Continued from EC 5.3.1 and EC 5.3.2
EC 5.3.3 Transposing C=C Bonds
EC 5.3.4 Transposing S-S Bonds
EC 5.3.99 Other Intramolecular Oxidoreductases
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 Δ5-Δ4-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.
Accepted name: isopentenyl-diphosphate Δ-isomerase
Reaction: 3-methylbut-3-en-1-yl diphosphate = prenyl diphosphate
For reaction pathway click here.
Other name(s): isopentenylpyrophosphate Δ-isomerase; methylbutenylpyrophosphate isomerase; isopentenylpyrophosphate isomerase
Systematic name: 3-methylbut-3-en-1-yl-diphosphate Δ3-Δ2-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.
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 Δ3-Δ2-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.
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 Δ3-Δ2-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.
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 Δ7-Δ8-isomerase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, 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]
Accepted name: methylitaconate Δ-isomerase
Reaction: methylitaconate = 2,3-dimethylmaleate
For diagram click here.
Other name(s): methylitaconate isomerase
Systematic name: methylitaconate Δ2-Δ3-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]
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 Δ2-Δ3-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.
Accepted name: Δ3-Δ2-enoyl-CoA isomerase
Reaction: (1) a (3Z)-alk-3-enoyl-CoA = a (2E)-alk-2-enoyl-CoA
(2) a (3E)-alk-3-enoyl-CoA = a (2E)-alk-2-enoyl-CoA
For diagram of reaction click here.
Other name(s): ECI (gene name); dodecenoyl-CoA isomerase; dodecenoyl-CoA Δ-isomerase; Δ3-cis-Δ2-trans-enoyl-CoA isomerase; acetylene-allene isomerase; dodecenoyl-CoA Δ3-cis-Δ2-trans-isomerase; dodecenoyl-CoA (3Z)-(2E)-isomerase
Systematic name: (3Z/3E)-alk-3-enoyl-CoA (2E)-isomerase
Comments: The enzyme participates in the β-oxidation of fatty acids with double bonds at an odd position. Processing of these substrates via the β-oxidation system results in intermediates with a cis- or trans-double bond at position C3, which cannot be processed further by the regular enzymes of the β-oxidation system. This enzyme isomerizes the bond to a trans bond at position C2, which can be processed further. The reaction rate is ten times higher for the (3Z) isomers than for (3E) isomers. The enzyme can also catalyse the isomerization of 3-acetylenic fatty acyl thioesters to 2,3-dienoyl fatty acyl thioesters.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 62213-29-0
References:
1. 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]
2. Stoffel, W. and Ecker, W. Δ3-cis,-Δ2-trans-Enoyl-CoA isomerase from rat liver mitochondria. Methods Enzymol. 14 (1969) 99-105.
3. 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]
4. 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]
5. Engeland, K. and Kindl, H. Purification and characterization of a plant peroxisomal Δ2,Δ3-enoyl-CoA isomerase acting on 3-cis-enoyl-CoA and 3-trans-enoyl-CoA. Eur. J. Biochem. 196 (1991) 699-705. [PMID: 2013292]
6. Geisbrecht, B.V., Zhang, D., Schulz, H. and Gould, S.J. Characterization of PECI, a novel monofunctional Δ3, Δ2-enoyl-CoA isomerase of mammalian peroxisomes. J. Biol. Chem. 274 (1999) 21797-21803. [PMID: 10419495]
7. Zhang, D., Yu, W., Geisbrecht, B.V., Gould, S.J., Sprecher, H. and Schulz, H. Functional characterization of Δ3,Δ2-enoyl-CoA isomerases from rat liver. J. Biol. Chem. 277 (2002) 9127-9132. [PMID: 11781327]
8. Goepfert, S., Vidoudez, C., Tellgren-Roth, C., Delessert, S., Hiltunen, J.K. and Poirier, Y. Peroxisomal Δ3,Δ2-enoyl CoA isomerases and evolution of cytosolic paralogues in embryophytes. Plant J. 56 (2008) 728-742. [PMID: 18657232]
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 Δ10-Δ11-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]
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 Δ2,Δ4-2-oxo,Δ3-isomerase
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, 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]
Accepted name: isopiperitenone Δ-isomerase
Reaction: isopiperitenone = piperitenone
Systematic name: isopiperitenone Δ8-Δ4-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]
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 Δ7,Δ2-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]
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 Δ8,11-Δ7,8-isomerase (incorrect); (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate Δ8,11-Δ7,9-isomerase (trans-double-bond-forming)
Systematic name: (5Z,8Z,11Z,14Z,17Z)-icosapentaenoate Δ8,11-Δ7,9-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]
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 5.3.3.15 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)]
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
For diagram of reaction click here.
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]
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, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, 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]
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, PDB, 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 5.3.3.20 Transferred entry: 2-hydroxyisobutanoyl-CoA mutase. Now EC 5.4.99.64, 2-hydroxyisobutanoyl-CoA mutase (EC 5.3.3.20 created 2016, deleted 2017)]
Accepted name: Δ3,5-Δ2,4-dienoyl-CoA isomerase
Reaction: a (3E,5Z)-alka-3,5-dienoyl-CoA = a (2E,4E)-alka-2,4-dienoyl-CoA
Other name(s): 3,5-tetradecadienoyl-CoA isomerase; DCI1 (gene name)
Systematic name: (3E,5Z)-alka-3,5-dienoyl-CoA Δ3,5-Δ2,4 isomerase
Comments: The enzyme participates in an alternative degradation route of fatty acids with cis-double bonds on odd-number carbons such as oleate and linoleate. The main physiological substrate is (3E,5Z)-tetradeca-3,5-dienoyl-CoA, but other (3E,5Z)-dienoyl-CoAs with varying carbon chain lengths are also substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Filppula, S.A., Yagi, A.I., Kilpelainen, S.H., Novikov, D., FitzPatrick, D.R., Vihinen, M., Valle, D. and Hiltunen, J.K. Δ3,5-Δ2,4-dienoyl-CoA isomerase from rat liver. Molecular characterization. J. Biol. Chem. 273 (1998) 349-355. [PMID: 9417087]
2. Modis, Y., Filppula, S.A., Novikov, D.K., Norledge, B., Hiltunen, J.K. and Wierenga, R.K. The crystal structure of dienoyl-CoA isomerase at 1.5 Å resolution reveals the importance of aspartate and glutamate sidechains for catalysis. Structure 6 (1998) 957-970. [PMID: 9739087]
3. Geisbrecht, B.V., Schulz, K., Nau, K., Geraghty, M.T., Schulz, H., Erdmann, R. and Gould, S.J. Preliminary characterization of Yor180Cp: identification of a novel peroxisomal protein of saccharomyces cerevisiae involved in fatty acid metabolism. Biochem. Biophys. Res. Commun. 260 (1999) 28-34. [PMID: 10381339]
4. Gurvitz, A., Mursula, A.M., Yagi, A.I., Hartig, A., Ruis, H., Rottensteiner, H. and Hiltunen, J.K. Alternatives to the isomerase-dependent pathway for the β-oxidation of oleic acid are dispensable in Saccharomyces cerevisiae. Identification of YOR180c/DCI1 encoding peroxisomal Δ(3,5)-Δ(2,4)-dienoyl-CoA isomerase. J. Biol. Chem. 274 (1999) 24514-24521. [PMID: 10455114]
5. Zhang, D., Liang, X., He, X.Y., Alipui, O.D., Yang, S.Y. and Schulz, H. Δ3,5,Δ2,4-dienoyl-CoA isomerase is a multifunctional isomerase. A structural and mechanistic study. J. Biol. Chem. 276 (2001) 13622-13627. [PMID: 11278886]
6. Goepfert, S., Vidoudez, C., Rezzonico, E., Hiltunen, J.K. and Poirier, Y. Molecular identification and characterization of the Arabidopsis Δ3,5,Δ2,4-dienoyl-coenzyme A isomerase, a peroxisomal enzyme participating in the β-oxidation cycle of unsaturated fatty acids. Plant Physiol. 138 (2005) 1947-1956. [PMID: 16040662]
Accepted name: lutein isomerase
Reaction: lutein = meso-zeaxanthin
For diagram of reaction click here.
Glossary: lutein = (3R,3'R)-dihydroxy-α-carotene
meso-zeaxanthin = (3R,3'S)-β,β-carotene-3,3'-diol
Other name(s): RPE65 (gene name); meso-zeaxanthin isomerase
Systematic name: lutein Δ4-Δ5-isomerase
Comments: The enzyme is found in the retinal pigment epithelium (RPE) of vertebrates. It also has the activity of EC 3.1.1.64, retinoid isomerohydrolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Shyam, R., Gorusupudi, A., Nelson, K., Horvath, M.P. and Bernstein, P.S. RPE65 has an additional function as the lutein to meso-zeaxanthin isomerase in the vertebrate eye. Proc. Natl Acad. Sci. USA 114 (2017) 10882-10887. [PMID: 28874556]
Accepted name: S-methyl-5-thioribulose 1-phosphate isomerase
Reaction: (1) S-methyl-5-thio-D-ribulose 1-phosphate = S-methyl-1-thio-D-xylulose 5-phosphate
(2) S-methyl-5-thio-D-ribulose 1-phosphate = S-methyl-1-thio-D-ribulose 5-phosphate
Other name(s): rlp (gene name); 5-methylthioribulose-1-phosphate isomerase (incorrect)
Systematic name: S-methyl-5-thio-D-ribulose 1-phosphate 1,3-isomerase
Comments: The enzyme, characterized from the bacterium Rhodospirillum rubrum, participates in methionine salvage from S-methyl-5'-thioadenosine. It is a RubisCO-like protein (RLP) that is not capable of carbon fixation, and catalyses an isomerization reaction that converts S-methyl-5-thio-D-ribulose 1-phosphate to a 3:1 mixture of S-methyl-1-thioxylulose 5-phosphate and S-methyl-1-thioribulose 5-phosphate. The reaction is an overall 1,3-proton transfer, which likely consists of two 1,2-proton transfer events.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Imker, H.J., Singh, J., Warlick, B.P., Tabita, F.R. and Gerlt, J.A. Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum. Biochemistry 47 (2008) 11171-11173. [PMID: 18826254]
2. Erb, T.J., Evans, B.S., Cho, K., Warlick, B.P., Sriram, J., Wood, B.M., Imker, H.J., Sweedler, J.V., Tabita, F.R. and Gerlt, J.A. A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis. Nat. Chem. Biol. 8 (2012) 926-932. [PMID: 23042035]
Accepted name: neopinone isomerase
Reaction: neopinone = codeinone
For diagram of reaction click here
Glossary: neopinone = 3-methoxy-17-methyl-8,14-didehydro-4,5α-epoxymorphinan-6-one
codeinone = 3-methoxy-17-methyl-7,8-didehydro-4,5α-epoxymorphinan-6-one
Other name(s): NISO (gene name)
Systematic name: neopinone Δ8-Δ7-isomerase
Comments: The enzyme, characterized from the opium poppy (Papaver somniferum), participates in the biosynthesis of morphine. It also catalyses the isomerization of neomorphinone and morphinone.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Dastmalchi, M., Chen, X., Hagel, J.M., Chang, L., Chen, R., Ramasamy, S., Yeaman, S. and Facchini, P.J. Neopinone isomerase is involved in codeine and morphine biosynthesis in opium poppy. Nat. Chem. Biol. 15 (2019) 384-390. [PMID: 30886433]
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]
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]
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]
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]
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.
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]
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, EAWAG-BBD, EXPASY, KEGG, Metacyc, 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.
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]
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]
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 = 4-methyl-5-[2-(phosphooxy)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, PDB, 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]
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, PDB, 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]
Accepted name: lachrymatory-factor synthase
Reaction: (E)-alk-1-en-1-SO-peroxol = (Z)-alkanethial oxide
Glossary: alk-1-en-1-SO-peroxol = S-alk-1-en-1-ylthiohydroperoxide
alkanethial oxide = alkylidene-λ4-sulfanone = (alkylidenesulfaniumyl)oxidanide
Other name(s): LFS
Systematic name: (E)-alk-1-en-1-SO-peroxol isomerase [(Z)-alkanethial S-oxide-forming]
Comments: The enzyme is responsible for production of the irritating lachrymatory factor that is released by onions and related species when they are chopped. It acts of the product of EC 4.4.1.4, alliin lyase. The enzyme from Allium cepa (onion) acts on (E)-prop-1-en-1-SO-peroxol and produces (Z)-propanethial oxide, while the enzyme from Allium siculum (honey garlic) acts on (E)-but-1-en-1-SO-peroxol and produces (Z)-butanethial oxide.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Norris, P.G., Nunn, A.V., Hawk, J.L. and Cox, T.M. Genetic heterogeneity in erythropoietic protoporphyria: a study of the enzymatic defect in nine affected families. J. Invest. Dermatol. 95 (1990) 260-263. [PMID: 2384686]
2. Imai, S., Tsuge, N., Tomotake, M., Nagatome, Y., Sawada, H., Nagata, T. and Kumagai, H. Plant biochemistry: an onion enzyme that makes the eyes water. Nature 419 (2002) 685. [PMID: 12384686]
3. Eady, C.C., Kamoi, T., Kato, M., Porter, N.G., Davis, S., Shaw, M., Kamoi, A. and Imai, S. Silencing onion lachrymatory factor synthase causes a significant change in the sulfur secondary metabolite profile. Plant Physiol. 147 (2008) 2096-2106. [PMID: 18583530]
4. Kubec, R., Cody, R.B., Dane, A.J., Musah, R.A., Schraml, J., Vattekkatte, A. and Block, E. Applications of direct analysis in real time-mass spectrometry (DART-MS) in Allium chemistry. (Z)-butanethial S-oxide and 1-butenyl thiosulfinates and their S-(E)-1-butenylcysteine S-oxide precursor from Allium siculum. J. Agric. Food Chem. 58 (2010) 1121-1128. [PMID: 20047275]
Accepted name: 4'-phospho-dehydrooxetanocin synthase
Reaction: dAMP + S-adenosyl-L-methionine = 4'-phospho-dehydrooxetanocin + 5'-deoxyadenosine + L-methionine (overall reaction)
(1a) S-adenosyl-L-methionine + reduced acceptor = 5'-deoxyadenosin-5'-yl radical + L-methionine + acceptor
(1b) 5'-deoxyadenosin-5'-yl radical + dAMP + acceptor = 4'-phospho-dehydrooxetanocin + 5'-deoxyadenosine + reduced acceptor
Glossary: oxetanocin A = [(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)oxetane-2,3-diyl]dimethanol
Other name(s): oxsB (gene name)
Systematic name: dAMP isomerase (4'-phospho-dehydrooxetanocin-forming)
Comments: The enzyme is a B12-dependent radical SAM (AdoMet) enzyme involved in the biosynthesis of oxetanocin A. The enzyme catalyses an oxidative ring contraction, forming an oxetane aldehyde. The reaction requires S-adenosyl-L-methionine, a cobalamin cofactor, and a reductant (the reductant does not show in the overall reaction because it is being restored during the cycle). The reaction is initiated by formation of 5'-deoxyadenosin-5'-yl radical, which then abstracts a hydrogen atom from C2'. The enzyme is also able to catalyse the radical mediated, stereoselective C2'-methylation of dAMP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Bridwell-Rabb, J., Zhong, A., Sun, H.G., Drennan, C.L. and Liu, H.W. A B12-dependent radical SAM enzyme involved in oxetanocin A biosynthesis. Nature 544 (2017) 322-326. [PMID: 28346939]
2. Lee, Y.H., Yeh, Y.C., Fan, P.H., Zhong, A., Ruszczycky, M.W. and Liu, H.W. Changing Fates of the Substrate Radicals Generated in the Active Sites of the B12-Dependent Radical SAM Enzymes OxsB and AlsB. J. Am. Chem. Soc. 145 (2023) 3656-3664. [PMID: 36719327]