carbon enoyl-ACPs [3]. ACP can be replaced by either CoA or N-acetylcysteamine thioesters. The cis-3-enoyl product is required to form unsaturated fatty acids, such as palmitoleic acid and cis-vaccenic acid, in dissociated (or type II) fatty-acid biosynthesis.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9030-80-2

References:

1. Brock, D.J.H., Kass, L.R. and Bloch, K. β-Hydroxydecanoyl thioester dehydrase. II. Mode of action. J. Biol. Chem. 242 (1967) 4432-4440. [PMID: 4863740]

2. Bloch, K. Enzymatic synthesis of monounsaturated fatty acids. Acc. Chem. Res. 2 (1969) 193-202.

3. Marrakchi, H., Choi, K.H. and Rock, C.O. A new mechanism for anaerobic unsaturated fatty acid formation in Streptococcus pneumoniae. J. Biol. Chem. 277 (2002) 44809-44816. [PMID: 12237320]

4. Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612-636.

[EC 5.3.3.14 created 2006]

[EC 5.3.3.15 Transferred entry: ascopyrone tautomerase. Now EC 5.3.2.7, ascopyrone tautomerase (EC 5.3.3.15 created 2006, deleted 2013)]

[EC 5.3.3.16 Transferred entry: 4-oxalomesaconate tautomerase. Now EC 5.3.2.8, 4-oxalomesaconate tautomerase (EC 5.3.3.16 created 2011, modified 2011, deleted 2013)]

EC 5.3.3.17

Accepted name: trans-2,3-dihydro-3-hydroxyanthranilate isomerase

Reaction: (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxyate = (1R,6S)-6-amino-5-oxocyclohex-2-ene-1-carboxylate

Glossary: (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate = trans-2,3-dihydro-3-hydroxyanthranilate

Other name(s): phzF (gene name); (5S,6S)-6-amino-5-hydroxycyclohexane-1,3-diene-1-carboxyate isomerase (incorrect)

Systematic name: (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxyate isomerase

Comments: The enzyme is involved in phenazine biosynthesis. The product probably spontaneously dimerises to 1,4,5a,6,9,10a-hexahydrophenazine-1,6-dicarboxylate

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

References:

1. Parsons, J.F., Song, F., Parsons, L., Calabrese, K., Eisenstein, E. and Ladner, J.E. Structure and function of the phenazine biosynthesis protein PhzF from Pseudomonas fluorescens 2-79. Biochemistry 43 (2004) 12427-12435. [PMID: 15449932]

2. Blankenfeldt, W., Kuzin, A.P., Skarina, T., Korniyenko, Y., Tong, L., Bayer, P., Janning, P., Thomashow, L.S. and Mavrodi, D.V. Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens. Proc. Natl. Acad. Sci. USA 101 (2004) 16431-16436. [PMID: 15545603]

3. Parsons, J.F., Calabrese, K., Eisenstein, E. and Ladner, J.E. Structure of the phenazine biosynthesis enzyme PhzG. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 2110-2113. [PMID: 15502343]

4. Mavrodi, D.V., Bleimling, N., Thomashow, L.S. and Blankenfeldt, W. The purification, crystallization and preliminary structural characterization of PhzF, a key enzyme in the phenazine-biosynthesis pathway from Pseudomonas fluorescens 2-79. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 184-186. [PMID: 14684924]

5. Ahuja, E.G., Janning, P., Mentel, M., Graebsch, A., Breinbauer, R., Hiller, W., Costisella, B., Thomashow, L.S., Mavrodi, D.V. and Blankenfeldt, W. PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis. J. Am. Chem. Soc. 130 (2008) 17053-17061. [PMID: 19053436]

[EC 5.3.3.17 created 2011]

EC 5.3.3.18

Accepted name: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Reaction: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA

For diagram of reaction click here.

Glossary: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-{7-oxabicyclo[4.1.0]hepta-2,4-dien-1-yl}acetyl-CoA
oxepin-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA

Other name(s): paaG (gene name); 1,2-epoxyphenylacetyl-CoA isomerase (misleading)

Systematic name: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Comments: The enzyme catalyses the reversible isomerization of 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA to the unusual unsaturated, oxygen-containing, seven-member heterocyclic enol ether 2-oxepin-2(3H)-ylideneacetyl-CoA, as part of an aerobic phenylacetate degradation pathway.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number:

References:

1. Ismail, W., El-Said Mohamed, M., Wanner, B.L., Datsenko, K.A., Eisenreich, W., Rohdich, F., Bacher, A. and Fuchs, G. Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli. Eur. J. Biochem. 270 (2003) 3047-3054. [PMID: 12846838]

2. Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390-14395. [PMID: 20660314]

[EC 5.3.3.18 created 2011]

EC 5.3.3.19

Accepted name: 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase

Reaction: 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate = 3-[(1E,4R)-4-hydroxycyclohex-2-en-1-ylidene]-2-oxopropanoate

For diagram of reaction click here.

Glossary: L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine

Other name(s): BacB

Systematic name: 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase

Comments: The enzyme, characterized from the bacterium Bacillus subtilis, is involved in the biosynthesis of the nonribosomally synthesized dipeptide antibiotic bacilysin, composed of L-alanine and L-anticapsin. The enzyme can interconvert the (E) isomer formed in the reaction into the (Z) isomer [2], although this isomerization is not part of the pathway leading to bacilysin [3].

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

References:

1. Mahlstedt, S.A. and Walsh, C.T. Investigation of anticapsin biosynthesis reveals a four-enzyme pathway to tetrahydrotyrosine in Bacillus subtilis. Biochemistry 49 (2010) 912-923. [PMID: 20052993]

2. Parker, J.B. and Walsh, C.T. Olefin isomerization regiochemistries during tandem action of BacA and BacB on prephenate in bacilysin biosynthesis. Biochemistry 51 (2012) 3241-3251. [PMID: 22483065]

3. Parker, J.B. and Walsh, C.T. Action and timing of BacC and BacD in the late stages of biosynthesis of the dipeptide antibiotic bacilysin. Biochemistry 52 (2013) 889-901. [PMID: 23317005]

[EC 5.3.3.19 created 2015]

EC 5.3.3.20

Accepted name: 2-hydroxyisobutanoyl-CoA mutase

Reaction: 2-hydroxyisobutanoyl-CoA = (S)-3-hydroxybutanoyl-CoA

Other name(s): hcmAB (gene names)

Systematic name: 2-hydroxyisobutanoyl-CoA mutase

Comments: The enzyme, characterized from the bacterium Aquincola tertiaricarbonis, uses radical chemistry to rearrange the positions of both a methyl group and a hydroxyl group. It consists of two subunits, the smaller one containing a cobalamin cofactor. It plays a central role in the degradation of assorted substrates containing a tert-butyl moiety.

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

References:

1. Yaneva, N., Schuster, J., Schafer, F., Lede, V., Przybylski, D., Paproth, T., Harms, H., Muller, R.H. and Rohwerder, T. Bacterial acyl-CoA mutase specifically catalyzes coenzyme B12-dependent isomerization of 2-hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA. J. Biol. Chem. 287 (2012) 15502-15511. [PMID: 22433853]

2. Kurteva-Yaneva, N., Zahn, M., Weichler, M.T., Starke, R., Harms, H., Muller, R.H., Strater, N. and Rohwerder, T. Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase. J. Biol. Chem. 290 (2015) 9727-9737. [PMID: 25720495]

[EC 5.3.3.20 created 2016]


EC 5.3.4 Transposing S-S Bonds

EC 5.3.4.1

Accepted name: protein disulfide-isomerase

Reaction: Catalyses the rearrangement of -S-S- bonds in proteins

Other name(s): S-S rearrangase

Systematic name: protein disulfide-isomerase

Comments: Needs reducing agents or partly reduced enzyme; the reaction depends on sulfhydryl-disulfide interchange.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37318-49-3

References:

1. De Lorenzo, F., Goldberger, R.F., Steers, E., Givol, D. and Anfinsen, C.B. Purification and properties of an enzyme from beef liver which catalyzes sulfhydryl-disulfide interchange in proteins. J. Biol. Chem. 241 (1966) 1562-1567. [PMID: 5946614]

2. Fuchs, S., De Lorenzo, F. and Anfinsen, C.B. Studies on the mechanism of the enzymic catalysis of disulfide interchange in proteins. J. Biol. Chem. 242 (1967) 398-402. [PMID: 6022836]

[EC 5.3.4.1 created 1972]


EC 5.3.99 Other Intramolecular Oxidoreductases

Contents

EC 5.3.99.1 deleted
EC 5.3.99.2 prostaglandin-D synthase
EC 5.3.99.3 prostaglandin-E synthase
EC 5.3.99.4 prostaglandin-I synthase
EC 5.3.99.5 thromboxane-A synthase
EC 5.3.99.6 allene-oxide cyclase
EC 5.3.99.7 styrene-oxide isomerase
EC 5.3.99.8 capsanthin/capsorubin synthase
EC 5.3.99.9 neoxanthin synthase
EC 5.3.99.10 thiazole tautomerase
EC 5.3.99.11 2-keto-myo-inositol isomerase


Entries

[EC 5.3.99.1 Deleted entry: hydroperoxide isomerase. Reaction due to combined action of EC 4.2.1.92 (hydroperoxide dehydratase) and EC 5.3.99.6 (allene-oxide cyclase) (EC 5.3.99.1 created 1972, deleted 1992)]

EC 5.3.99.2

Accepted name: prostaglandin-D synthase

Reaction: (5Z,13E,15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-9α,15-dihydroxy-11-oxoprosta-5,13-dienoate

Other name(s): prostaglandin-H2 Δ-isomerase; prostaglandin-R-prostaglandin D isomerase; PGH-PGD isomerase; prostaglandin endoperoxide Δ-isomerase; prostaglandin D synthetase; (5Z,13E)-(15S)-9a,11a-epidioxy-15-hydroxyprosta-5,13-dienoate D-isomerase

Systematic name: (5Z,13E,15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate Δ-isomerase

Comments: Brings about the opening of the epidioxy bridge. Some enzymes require glutathione.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 65802-85-9

References:

1. Christ-Hazelhof, E. and Nugteren, D.H. Purification and characterisation of prostaglandin endoperoxide Δ-isomerase, a cytoplasmic, glutathione-requiring enzyme. Biochim. Biophys. Acta 572 (1979) 43-51. [PMID: 32914]

2. Shimizu, T., Yamamoto, S. and Hayaishi, O. Purification and properties of prostaglandin D synthetase from rat brain. J. Biol. Chem. 254 (1979) 5222-5228. [PMID: 109431]

[EC 5.3.99.2 created 1976, modified 1990]

EC 5.3.99.3

Accepted name: prostaglandin-E synthase

Reaction: (5Z,13E,15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-11α,15-dihydroxy-9-oxoprosta-5,13-dienoate

Other name(s): prostaglandin-H2 E-isomerase; endoperoxide isomerase; endoperoxide isomerase; prostaglandin R-prostaglandin E isomerase; prostaglandin endoperoxide E isomerase; PGE isomerase; PGH-PGE isomerase; PGE2 isomerase; prostaglandin endoperoxide E2 isomerase; prostaglandin H-E isomerase; (5Z,13E)-(15S)-9a,11a-epidioxy-15-hydroxyprosta-5,13-dienoate E-isomerase

Systematic name: (5Z,13E,15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate E-isomerase

Comments: Brings about the opening of the epidioxy bridge. Requires glutathione.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 52227-79-9

References:

1. Ogino, N., Miyamoto, T., Yamamoto, S. and Hayaishi, O. Prostaglandin endoperoxide E isomerase from bovine vesicular gland microsomes, a glutathione-requiring enzyme. J. Biol. Chem. 252 (1977) 890-895. [PMID: 838703]

2. Tanaka, Y., Ward, S.L. and Smith, W.L. Immunochemical and kinetic evidence for two different prostaglandin H-prostaglandin E isomerases in sheep vesicular gland microsomes. J. Biol. Chem. 262 (1987) 1374-1381. [PMID: 3100531]

[EC 5.3.99.3 created 1976, modified 1990]

EC 5.3.99.4

Accepted name: prostaglandin-I synthase

Reaction: (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E)-(15S)-6,9α-epoxy-11α,15-dihydroxyprosta-5,13-dienoate

Other name(s): prostacyclin synthase; prostacycline synthetase; prostagladin I2 synthetase; PGI2 synthase; PGI2 synthetase

Systematic name: (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate 6-isomerase

Comments: A cytochrome P-450 heme-thiolate enzyme. Converts prostaglandin H2 into prostaglandin I2 (prostacyclin).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 65802-86-0

References:

1. DeWitt, D.L. and Smith, W.L. Purification of prostacyclin synthase from bovine aorta by immunoaffinity chromatography. Evidence that the enzyme is a hemoprotein. J. Biol. Chem. 258 (1983) 3285-3293. [PMID: 6338016]

2. Ullrich, V., Castle, L. and Weber, P. Spectral evidence for the cytochrome P450 nature of prostacyclin synthetase. Biochem. Pharmacol. 30 (1981) 2033-2036. [PMID: 7023490]

[EC 5.3.99.4 created 1984, modified 1990]

EC 5.3.99.5

Accepted name: thromboxane-A synthase

Reaction: (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E)-(15S)-9α,11α-epoxy-15-hydroxythromboxa-5,13-dienoate

Other name(s): thromboxane synthase; (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate thromboxane-A2-isomerase

Systematic name: (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate isomerase

Comments: A cytochrome P-450 heme-thiolate enzyme. Converts prostaglandin H2 into thromboxane A2.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 61276-89-9

References:

1. Shen, R.-F. and Tai, H.-H. Immunoaffinity purification and characterization of thromboxane synthase from porcine lung. J. Biol. Chem. 261 (1986) 11592-11599. [PMID: 3745158]

2. Ullrich, V. and Haurand, M. Thromboxane synthase as a cytochrome P450 enzyme. Adv. Prostaglandin Thromboxane Res. 11 (1983) 105-110.

[EC 5.3.99.5 created 1984, modified 1990]

EC 5.3.99.6

Accepted name: allene-oxide cyclase

Reaction: (9Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate = (15Z)-12-oxophyto-10,15-dienoate

Systematic name: (9Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate isomerase (cyclizing)

Comments: Allene oxides formed by the action of EC 4.2.1.92 hydroperoxide dehydratase, are converted into cyclopentenone derivatives.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 118390-59-3

References:

1. Hamberg, M. Biosynthesis of 12-oxo-10,15(Z)-phytodienoic acid: identification of an allene oxide cyclase. Biochem. Biophys. Res. Commun. 156 (1988) 543-550. [PMID: 3178850]

[EC 5.3.99.6 created 1992]

EC 5.3.99.7

Accepted name: styrene-oxide isomerase

Reaction: styrene oxide = phenylacetaldehyde

Other name(s): SOI

Systematic name: styrene-oxide isomerase (epoxide-cleaving)

Comments: Highly specific.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number: 124541-89-5

References:

1. Hartmans, S., Smits, J.P., van der Werf, M.J., Volkering, F. and de Bont, J.A.M. Metabolism of styrene oxide and 2-phenylethanol in the styrene-degrading Xanthobacter strain 124X. Appl. Environ. Microbiol. 55 (1989) 2850-2855.

[EC 5.3.99.7 created 1992]

EC 5.3.99.8

Accepted name: capsanthin/capsorubin synthase

Reaction: (1) violaxanthin = capsorubin

(2) antheraxanthin = capsanthin

For diagram click here (mechanism).

Other name(s): CCS; ketoxanthophyll synthase; capsanthin-capsorubin synthase

Systematic name: violaxanthin—capsorubin isomerase (ketone-forming)

Comments: This multifunctional enzyme is induced during chromoplast differentiation in plants [1]. Isomerization of the epoxide ring of violaxanthin gives the cyclopentyl-ketone of capsorubin or capsanthin.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 162032-85-1

References:

1. Bouvier, F., Hugueney, P., d'Harlingue, A., Kuntz, M. and Camara, B. Xanthophyll biosynthesis in chromoplasts: isolation and molecular cloning of an enzyme catalyzing the conversion of 5,6-epoxycarotenoid into ketocarotenoid. Plant J. 6 (1994) 45-54. [PMID: 7920703]

2. Lefebvre, V., Kuntz, M., Camara, B. and Palloix, A. The capsanthin-capsorubin synthase gene: a candidate gene for the y locus controlling the red fruit colour in pepper. Plant Mol. Biol. 36 (1998) 785-789. [PMID: 9526511]

3. Xu, C.J., Chen, D.M. and Zhang, S.L. [Molecular cloning of full length capsanthin/capsorubin synthase homologous gene from orange (Citrus sinensis).] Shi Yan Sheng Wu Xue Bao 34 (2001) 147-150. [PMID: 12549109] [Article in Chinese]

[EC 5.3.99.8 created 2005]

EC 5.3.99.9

Accepted name: neoxanthin synthase

Reaction: violaxanthin = neoxanthin

For diagram click here (mechanism).

Other name(s): NSY

Systematic name: violaxanthin—neoxanthin isomerase (epoxide-opening)

Comments: The opening of the epoxide ring of violaxanthin generates a chiral allene. Neoxanthin is a precursor of the plant hormone abscisic acid and the last product of carotenoid synthesis in green plants [2].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 318960-21-3

References:

1. Al-Babili, S., Hugueney, P., Schledz, M., Welsch, R., Frohnmeyer, H., Laule, O. and Beyer, P. Identification of a novel gene coding for neoxanthin synthase from Solanum tuberosum. FEBS Lett. 485 (2000) 168-172. [PMID: 11094161]

2. Bouvier, F., d'Harlingue, A., Backhaus, R.A., Kumagai, M.H. and Camara, B. Identification of neoxanthin synthase as a carotenoid cyclase paralog. Eur. J. Biochem. 267 (2000) 6346-6352. [PMID: 11029576]

[EC 5.3.99.9 created 2005]

EC 5.3.99.10

Accepted name: thiazole tautomerase

Reaction: 2-[(2R,5Z)-(2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate = 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate

For diagram of reaction click here.

Glossary: cThz*-P = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate
cThz-P = 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate = 4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylate

Other name(s): tenI (gene name)

Systematic name: 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate isomerase

Comments: The enzyme catalyses the irreversible aromatization of the thiazole moiety of 2-[(2R,5Z)-(2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate.

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

References:

1. Hazra, A.B., Han, Y., Chatterjee, A., Zhang, Y., Lai, R.Y., Ealick, S.E. and Begley, T.P. A missing enzyme in thiamin thiazole biosynthesis: identification of TenI as a thiazole tautomerase. J. Am. Chem. Soc. 133 (2011) 9311-9319. [PMID: 21534620]

[EC 5.3.99.10 created 2012]

EC 5.3.99.11

Accepted name: 2-keto-myo-inositol isomerase

Reaction: 2,4,6/3,5-pentahydroxycyclohexanone = 2D-2,3,5/4,6-pentahydroxycyclohexanone

For diagram of reaction click here.

Glossary: 2,4,6/3,5-pentahydroxycyclohexanone = (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone = scyllo-inosose

Other name(s): IolI; inosose isomerase; 2KMI isomerase.

Systematic name: 2,4,6/3,5-pentahydroxycyclohexanone 2-isomerase

Comments: Requires a divalent metal ion for activity. Mn2+, Fe2+ and Co2+ can be used. The enzyme, found in the bacterium Bacillus subtilis, is part of the myo-inositol/D-chiro-inositol degradation pathway leading to acetyl-CoA.

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

References:

1. Zhang, R.G., Dementieva, I., Duke, N., Collart, F., Quaite-Randall, E., Alkire, R., Dieckman, L., Maltsev, N., Korolev, O. and Joachimiak, A. Crystal structure of Bacillus subtilis ioli shows endonuclase IV fold with altered Zn binding. Proteins 48 (2002) 423-426. [PMID: 12112707]

2. Yoshida, K., Yamaguchi, M., Morinaga, T., Ikeuchi, M., Kinehara, M. and Ashida, H. Genetic modification of Bacillus subtilis for production of D-chiro-inositol, an investigational drug candidate for treatment of type 2 diabetes and polycystic ovary syndrome. Appl. Environ. Microbiol. 72 (2006) 1310-1315. [PMID: 16461681]

[EC 5.3.99.11 created 2014]


Continued with EC 5.4
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