Continued from EC 4.3.1 to EC 4.3.99
EC 4.4 Carbon-Sulfur Lyases
EC 4.5 Carbon-Halide Lyases
EC 4.6 Phosphorus-Oxygen Lyases
EC 4.8 Nitrogen-oxygen Lyases
EC 4.98 ATP-independent Chelatases
EC 4.99 Other Lyases
Accepted name: cystathionine γ-lyase
Reaction: L-cystathionine + H2O = L-cysteine + 2-oxobutanoate + NH3 (overall reaction)
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
(1b) 2-aminobut-2-enoate = 2-iminobutanoate (spontaneous)
(1c) 2-iminobutanoate + H2O = 2-oxobutanoate + NH3 (spontaneous)
For diagram of reaction click here and mechanism click here.
Other name(s): homoserine deaminase; homoserine dehydratase; cystine desulfhydrase; cysteine desulfhydrase; γ-cystathionase; cystathionase; homoserine deaminase-cystathionase; γ-CTL; cystalysin; cysteine lyase; L-cystathionine cysteine-lyase (deaminating)
Systematic name: L-cystathionine cysteine-lyase (deaminating; 2-oxobutanoate-forming)
Comments: A multifunctional pyridoxal-phosphate protein. The enzyme cleaves a carbon-sulfur bond, releasing L-cysteine and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form 2-oxobutanoate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. Also catalyses the conversion of L-homoserine to 2-oxobutanoate and ammonia, of L-cystine to thiocysteine, pyruvate and ammonia, and of L-cysteine to pyruvate, hydrogen sulfide and ammonia.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9012-96-8
References:
1. Braunstein, A.E. and Azarkh, R.M. [Participation of vitamin B6 in enzymic formation of hydrogen sulfide from L-cysteine.] Dokl. Akad. Nauk. S.S.S.R. 71 (1950) 93-96. (in Russian)
2. Braunstein, A.E. and Azarkh, R.M. [Phosphopyridoxal in aerobic deamination of homoserine and serine.] Dokl. Akad. Nauk. S.S.S.R. 85 (1952) 385-388. (in Russian)
3. Flavin, M. and Segal, A. Purification and properties of the cystathionine γ-cleavage enzyme of Neurospora. J. Biol. Chem. 239 (1964) 2220-2227. [PMID: 14209951]
4. Matsuo, Y. and Greenberg, D.M. A crystalline enzyme that cleaves homoserine and cystathionine. III. Coenzyme resolution, activation, and inhibitors. J. Biol. Chem. 234 (1959) 507-515. [PMID: 13641250]
5. Matsuo, Y. and Greenberg, D.M. A crystalline enzyme that cleaves homoserine and cystathionine. IV. Mechanism of action, reversibility, and substrate specificity. J. Biol. Chem. 234 (1959) 516-519. [PMID: 13641251]
Accepted name: homocysteine desulfhydrase
Reaction: L-homocysteine + H2O = hydrogen sulfide + NH3 + 2-oxobutanoate (overall reaction)
(1a) L-homocysteine = hydrogen sulfide + 2-aminobut-2-enoate
(1b) 2-aminobut-2-enoate = 2-iminobutanoate (spontaneous)
(1c) 2-iminobutanoate + H2O = 2-oxobutanoate + NH3 (spontaneous)
For diagram click here.
Other name(s): homocysteine desulfurase; L-homocysteine hydrogen-sulfide-lyase (deaminating)
Systematic name: L-homocysteine hydrogen-sulfide-lyase (deaminating; 2-oxobutanoate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme cleaves a carbon-sulfur bond, releasing hydrogen sulfide and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form 2-oxobutanoate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-41-3
References:
1. Kallio, R.E. Function of pyridoxal phosphate in desulfhydrase systems of Proteus morganii. J. Biol. Chem. 192 (1951) 371-377. [PMID: 14917685]
Accepted name: dimethylpropiothetin dethiomethylase
Reaction: S,S-dimethyl-β-propiothetin = dimethyl sulfide + acrylate
For diagram of reaction click here.
Other name(s): desulfhydrase; S,S-dimethyl-β-propiothetin dimethyl-sulfide-lyase
Systematic name: S,S-dimethyl-β-propiothetin dimethyl-sulfide-lyase (acrylate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9026-85-1
References:
1. Cantoni, G.L. and Anderson, D.G. Enzymatic cleavage of dimethylpropiothetin by Polysiphonia lanosa. J. Biol. Chem. 222 (1956) 171-177. [PMID: 13366990]
Accepted name: alliin lyase
Reaction: an S-alkyl-L-cysteine S-oxide = an alkyl sulfenate + 2-aminoacrylate
Other name(s): alliinase; cysteine sulfoxide lyase; alkylcysteine sulfoxide lyase; S-alkylcysteine sulfoxide lyase; L-cysteine sulfoxide lyase; S-alkyl-L-cysteine sulfoxide lyase; alliin alkyl-sulfenate-lyase
Systematic name: S-alkyl-L-cysteine S-oxide alkyl-sulfenate-lyase (2-aminoacrylate-forming)
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9031-77-0
References:
1. Durbin, R.D. and Uchytil, T.F. Purification and properties of alliin lyase from the fungus Penicillium corymbiferum. Biochim. Biophys. Acta 235 (1971) 518-520.
2. Goryachenkova, E.V. [Enzyme in garlic which forms allycine (allyinase), a protein with phosphopyridoxal.] Dokl. Akad. Nauk. S.S.S.R. 87 (1952) 457-460. (in Russian)
3. Jacobsen, J.V., Yamaguchi, M., Howard, F.D. and Bernhard, R.A. Product inhibition of the cysteine sulfoxide lyase of Tulbaghia violacea. Arch. Biochem. Biophys. 127 (1968) 252-258.
Accepted name: lactoylglutathione lyase
Reaction: (R)-S-lactoylglutathione = glutathione + methylglyoxal
Glossary: methylglyoxal = 2-oxopropanal
Other name(s): methylglyoxalase; aldoketomutase; ketone-aldehyde mutase; glyoxylase I; (R)-S-lactoylglutathione methylglyoxal-lyase (isomerizing)
Systematic name: (R)-S-lactoylglutathione methylglyoxal-lyase (isomerizing; glutathione-forming)
Comments: Also acts on 3-phosphoglycerol-glutathione.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9033-12-9
References:
1. Ekwall, K. and Mannervik, B. The stereochemical configuration of the lactoyl group of S-lactoylglutathionine formed by the action of glyoxalase I from porcine erythrocytes and yeast. Biochim. Biophys. Acta 297 (1973) 297-299. [PMID: 4574550]
2. Racker, E. The mechanism of action of glyoxalase. J. Biol. Chem. 190 (1951) 685-696. [PMID: 14841219]
[EC 4.4.1.6 Transferred entry: S-alkylcysteine lyase. Now included in EC 4.4.1.13, cysteine-S-conjugate β-lyase (EC 4.4.1.6 created 1965, deleted 1972, reinstated 1976, deleted 2018)]
[EC 4.4.1.7 Deleted entry: S-(hydroxyalkyl)glutathione lyase. Now included with EC 2.5.1.18 glutathione transferase (EC 4.4.1.7 created 1972, deleted 1976)]
[EC 4.4.1.8 Transferred entry: cystathionine β-lyase. Now included in EC 4.4.1.13, cysteine-S-conjugate β-lyase (EC 4.4.1.8 created 1972, deleted 2018)]
Accepted name: L-3-cyanoalanine synthase
Reaction: L-cysteine + hydrogen cyanide = hydrogen sulfide + L-3-cyanoalanine
Other name(s): β-cyanoalanine synthase; β-cyanoalanine synthetase; β-cyano-L-alanine synthase; L-cysteine hydrogen-sulfide-lyase (adding HCN)
Systematic name: L-cysteine hydrogen-sulfide-lyase (adding hydrogen cyanide; L-3-cyanoalanine-forming)
Comments: Contains pyridoxal phospate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9059-53-4
References:
1. Akopyan, T.N., Braunstein, A.E. and Goryachenkova, E.V. β-Cyanoalanine synthase: purification and characterization. Proc. Natl. Acad. Sci. USA 72 (1975) 1617-1621. [PMID: 1055433]
2. Castric, P.A. and Conn, E.E. Formation of β-cyanoalanine by O-acetylserine sulfhydrylase. J. Bacteriol. 108 (1971) 132-136. [PMID: 5001194]
3. Hendrickson, H.R. The β-cyanoalanine synthase of blue lupine. Fed. Proc. 27 (1968) 593 only.
4. Hendrickson, H.R. and Conn, E.E. Cyanide metabolism in higher plants. IV. Purification and properties of the β-cyanoalanine synthase of blue lupine. J. Biol. Chem. 244 (1969) 2632-2640. [PMID: 5769995]
Accepted name: cysteine lyase
Reaction: L-cysteine + sulfite = L-cysteate + hydrogen sulfide
For diagram click here.
Other name(s): cysteine (sulfite) lyase; L-cysteine hydrogen-sulfide-lyase (adding sulfite)
Systematic name: L-cysteine hydrogen-sulfide-lyase (adding sulfite; L-cysteate-forming)
Comments: A pyridoxal-phosphate protein. Can use a second molecule of cysteine (producing lanthionine), or other alkyl thiols, as a replacing agent.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9079-86-1
References:
1. Tolosa, E.A., Chepurnova, N.K., Khomutov, R.M. and Severin, E.S. Reactions catalysed by cysteine lyase from the yolk sac of chicken embryo. Biochim. Biophys. Acta 171 (1969) 369-371. [PMID: 5813025]
Accepted name: methionine γ-lyase
Reaction: L-methionine + H2O = methanethiol + NH3 + 2-oxobutanoate (overall reaction)
(1a) L-methionine = methanethiol + 2-aminobut-2-enoate
(1b) 2-aminobut-2-enoate = 2-iminobutanoate (spontaneous)
(1c) 2-iminobutanoate + H2O = 2-oxobutanoate + NH3 (spontaneous)
For diagram click here.
Other name(s): L-methioninase; methionine lyase; methioninase; methionine dethiomethylase; L-methionine γ-lyase; L-methionine methanethiol-lyase (deaminating)
Systematic name: L-methionine methanethiol-lyase (deaminating; 2-oxobutanoate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme cleaves a carbon-sulfur bond, releasing methanethiol and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form 2-oxobutanoate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. The enzyme is involved in L-methionine catabolism.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 42616-25-1
References:
1. Kreis, W. and Hession, C. Isolation and purification of L-methionine-α-deamino-γ-mercaptomethane-lyase (L-methioninase) from Clostridium sporogenes. Cancer Res. 33 (1973) 1862-1865. [PMID: 4720797]
[EC 4.4.1.12 Deleted entry: sulfoacetaldehyde lyase. Activity due to EC 2.3.3.15, sulfoacetaldehyde acetyltransferase. (EC 4.4.1.12 created 1976, deleted 2003)]
Accepted name: cysteine-S-conjugate β-lyase
Reaction: an L-cysteine-S-conjugate + H2O = a thiol + NH3 + pyruvate (overall reaction)
(1a) an L-cysteine-S-conjugate = a thiol + 2-aminoprop-2-enoate
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + NH3 (spontaneous)
Other name(s): cysteine conjugate β-lyase; glutamine transaminase K/cysteine conjugate β-lyase; L-cysteine-S-conjugate thiol-lyase (deaminating); cystathionine β-lyase; β-cystathionase; cystine lyase; cystathionine L-homocysteine-lyase (deaminating); L-cystathionine L-homocysteine-lyase (deaminating); CBL; S-alkylcysteine lyase; S-alkylcysteinase; alkylcysteine lyase; S-alkyl-L-cysteine lyase; S-alkyl-L-cysteinase; alkyl cysteine lyase; S-alkyl-L-cysteine alkylthiol-lyase (deaminating)
Systematic name: L-cysteine-S-conjugate thiol-lyase (deaminating; pyruvate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme can act on a broad range of L-cysteine-S-conjugates, including aromatic conjugates such as 4-bromobenzene and 2,4-dinitrobenzene. The enzyme cleaves a carbon-sulfur bond, releasing a thiol and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 68652-57-3
References:
1. Tateishi, M., Suzuki, S. and Shimizu, H. Cysteine conjugate β-lyase in rat liver. A novel enzyme catalyzing formation of thiol-containing metabolites of drugs. J. Biol. Chem. 253 (1978) 8854-8859. [PMID: 721818]
Accepted name: 1-aminocyclopropane-1-carboxylate synthase
Reaction: S-adenosyl-L-methionine = 1-aminocyclopropane-1-carboxylate + S-methyl-5'-thioadenosine
For diagram of reaction click here
Glossary: S-methyl-5'-thioadenosine = 5'-deoxy-5'-(methylsulfanyl)adenosine
Other name(s): 1-aminocyclopropanecarboxylate synthase; 1-aminocyclopropane-1-carboxylic acid synthase; 1-aminocyclopropane-1-carboxylate synthetase; aminocyclopropanecarboxylic acid synthase; aminocyclopropanecarboxylate synthase; ACC synthase; S-adenosyl-L-methionine methylthioadenosine-lyase; S-adenosyl-L-methionine methylthioadenosine-lyase (1-aminocyclopropane-1-carboxylate-forming)
Systematic name: S-adenosyl-L-methionine S-methyl-5'-thioadenosine-lyase (1-aminocyclopropane-1-carboxylate-forming)
Comments: A pyridoxal 5'-phosphate protein. The enzyme catalyses an α,γ-elimination.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 72506-68-4
References:
1. Boller, T., Herner, R.C. and Kende, H. Assay for and enzymatic formation of an ethylene precursor, 1-aminocyclopropane-1-carboxylic acid. Planta 145 (1979) 293-303. [PMID: 24317737]
2. Yu, Y.-B., Adams, D.O. and Yang, S.F. 1-Aminocyclopropanecarboxylate synthase, a key enzyme in ethylene biosynthesis. Arch. Biochem. Biophys. 198 (1979) 280-296. [PMID: 507845]
Accepted name: D-cysteine desulfhydrase
Reaction: D-cysteine + H2O = sulfide + NH3 + pyruvate
Other name(s): D-cysteine lyase; D-cysteine sulfide-lyase (deaminating)
Systematic name: D-cysteine sulfide-lyase (deaminating; pyruvate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 84012-74-8
References:
1. Nagasawa, T., Ishii, T., Kumagai, H. and Yamada, H. D-Cysteine desulfhydrase of Escherichia coli. Purification and characterization. Eur. J. Biochem. 153 (1985) 541-551. [PMID: 3908101]
2. Schmidt, A. A cysteine desulfhydrase from spinach leaves specific for D-cysteine. Z. Pflanzenphysiol. 107 (1982) 301-312.
3. Schmidt, A. and Erdle, I. A cysteine desulfhydrase specific for D-cysteine from the green-alga Chlorella fusca. Z. Naturforsch. C: Biosci. 38 (1983) 428-435.
Accepted name: selenocysteine lyase
Reaction: L-selenocysteine + reduced acceptor = selenide + L-alanine + acceptor
Glossary: dithiothreitol = 1,4-bis(sulfanyl)butane-2,3-diol
Other name(s): selenocysteine reductase; selenocysteine β-lyase
Systematic name: L-selenocysteine selenide-lyase (L-alanine-forming)
Comments: A pyridoxal-phosphate protein. Dithiothreitol or 2-sulfanylethan-1-ol (2-mercaptoethanol) can act as the reducing agent in the reaction. The enzyme from animals does not act on cysteine, serine or chloroalanine [1,3], while the enzyme from bacteria shows activity with cysteine (cf. EC 2.8.1.7, cysteine desulfurase) [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 82047-76-5
References:
1. Esaki, N., Nakamura, T., Tanaka, H. and Soda, K. Selenocysteine lyase, a novel enzyme that specifically acts on selenocysteine. Mammalian distribution and purification and properties of pig liver enzyme. J. Biol. Chem. 257 (1982) 4386-4391. [PMID: 6461656]
2. Mihara, H., Kurihara, T., Yoshimura, T., Soda, K. and Esaki, N. Cysteine sulfinate desulfinase, a NIFS-like protein of Escherichia coli with selenocysteine lyase and cysteine desulfurase activities. Gene cloning, purification, and characterization of a novel pyridoxal enzyme. J. Biol. Chem. 272 (1997) 22417-22424. [PMID: 9278392]
3. Omi, R., Kurokawa, S., Mihara, H., Hayashi, H., Goto, M., Miyahara, I., Kurihara, T., Hirotsu, K. and Esaki, N. Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase. J. Biol. Chem. 285 (2010) 12133-12139. [PMID: 20164179]
Accepted name: holocytochrome-c synthase
Reaction: holocytochrome c = apocytochrome c + heme
Other name(s): cytochrome c heme-lyase; holocytochrome c synthetase; holocytochrome-c apocytochrome-c-lyase
Systematic name: holocytochrome-c apocytochrome-c-lyase (heme-forming)
Comments: In the reverse direction, the enzyme catalyses the attachment of heme to two cysteine residues in the protein, forming thioether links.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 75139-03-6
References:
1. Dumont, M.E., Ernst, J.F., Hampsey, D.M. and Sherman, F. Identification and sequence of the gene encoding cytochrome c heme lyase in the yeast Saccharomyces cerevisiae. EMBO J. 6 (1987) 235-241. [PMID: 3034577]
[EC 4.4.1.18 Transferred entry: now EC 1.8.3.5, prenylcysteine lyase (EC 4.4.1.18 created 2000, deleted 2002)]
Accepted name: phosphosulfolactate synthase
Reaction: (2R)-2-O-phospho-3-sulfolactate = phosphoenolpyruvate + sulfite
For diagram of reaction click here (mechanism)
Glossary: bisulfite = HSO3–
Other name(s): (2R)-phospho-3-sulfolactate synthase; (2R)-O-phospho-3-sulfolactate sulfo-lyase
Systematic name: (2R)-2-O-phospho-3-sulfolactate hydrogen-sulfite-lyase (phosphoenolpyruvate-forming)
Comments: Requires Mg2+. The enzyme from the archaeon Methanococcus jannaschii catalyses the Michael addition of sulfite to phosphoenolpyruvate. It specifically requires phosphoenolpyruvate and its broad alkaline pH optimum suggests that it uses sulfite rather than hydrogensulfite.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 473575-53-0
References:
1. Graham, D.E., Xu, H. and White, R.H. Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes. J. Biol. Chem. 277 (2002) 13421-13429. [PMID: 11830598]
Accepted name: leukotriene-C4 synthase
Reaction: leukotriene C4 = leukotriene A4 + glutathione
For diagram click here.
Other name(s): leukotriene C4 synthetase; LTC4 synthase; LTC4 synthetase; leukotriene A4:glutathione S-leukotrienyltransferase; (7E,9E,11Z,14Z)-(5S,6R)-5,6-epoxyicosa-7,9,11,14-tetraenoate:glutathione leukotriene-transferase (epoxide-ring-opening); (7E,9E,11Z,14Z)-(5S,6R)-6-(glutathion-S-yl)-5-hydroxyicosa-7,9,11,14-tetraenoate glutathione-lyase (epoxide-forming)
Systematic name: leukotriene-C4 glutathione-lyase (leukotriene-A4-forming)
Comments: The reaction proceeds in the direction of addition. Not identical with EC 2.5.1.18, glutathione transferase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 90698-32-1
References:
1. Bach, M.K., Brashler, J.R. and Morton, D.R., Jr. Solubilization and characterization of the leukotriene C4 synthetase of rat basophil leukemia cells: a novel, particulate glutathione S-transferase. Arch. Biochem. Biophys. 230 (1984) 455-465. [PMID: 6324687]
2. Shimizu, T. Enzymes functional in the syntheses of leukotrienes and related compounds. Int. J. Biochem. 20 (1988) 661-666. [PMID: 2846379]
3. Lam, B.K. and Austen, K.F. Leukotriene C4 synthase: a pivotal enzyme in cellular biosynthesis of the cysteinyl leukotrienes. Prostaglandins Other Lipid Mediat. 68-69 (2002) 511-520. [PMID: 12432940]
4. Christmas, P., Weber, B.M., McKee, M., Brown, D. and Soberman, R.J. Membrane localization and topology of leukotriene C4 synthase. J. Biol. Chem. 277 (2002) 28902-28908. [PMID: 12023288]
Accepted name: S-ribosylhomocysteine lyase
Reaction: S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione
For diagram click here.
Other name(s): S-ribosylhomocysteinase; LuxS
Systematic name: S-(5-deoxy-D-ribos-5-yl)-L-homocysteine L-homocysteine-lyase [(4S)-4,5-dihydroxypentan-2,3-dione-forming]
Comments: Contains Fe2+. The 4,5-dihydroxypentan-2,3-dione formed spontaneously cyclizes and combines with borate to form an autoinducer (AI-2) in the bacterial quorum-sensing mechanism, which is used by many bacteria to control gene expression in response to cell density [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37288-63-4
References:
1. Zhu, J., Dizin, E., Hu, X., Wavbreille, A.S., Park, J. and Pei, D. S-Ribosylhomocysteinase (LuxS) is a mononuclear iron protein. Biochemistry 42 (2003) 4717-4726. [PMID: 12705835]
2. Miller, M.B. and Bassler, B.L. Quorum sensing in bacteria. Annu. Rev. Microbiol. 55 (2001) 165-199. [PMID: 11544353]
Accepted name: S-(hydroxymethyl)glutathione synthase
Reaction: S-(hydroxymethyl)glutathione = glutathione + formaldehyde
Other name(s): glutathione-dependent formaldehyde-activating enzyme; Gfa; S-(hydroxymethyl)glutathione formaldehyde-lyase
Systematic name: S-(hydroxymethyl)glutathione formaldehyde-lyase (glutathione-forming)
Comments: The enzyme from Paracoccus denitrificans accelerates the spontaneous reaction in which the adduct of formaldehyde and glutathione is formed, i.e. the substrate for EC 1.1.1.284, S-(hydroxymethyl)glutathione dehydrogenase, in the formaldehyde-detoxification pathway.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 425642-27-9
References:
1. Goenrich, M., Bartoschek, S., Hagemeier, C.H., Griesinger, C. and Vorholt, J.A. A glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans detected and purified via two-dimensional proton exchange NMR spectroscopy. J. Biol. Chem. 277 (2002) 3069-3072. [PMID: 11741920]
Accepted name: 2-hydroxypropyl-CoM lyase
Reaction: (1) (R)-2-hydroxypropyl-CoM = (R)-1,2-epoxypropane + HS-CoM
(2) (S)-2-hydroxypropyl-CoM = (S)-1,2-epoxypropane + HS-CoM
For diagram click here.
Glossary:
coenzyme M (CoM) = 2-sulfanylethan-1-ol = 2-mercaptoethanesulfonate (deprecated)
Other name(s): epoxyalkane:coenzyme M transferase; epoxyalkane:CoM transferase; epoxyalkane:2-mercaptoethanesulfonate transferase; coenzyme M-epoxyalkane ligase; epoxyalkyl:CoM transferase; epoxypropane:coenzyme M transferase; epoxypropyl:CoM transferase; EaCoMT; 2-hydroxypropyl-CoM:2-mercaptoethanesulfonate lyase (epoxyalkane-ring-forming); (R)-[or (S)-]2-hydroxypropyl-CoM:2-mercaptoethanesulfonate lyase (epoxyalkane-ring-forming); (R)-2-hydroxypropyl-CoM 2-mercaptoethanesulfonate lyase (cyclizing; (R)-1,2-epoxypropane-forming)
Systematic name: (R)-2-hydroxypropyl-CoM:2-sulfanylethanesulfonate lyase (cyclizing; (R)-1,2-epoxypropane-forming)
Comments: Requires zinc. Acts on both enantiomers of chiral epoxyalkanes to form the corresponding (R)- and (S)-2-hydroxyalkyl-CoM adducts. The enzyme will function with some other thiols (e.g., 2-sulfanylethanol) as the nucleophile. Uses short-chain epoxyalkanes from C2 (epoxyethane) to C6 (1,2-epoxyhexane). This enzyme forms component I of a four-component enzyme system {comprising EC 4.4.1.23 (2-hydroxypropyl-CoM lyase; component I), EC 1.8.1.5 [2-oxopropyl-CoM reductase (carboxylating); component II], EC 1.1.1.268 [2-(R)-hydroxypropyl-CoM dehydrogenase; component III] and EC 1.1.1.269 [2-(S)-hydroxypropyl-CoM dehydrogenase; component IV]} that is involved in epoxyalkane carboxylation in Xanthobacter sp. strain Py2.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 244301-07-3
References:
1. Allen, J.R., Clark, D.D., Krum, J.G. and Ensign, S.A. A role for coenzyme M (2-mercaptoethanesulfonic acid) in a bacterial pathway of aliphatic epoxide carboxylation. Proc. Natl. Acad. Sci. USA 96 (1999) 8432-8437. [PMID: 10411892]
2. Krum, J.G., Ellsworth, H., Sargeant, R.R., Rich, G. and Ensign, S.A. Kinetic and microcalorimetric analysis of substrate and cofactor interactions in epoxyalkane:CoM transferase, a zinc-dependent epoxidase. Biochemistry 41 (2002) 5005-5014. [PMID: 11939797]
3. Coleman, N.V. and Spain, J.C. Epoxyalkane: coenzyme M transferase in the ethene and vinyl chloride biodegradation pathways of Mycobacterium strain JS60. J. Bacteriol. 185 (2003) 5536-5545. [PMID: 12949106]
Accepted name: (2R)-sulfolactate sulfo-lyase
Reaction: (2R)-3-sulfolactate = pyruvate + hydrogensulfite
Other name(s): Suy; SuyAB; 3-sulfolactate bisulfite-lyase; sulfolactate sulfo-lyase (ambigious); (2R)-3-sulfolactate bisulfite-lyase (pyruvate-forming)
Systematic name: (2R)-3-sulfolactate hydrogensulfite-lyase (pyruvate-forming)
Comments: Requires iron(II). This inducible enzyme participates in cysteate degradation by the bacterium Paracoccus pantotrophus NKNCYSA and in 3-sulfolactate degradation by the bacterium Chromohalobacter salexigens. The enzyme is specific for the (R) isomer of its substrate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 1256650-35-7
References:
1. Graham, D.E. and White, R.H. Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat. Prod. Rep. 19 (2002) 133-147. [PMID: 12013276]
2. Rein, U., Gueta, R., Denger, K., Ruff, J., Hollemeyer, K. and Cook, A.M. Dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in Paracoccus pantotrophus NKNCYSA. Microbiology 151 (2005) 737-747. [PMID: 15758220]
3. Denger, K. and Cook, A.M. Racemase activity effected by two dehydrogenases in sulfolactate degradation by Chromohalobacter salexigens: purification of (S)-sulfolactate dehydrogenase. Microbiology 156 (2010) 967-974. [PMID: 20007648]
Accepted name: L-cysteate sulfo-lyase
Reaction: L-cysteate + H2O = HSO3– + pyruvate + NH3 (overall reaction)
(1a) L-cysteate = HSO3– + 2-aminoprop-2-enoate
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + NH3 (spontaneous)
Glossary: L-cysteate = (2S)-2-amino-3-sulfopropanoate
bisulfite = HSO3–
Other name(s): L-cysteate sulfo-lyase (deaminating); CuyA
Systematic name: L-cysteate bisulfite-lyase (deaminating; pyruvate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme cleaves a carbon-sulfur bond, releasing bisulfite and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. D-Cysteine can also act as a substrate, but more slowly. It is converted into hydrogen sulfide, pyruvate, and ammonia. This inducible enzyme from the marine bacterium Silicibacter pomeroyi DSS-3 forms part of the cysteate-degradation pathway.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Denger, K., Smits, T.H. and Cook, A.M. L-cysteate sulpho-lyase, a widespread, pyridoxal 5'-phosphate-coupled desulphonative enzyme purified from Silicibacter pomeroyi DSS-3 T. Biochem. J. 394 (2005) 657-664. [PMID: 16302849]
Accepted name: olivetolic acid cyclase
Reaction: 3,5,7-trioxododecanoyl-CoA = CoA + 2,4-dihydroxy-6-pentylbenzoate
For diagram of reaction click here.
Glossary: 2,4-dihydroxy-6-pentylbenzoate = olivetolate
Other name(s): OAC
Systematic name: 3,5,7-trioxododecanoyl-CoA CoA-lyase (olivetolate-forming)
Comments: Part of the cannabinoids biosynthetic pathway in the plant Cannabis sativa.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Gagne, S.J., Stout, J.M., Liu, E., Boubakir, Z., Clark, S.M. and Page, J.E. Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides. Proc. Natl. Acad. Sci. USA 109 (2012) 12811-12816. [PMID: 22802619]
[EC 4.4.1.27 Transferred entry: carbon disulfide lyase. Now EC 3.13.1.5, carbon disulfide hydrolase (EC 4.4.1.27 created 2013, deleted 2017)]
Accepted name: L-cysteine desulfidase
Reaction: L-cysteine + H2O = sulfide + NH3 + pyruvate (overall reaction)
(1a) L-cysteine = 2-aminoprop-2-enoate + sulfide
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + NH3 (spontaneous)
Other name(s): L-cysteine desulfhydrase
Systematic name: L-cysteine sulfide-lyase (deaminating; pyruvate-forming)
Comments: The enzyme from the archaeon Methanocaldococcus jannaschii contains a [4Fe-4S] cluster and is specific for L-cysteine (cf. EC 4.4.1.1, cystathionine γ-lyase). It cleaves a carbon-sulfur bound releasing sulfide and the unstable enamine product 2-aminoprop-2-enoate that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The same reaction can also be catalysed by some pyridoxal-phosphate proteins (cf. EC 4.4.1.1, cystathionine γ-lyase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Tchong, S.I., Xu, H. and White, R.H. L-Cysteine desulfidase: an [4Fe-4S] enzyme isolated from Methanocaldococcus jannaschii that catalyzes the breakdown of L-cysteine into pyruvate, ammonia, and sulfide. Biochemistry 44 (2005) 1659-1670. [PMID: 15683250]
Accepted name: phycobiliprotein cysteine-84 phycobilin lyase
Reaction: (1) [C-phycocyanin β-subunit]-Cys84-phycocyanobilin = apo-[C-phycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(2) [phycoerythrocyanin β-subunit]-Cys84-phycocyanobilin = apo-[phycoerythrocyanin β-subunit] + (2R,3E)-phycocyanobilin
(3) [allophycocyanin α-subunit]-Cys84-phycocyanobilin = apo-[allophycocyanin α-subunit] + (2R,3E)-phycocyanobilin
(4) [allophycocyanin β-subunit]-Cys84-phycocyanobilin = apo-[allophycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(5) [C-phycoerythrin α-subunit]-Cys84-phycoerythrobilin = apo-[C-phycoerythrin α-subunit] + (2R,3E)-phycoerythrobilin
(6) [C-phycoerythrin β-subunit]-Cys84-phycoerythrobilin = apo-[C-phycoerythrin β-subunit] + (2R,3E)-phycoerythrobilin
Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
phycoerythrobilin = 3,31,181,182-tetradehydro-2,3,15,16-tetrahydromesobiliverdin
Other name(s): cpcS (gene name); cpeS (gene name); cpcS1 (gene name); cpcU (gene name); phycocyanobilin:Cys-β84-phycobiliprotein lyase
Systematic name: [phycobiliprotein]-Cys84-phycobilin:phycobilin lyase
Comments: The enzyme, found in cyanobacteria and red algae, catalyses the attachment of phycobilin chromophores to cysteine 84 of several phycobiliproteins (the numbering used here corresponds to the enzyme from Anabaena, in other organisms the number may vary slightly). It can attach phycocyanobilin to the β subunits of C-phycocyanin and phycoerythrocyanin and to both subunits of allophycocyanin. In addition, it can attach phycoerythrobilin to both subunits of C-phycoerythrin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Zhao, K.H., Su, P., Li, J., Tu, J.M., Zhou, M., Bubenzer, C. and Scheer, H. Chromophore attachment to phycobiliprotein β-subunits: phycocyanobilin:cysteine-β84 phycobiliprotein lyase activity of CpeS-like protein from Anabaena Sp. PCC7120. J. Biol. Chem. 281 (2006) 8573-8581. [PMID: 16452471]
2. Zhao, K.H., Su, P., Tu, J.M., Wang, X., Liu, H., Ploscher, M., Eichacker, L., Yang, B., Zhou, M. and Scheer, H. Phycobilin:cystein-84 biliprotein lyase, a near-universal lyase for cysteine-84-binding sites in cyanobacterial phycobiliproteins. Proc. Natl. Acad. Sci. USA 104 (2007) 14300-14305. [PMID: 17726096]
3. Saunee, N.A., Williams, S.R., Bryant, D.A. and Schluchter, W.M. Biogenesis of phycobiliproteins: II. CpcS-I and CpcU comprise the heterodimeric bilin lyase that attaches phycocyanobilin to Cys-82 of β-phycocyanin and Cys-81 of allophycocyanin subunits in Synechococcus sp. PCC 7002. J. Biol. Chem. 283 (2008) 7513-7522. [PMID: 18199753]
4. Kupka, M., Zhang, J., Fu, W.L., Tu, J.M., Bohm, S., Su, P., Chen, Y., Zhou, M., Scheer, H. and Zhao, K.H. Catalytic mechanism of S-type phycobiliprotein lyase: chaperone-like action and functional amino acid residues. J. Biol. Chem. 284 (2009) 36405-36414. [PMID: 19864423]
Accepted name: phycobiliprotein β-cysteine-155 phycobilin lyase
Reaction: (1) [C-phycocyanin β-subunit]-Cys155-phycocyanobilin = apo-[C-phycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(2) [phycoerythrocyanin β-subunit]-Cys155-phycocyanobilin = apo-[phycoerythrocyanin β-subunit] + (2R,3E)-phycocyanobilin
Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
Other name(s): cpcT (gene name); cpeT1 (gene name); cpcT1 (gene name)
Systematic name: [phycobiliprotein β-subunit]-Cys155-phycocyanobilin:phycocyanobilin lyase
Comments: The enzyme, found in cyanobacteria and red algae, catalyses the attachment of the phycobilin chromophore phycocyanobilin to cysteine 155 of the β subunits of the phycobiliproteins C-phycocyanin and phycoerythrocyanin. The numbering used here corresponds to the enzyme from Anabaena, and could vary slightly in other organisms.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Zhao, K.H., Zhang, J., Tu, J.M., Bohm, S., Ploscher, M., Eichacker, L., Bubenzer, C., Scheer, H., Wang, X. and Zhou, M. Lyase activities of CpcS- and CpcT-like proteins from Nostoc PCC7120 and sequential reconstitution of binding sites of phycoerythrocyanin and phycocyanin β-subunits. J. Biol. Chem. 282 (2007) 34093-34103. [PMID: 17895251]
2. Zhang, R., Feng, X.T., Wu, F., Ding, Y., Zang, X.N., Zhang, X.C., Yuan, D.Y. and Zhao, B.R. Molecular cloning and expression analysis of a new bilin lyase: the cpcT gene encoding a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the β-subunit of phycocyanin in Arthrospira platensis FACHB314. Gene 544 (2014) 191-197. [PMID: 24768724]
3. Zhou, W., Ding, W.L., Zeng, X.L., Dong, L.L., Zhao, B., Zhou, M., Scheer, H., Zhao, K.H. and Yang, X. Structure and mechanism of the phycobiliprotein lyase CpcT. J. Biol. Chem. 289 (2014) 26677-26689. [PMID: 25074932]
Accepted name: phycoerythrocyanin α-cysteine-84 phycoviolobilin lyase/isomerase
Reaction: [phycoerythrocyanin α-subunit]-Cys84-phycoviolobilin = apo-[phycoerythrocyanin α-subunit] + (2R,3E)-phycocyanobilin
Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
phycoviolobilin = 15,16-dihydrobiliverdin IIIa
Other name(s): pecE (gene name); pecF (gene name); phycoviolobilin phycoerythrocyanin-α84-cystein-lyase; PecE/PecF; PEC-Cys-R84 PCB lyase/isomerase
Systematic name: [phycoerythrocyanin α-subunit]-Cys84-phycoviolobilin:(2R,3E)-phycocyanobilin lyase/isomerase
Comments: The enzyme, characterized from the cyanobacteria Nostoc sp. PCC 7120 and Mastigocladus laminosus, catalyses the covalent attachment of the phycobilin chromophore phycocyanobilin to cysteine 84 of the β subunit of the phycobiliprotein phycoerythrocyanin and its isomerization to phycoviolobilin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Jung, L.J., Chan, C.F. and Glazer, A.N. Candidate genes for the phycoerythrocyanin α subunit lyase. Biochemical analysis of pecE and pecF interposon mutants. J. Biol. Chem. 270 (1995) 12877-12884. [PMID: 7759546]
2. Zhao, K.H., Deng, M.G., Zheng, M., Zhou, M., Parbel, A., Storf, M., Meyer, M., Strohmann, B. and Scheer, H. Novel activity of a phycobiliprotein lyase: both the attachment of phycocyanobilin and the isomerization to phycoviolobilin are catalyzed by the proteins PecE and PecF encoded by the phycoerythrocyanin operon. FEBS Lett 469 (2000) 9-13. [PMID: 10708746]
3. Storf, M., Parbel, A., Meyer, M., Strohmann, B., Scheer, H., Deng, M.G., Zheng, M., Zhou, M. and Zhao, K.H. Chromophore attachment to biliproteins: specificity of PecE/PecF, a lyase-isomerase for the photoactive 31-cys-α 84-phycoviolobilin chromophore of phycoerythrocyanin. Biochemistry 40 (2001) 12444-12456. [PMID: 11591166]
4. Zhao, K.H., Wu, D., Wang, L., Zhou, M., Storf, M., Bubenzer, C., Strohmann, B. and Scheer, H. Characterization of phycoviolobilin phycoerythrocyanin-α 84-cystein-lyase-(isomerizing) from Mastigocladus laminosus. Eur. J. Biochem. 269 (2002) 4542-4550. [PMID: 12230566]
Accepted name: C-phycocyanin α-cysteine-84 phycocyanobilin lyase
Reaction: [C-phycocyanin α-subunit]-Cys84-phycocyanobilin = apo-[C-phycocyanin α-subunit] + (2R,3E)-phycocyanobilin
Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
Other name(s): cpcE (gene name); cpcF (gene name)
Systematic name: [C-phycocyanin α-subunit]-Cys84-phycocyanobilin:(2R,3E)-phycocyanobilin lyase
Comments: The enzyme, characterized from the cyanobacterium Synechococcus elongatus PCC 7942, catalyses the covalent attachment of the phycobilin chromophore phycocyanobilin to cysteine 84 of the α subunit of the phycobiliprotein C-phycocyanin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Fairchild, C.D., Zhao, J., Zhou, J., Colson, S.E., Bryant, D.A. and Glazer, A.N. Phycocyanin α-subunit phycocyanobilin lyase. Proc. Natl. Acad. Sci. USA 89 (1992) 7017-7021. [PMID: 1495995]
2. Fairchild, C.D. and Glazer, A.N. Oligomeric structure, enzyme kinetics, and substrate specificity of the phycocyanin α subunit phycocyanobilin lyase. J. Biol. Chem. 269 (1994) 8686-8694. [PMID: 8132596]
3. Bhalerao, R.P., Lind, L.K. and Gustafsson, P. Cloning of the cpcE and cpcF genes from Synechococcus sp. PCC 6301 and their inactivation in Synechococcus sp. PCC 7942. Plant Mol. Biol. 26 (1994) 313-326. [PMID: 7524727]
Accepted name: R-phycocyanin α-cysteine84 phycourobilin lyase/isomerase
Reaction: [R-phycocyanin α-subunit]-Cys84-phycourobilin = apo-[R-phycocyanin α-subunit] + (2R,3E)-phycoerythrobilin
Other name(s): rpcG (gene name)
Systematic name: [R-phycocyanin α-subunit]-Cys84-phycourobilin:(2R,3E)-phycoerythrobilin lyase/isomerase
Comments: The enzyme, characterized from the cyanobacterium Synechococcus sp. WH8102, catalyses the covalent attachment of the phycobilin chromophore phycoerythrobilin to cysteine 84 of the α subunit of the phycobiliprotein R-phycocyanin and its isomerization to phycourobilin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Blot, N., Wu, X.J., Thomas, J.C., Zhang, J., Garczarek, L., Bohm, S., Tu, J.M., Zhou, M., Ploscher, M., Eichacker, L., Partensky, F., Scheer, H. and Zhao, K.H. Phycourobilin in trichromatic phycocyanin from oceanic cyanobacteria is formed post-translationally by a phycoerythrobilin lyase-isomerase. J. Biol. Chem. 284 (2009) 9290-9298. [PMID: 19182270]
Accepted name: isoprene-epoxide—glutathione S-transferase
Reaction: 2-(glutathion-S-yl)-2-methylbut-3-en-1-ol = (3R)-3,4-epoxy-3-methylbut-1-ene + glutathione
For diagram of reaction click here.
Other name(s): isoI (gene name)
Systematic name: 2-(glutathion-S-yl)-2-methylbut-3-en-1-ol lyase [(3R)-3,4-epoxy-3-methylbut-1-ene forming]
Comments: The enzyme, characterized from the bacterium Rhodococcus sp. AD45, is involved in isoprene degradation. The enzyme can catalyse the glutathione-dependent ring opening of various epoxides, but the highest activity is with (3R)-3,4-epoxy-3-methylbut-1-ene, which is derived from isoprene by EC 1.14.13.69, alkene monooxygenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. van Hylckama Vlieg, J.E., Kingma, J., van den Wijngaard, A.J. and Janssen, D.B. A glutathione S-transferase with activity towards cis-1, 2-dichloroepoxyethane is involved in isoprene utilization by Rhodococcus sp. strain AD45. Appl. Environ. Microbiol. 64 (1998) 2800-2805. [PMID: 9687433]
2. van Hylckama Vlieg, J.E., Kingma, J., Kruizinga, W. and Janssen, D.B. Purification of a glutathione S-transferase and a glutathione conjugate-specific dehydrogenase involved in isoprene metabolism in Rhodococcus sp. strain AD45. J. Bacteriol. 181 (1999) 2094-2101. [PMID: 10094686]
Accepted name: L-cystine β-lyase
Reaction: L-cystine + H2O = L-thiocysteine + pyruvate + NH3 (overall reaction)
(1a) L-cystine = L-thiocysteine + 2-aminoprop-2-enoate
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + NH3 (spontaneous)
Glossary: L-thiocysteine = S-sulfanyl-L-cysteine
Other name(s): CORI3 (gene name)
Systematic name: L-cystine thiocysteine-lyase (deaminating; pyruvate-forming)
Comments: A pyridoxal 5'-phosphate protein. The enzyme cleaves a carbon-sulfur bond, releasing L-thiocysteine and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. The enzyme from Brassica oleracea var. italica (broccoli) does not act on cysteine or cystathionine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Ukai, K. and Sekiya, J. Purification and characterization of cystine lyase a from broccoli Inflorescence. Biosci. Biotechnol. Biochem. 61 (1997) 1890-1895. [PMID: 27396740]
2. Jones, P.R., Manabe, T., Awazuhara, M. and Saito, K. A new member of plant CS-lyases. A cystine lyase from Arabidopsis thaliana. J. Biol. Chem. 278 (2003) 10291-10296. [PMID: 12525491]
Accepted name: hercynylcysteine S-oxide lyase
Reaction: S-(hercyn-2-yl)-L-cysteine S-oxide + reduced acceptor = ergothioneine + pyruvate + NH3 + acceptor (overall reaction)
(1a) S-(hercyn-2-yl)-L-cysteine S-oxide + H2O = 2-(hydroxysulfanyl)hercynine + pyruvate + NH3
(1b) 2-(hydroxysulfanyl)hercynine + reduced acceptor = ergothioneine + acceptor + H2O (spontaneous)
Glossary: 2-(hydroxysulfanyl)hercynine = Nα,Nα,Nα-trimethyl-2-(hydroxysulfanyl)-L-histidine = 2-sulfenohercynine
ergothioneine = Nα,Nα,Nα-trimethyl-2-sulfanylidene-2,3-dihydro-L-histidine
Other name(s): egtE (gene name)
Systematic name: S-(hercyn-2-yl)-L-cysteine ergothioneine-hydroxysulfanolate-lyase
Comments: Contains pyridoxal 5'-phosphate. The enzyme, characterized from the bacterium Mycobacterium smegmatis, cayalyses the last step in the pathway of ergothioneine biosynthesis. The enzyme forms a 2-(hydroxysulfanyl)hercynine intermediate, which is reduced to ergothioneine non-enzymically by a thiol. In vitro, DTT can serve this function.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Seebeck, F.P. In vitro reconstitution of mycobacterial ergothioneine biosynthesis. J. Am. Chem. Soc. 132 (2010) 6632-6633. [PMID: 20420449]
2. Pluskal, T., Ueno, M. and Yanagida, M. Genetic and metabolomic dissection of the ergothioneine and selenoneine biosynthetic pathway in the fission yeast, S. pombe, and construction of an overproduction system. PLoS One 9 (2014) e97774. [PMID: 24828577]
3. Song, H., Hu, W., Naowarojna, N., Her, A.S., Wang, S., Desai, R., Qin, L., Chen, X. and Liu, P. Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate. Sci Rep 5 (2015) 11870. [PMID: 26149121]
Accepted name: pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
Reaction: (1) [LarE]-L-cysteine + pyridin-1-ium-3,5-dicarboxylate mononucleotide + ATP = [LarE]-dehydroalanine + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide + AMP + diphosphate (overall reaction)
(1a) ATP + pyridin-1-ium-3,5-dicarboxylate mononucleotide = diphosphate + 5-carboxy-1-(5-O-phospho-β-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate
(1b) 5-carboxy-1-(5-O-phospho-β-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate + [LarE]-L-cysteine = AMP + [LarE]-S-[5-carboxy-1-(5-O-phosphono-β-D-ribofuranosyl)pyridin-1-ium-3-carbonyl]-L-cysteine
(1c) [LarE]-S-[5-carboxy-1-(5-O-phosphono-β-D-ribofuranosyl)pyridin-1-ium-3-carbonyl]-L-cysteine = [LarE]-dehydroalanine + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide
(2) [LarE]-L-cysteine + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide + ATP = [LarE]-dehydroalanine + pyridin-1-ium-3,5-bisthiocarboxylate mononucleotide + AMP + diphosphate (overall reaction)
(2a) ATP + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide = diphosphate + 1-(5-O-phospho-β-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate
(2b) 1-(5-O-phospho-β-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate + [LarE]-L-cysteine = AMP + [LarE]-S-[1-(5-O-phosphono-β-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl]-L-cysteine
(2c) [LarE]-S-[1-(5-O-phosphono-β-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl]-L-cysteine = [LarE]-dehydroalanine + pyridin-1-ium-3,5-bisthiocarboxylate mononucleotide
Other name(s): LarE; P2CMN sulfurtransferase; pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase; P2TMN synthase
Systematic name: [LarE]-S-[1-(5-O-phosphono-β-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl]-L-cysteine pyridin-1-ium-3,5-dicarbothioate-mononucleotide-lyase (ATP-consuming)
Comments: This enzyme, found in Lactobacillus plantarum, is involved in the biosynthesis of a nickel-pincer cofactor. The process starts when one enzyme molecule adenylates pyridinium-3,5-dicarboxylate mononucleotide (P2CMN) and covalently binds the adenylated product to an intrinsic cysteine residue. Next, the enzyme cleaves the carbon-sulfur bond, liberating pyridinium-3-carboxylate-5-thiocarboxylate mononucleotide (PCTMN) and leaving a 2-aminoprop-2-enoate (dehydroalanine) residue attached to the protein. Since the cysteine residue is not regenerated in vivo, the enzyme is inactivated during the process. A second enzyme molecule then repeats the process with PCTMN, adenylating it and covalently binding it to the same cysteine residue, followed by liberation of pyridinium-3,5-bisthiocarboxylate mononucleotide (P2TMN) and the inactivation of the second enzyme molecule.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Desguin, B., Goffin, P., Viaene, E., Kleerebezem, M., Martin-Diaconescu, V., Maroney, M.J., Declercq, J.P., Soumillion, P. and Hols, P. Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Nat Commun 5 (2014) 3615. [PMID: 24710389]
2. Desguin, B., Soumillion, P., Hols, P. and Hausinger, R.P. Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion. Proc. Natl Acad. Sci. USA 113 (2016) 5598-5603. [PMID: 27114550]
3. Fellner, M., Desguin, B., Hausinger, R.P. and Hu, J. Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. Proc. Natl Acad. Sci. USA 114 (2017) 9074-9079. [PMID: 28784764]
Accepted name: isethionate sulfite-lyase
Reaction: isethionate = acetaldehyde + sulfite
Glossary: isethionate = 2-hydroxyethanesulfonate
Other name(s): islA (gene name)
Systematic name: isethionate sulfite-lyase
Comments: The enzyme, characterized from the human gut bacterium Bilophila wadsworthia, participates in a taurine degradation pathway that leads to sulfide production. The active form of the enzyme contains a glycyl radical that is generated by a dedicated activating enzyme via chemistry involving S-adenosyl-L-methionine (SAM) and a [4Fe-4S] cluster.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Peck, S.C., Denger, K., Burrichter, A., Irwin, S.M., Balskus, E.P. and Schleheck, D. A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia. Proc. Natl. Acad. Sci. USA 116 (2019) 3171-3176. [PMID: 30718429]
2. Xing, M., Wei, Y., Zhou, Y., Zhang, J., Lin, L., Hu, Y., Hua, G.,, N. Nanjaraj Urs, A., Liu, D., Wang, F., Guo, C., Tong, Y., Li, M., Liu, Y., Ang, E.L., Zhao, H., Yuchi, Z. and Zhang, Y. Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria. Nat. Commun. 10 (2019) 1609. [PMID: 30962433]
Accepted name: C-phycoerythrin α-cysteine-82 phycoerythrobilin lyase
Reaction: a [C-phycoerythrin α-subunit]-Cys82-phycoerythrobilin = apo-[C-phycoerythrin α-subunit] + (3E)-phycoerythrobilin
Other name(s): cpeY (gene name)
Systematic name: [C-phycoerythrin α-subunit]-Cys82-phycoerythrobilin:phycoerythrobilin lyase
Comments: The enzyme, characterized from the cyanobacterium Microchaete diplosiphon, catalyses the attachment of the phycobilin chromophore (3E)-phycoerythrobilin (PEB) to cysteine 82 of the α subunit of the phycobiliprotein C-phycoerythrin. The numbering used here corresponds to the enzyme from Microchaete diplosiphon, and could vary slightly in other organisms. Activity is greatly enhanced in the presence of the chaperone-like protein CpeZ. The reaction could also be catalysed by EC 4.4.1.29, phycobiliprotein cysteine-84 phycobilin lyase, but much less efficiently.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Biswas, A., Boutaghou, M.N., Alvey, R.M., Kronfel, C.M., Cole, R.B., Bryant, D.A. and Schluchter, W.M. Characterization of the activities of the CpeY, CpeZ, and CpeS bilin lyases in phycoerythrin biosynthesis in Fremyella diplosiphon strain UTEX 481. J. Biol. Chem. 286 (2011) 35509-35521. [PMID: 21865169]
2. Kronfel, C.M., Biswas, A., Frick, J.P., Gutu, A., Blensdorf, T., Karty, J.A., Kehoe, D.M. and Schluchter, W.M. The roles of the chaperone-like protein CpeZ and the phycoerythrobilin lyase CpeY in phycoerythrin biogenesis. Biochim Biophys Acta Bioenerg 1860 (2019) S0005-2728(. [PMID: 31173730]
Accepted name: C-phycoerythrin β-cysteine-48/59 phycoerythrobilin lyase
Reaction: a [C-phycoerythrin β-subunit]-Cys48/59-phycoerythrobilin = apo-[C-phycoerythrobilin α-subunit] + (3E)-phycoerythrobilin
Other name(s): cpeF (gene name)
Systematic name: [C-phycoerythrin β-subunit]-Cys48/59-phycoerythrobilin:phycoerythrobilin lyase
Comments: The enzyme, characterized from the cyanobacterium Microchaete diplosiphon, catalyses the attachment of the phycobilin chromophore (3E)-phycoerythrobilin (PEB) to cysteine 48 and 59 of the β-subunits of the phycobiliprotein C-phycoerythrin. The enzyme first ligates the A ring of PEB to cysteine-48, followed by the attachment of the D ring to cysteine-59. The numbering used here corresponds to the enzyme from Microchaete diplosiphon, and could vary slightly in other organisms. The reaction requires the presence of the chaperone-like protein CpeZ.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Kronfel, C.M., Hernandez, C.V., Frick, J.P., Hernandez, L.S., Gutu, A., Karty, J.A., Boutaghou, M.N., Kehoe, D.M., Cole, R.B. and Schluchter, W.M. CpeF is the bilin lyase that ligates the doubly linked phycoerythrobilin on β-phycoerythrin in the cyanobacterium Fremyella diplosiphon. J. Biol. Chem. 294 (2019) 3987-3999. [PMID: 30670589]
Accepted name: (2S)-3-sulfopropanediol sulfolyase
Reaction: (2S)-2,3-dihydroxypropane-1-sulfonate = hydroxyacetone + sulfite
Glossary: (2S)-2,3-dihydroxypropane-1-sulfonate = (2S)-3-sulfopropanediol
Other name(s): DHPS sulfolyase; hpsG (gene name)
Systematic name: (2S)-2,3-dihydroxypropane-1-sulfonate sulfite-lyase
Comments: The enzyme, characterized from the human gut bacterium Bilophila wadsworthia, contains a glycyl radical that is generated by a dedicated activating enzyme via chemistry involving S-adenosyl-L-methionine (AdoMet) and a [4Fe-4S] cluster.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Liu, J., Wei, Y., Lin, L., Teng, L., Yin, J., Lu, Q., Chen, J., Zheng, Y., Li, Y., Xu, R., Zhai, W., Liu, Y., Liu, Y., Cao, P., Ang, E.L., Zhao, H., Yuchi, Z. and Zhang, Y. Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate. Proc. Natl. Acad. Sci. USA 117 (2020) 15599-15608. [PMID: 32571930]
Accepted name: S-adenosyl-L-methionine lyase
Reaction: S-adenosyl-L-methionine = L-homoserine lactone + S-methyl-5'-thioadenosine
Other name(s): T3p01 (gene name); SAM lyase; SAMase; adenosylmethionine cyclotransferase; S-adenosyl-L-methionine alkyltransferase (cyclizing)
Systematic name: S-adenosyl-L-methionine S-methyl-5'-thioadenosine-lyase (cyclizing; L-homoserine lactone-forming)
Comments: The enzyme was originally described from the yeast Saccharomyces cerevisiae (as EC 2.5.1.4), though it had not been well characterized. It was also incorrectly described from several bacteriophages as a hydrolase (EC 3.13.2.2). Later work has shown the bacteriophage enzyme to be a lyase. The enzyme binds its substrate at the border between two subunits of a trimeric complex in a position that prevents it from interacting with water. Instead, the substrate reacts with itself and splits in two. The product, L-homoserine lactone, spontaneously hydrolyses to L-homoserine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Mudd, S.H. The mechanism of the enzymatic cleavage of S-adenosylmethionine to α-amino-γ-butyrolactone. J. Biol. Chem. 234 (1959) 1784-1786. [PMID: 13672964]
2. Mudd, S.H. Enzymatic cleavage of S-adenosylmethionine. J. Biol. Chem. 234 (1959) 87-92. [PMID: 13610898]
3. Hausmann, R. Synthesis of an S-adenosylmethionine-cleaving enzyme in T3-infected Escherichia coli and its disturbance by co-infection with enzymatically incompetent bacteriophage. J. Virol. 1 (1967) 57-63. [PMID: 4918233]
4. Studier, F.W. and Movva, N.R. SAMase gene of bacteriophage T3 is responsible for overcoming host restriction. J. Virol. 19 (1976) 136-145. [PMID: 781304]
5. Guo, X., Soderholm, A., Kanchugal, P., S., Isaksen, G.V., Warsi, O., Eckhard, U., Triguis, S., Gogoll, A., Jerlstrom-Hultqvist, J., Aqvist, J., Andersson, D.I. and Selmer, M. Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family. Elife 10 (2021) . [PMID: 33567250]
Accepted name: canavanine-γ-lyase
Reaction: L-canavanine + H2O = L-homoserine + N-hydroxyguanidine (overall reaction)
(1a) L-canavanine = vinylglycine + N-hydroxyguanidine
(1b) vinylglycine = (2E)-2-aminobut-2-enoate (spontaneous)
(1c) (2E)-2-aminobut-2-enoate + H2O = L-homoserine (spontaneous)
Other name(s): CangL
Systematic name: L-canavanine N-hydroxyguanidine-lyase (L-homoserine-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, characterized from the bacterium Pseudomonas canavaninivorans, cleaves a carbon-oxygen bond, releasing N-hydroxyguanidine and an unstable enamine product that tautomerizes to an imine form, which is attacked by a water molecule to form L-homoserine.
References:
1. Hauth, F., Buck, H., Stanoppi, M., and Hartig, J. S. Canavanine utilization via homoserine and hydroxyguanidine by a PLP-dependent γ-lyase in Pseudomonadaceae and Rhizobiales. RSC Chemical Biology (0) .
Accepted name: DDT-dehydrochlorinase
Reaction: 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane = 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene + chloride
Other name(s): DDT-as; 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane chloride-lyase
Systematic name: 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane chloride-lyase [1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene-forming]
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9031-20-3
References:
1. Lipke, H. and Kearns, C.W. DDT dechlorinase. I. Isolation, chemical properties, and spectrophotometric assay. J. Biol. Chem. 234 (1959) 2123-2128. [PMID: 13673024]
2. Lipke, H. and Kearns, C.W. DDT dechlorinase. II. Substrate and cofactor specificity. J. Biol. Chem. 234 (1959) 2129-2132. [PMID: 13673025]
3. Moorefield, H.H. Purification of DDT-dehydrochlorinase from resistant houseflies. Contr. Boyce Thompson Inst. 18 (1956) 303-310.
Accepted name: 3-chloro-D-alanine dehydrochlorinase
Reaction: 3-chloro-D-alanine + H2O = pyruvate + chloride + NH3 (overall reaction)
(1a) 3-chloro-D-alanine = chloride + 2-aminoprop-2-enoate
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + NH3 (spontaneous)
Other name(s): β-chloro-D-alanine dehydrochlorinase; 3-chloro-D-alanine chloride-lyase (deaminating)
Systematic name: 3-chloro-D-alanine chloride-lyase (deaminating; pyruvate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme cleaves a carbon-chlorine bond, releasing a chloride and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. The enzyme's activity can also result in β-replacement reactions, e.g. in the presence of hydrogen sulfide it can convert 3-chloro-D-alanine into D-cysteine and chloride.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 78990-65-5
References:
1. Nagasawa, T., Ishii, T. and Yamada, H. Physiological comparison of D-cysteine desulfhydrase of Escherichia coli with 3-chloro-D-alanine dehydrochlorinase of Pseudomonas putida CR 1-1. Arch. Microbiol. 149 (1988) 413-416. [PMID: 3132906]
2. Yamada, H., Nagasawa, T., Ohkishi, H., Kawakami, B. and Tani, Y. Synthesis of D-cysteine from 3-chloro-D-alanine and hydrogen sulfide by 3-chloro-D-alanine hydrogen chloride-lyase (deaminating) of Pseudomonas putida. Biochem. Biophys. Res. Commun. 100 (1981) 1104-1110. [PMID: 6791643]
Accepted name: dichloromethane dehalogenase
Reaction: dichloromethane + H2O = formaldehyde + 2 chloride
Other name(s): dichloromethane chloride-lyase (chloride-hydrolysing); dichloromethane chloride-lyase (chloride-hydrolysing; formaldehyde-forming)
Systematic name: dichloromethane chloride-lyase (adding H2O; chloride-hydrolysing; formaldehyde-forming)
Comments: Requires glutathione.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, CAS registry number: 97002-70-5
References:
1. Kohler-Staub, D. and Leisinger, T. Dichloromethane dehalogenase of Hyphomicrobium sp. strain DM2. J. Bacteriol. 162 (1985) 676-681. [PMID: 3988708]
Accepted name: L-2-amino-4-chloropent-4-enoate dehydrochlorinase
Reaction: L-2-amino-4-chloropent-4-enoate + H2O = 2-oxopent-4-enoate + chloride + NH3
Other name(s): L-2-amino-4-chloro-4-pentenoate dehalogenase; L-2-amino-4-chloropent-4-enoate chloride-lyase (deaminating); L-2-amino-4-chloropent-4-enoate chloride-lyase (deaminating; 2-oxopent-4-enoate-forming)
Systematic name: L-2-amino-4-chloropent-4-enoate chloride-lyase (adding water; deaminating; 2-oxopent-4-enoate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 113066-37-8
References:
1. Moriguchi, M., Hoshino, S. and Hatanaka, S.-I. Dehalogenation and deamination of l-2-amino-4-chloro-4-pentenoic acid by Proteus mirabilis. Agric. Biol. Chem. 51 (1987) 3295.
Accepted name: S-carboxymethylcysteine synthase
Reaction: 3-chloro-L-alanine + thioglycolate = S-carboxymethyl-L-cysteine + chloride
Other name(s): S-carboxymethyl-L-cysteine synthase
Systematic name: 3-chloro-L-alanine chloride-lyase (adding thioglycolate; S-carboxymethyl-L-cysteine-forming)
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 124671-39-2
References:
1. Kumagai, H., Suzuki, H., Shigematsu, H. and Tuchikura, T. S-Carboxymethylcysteine synthase from Escherichia coli. Agric. Biol. Chem. 53 (1989) 2481-2487.
Accepted name: adenylate cyclase
Reaction: ATP = 3',5'-cyclic AMP + diphosphate
Other name(s): adenylylcyclase; adenyl cyclase; 3',5'-cyclic AMP synthetase; ATP diphosphate-lyase (cyclizing)
Systematic name: ATP diphosphate-lyase (cyclizing; 3',5'-cyclic-AMP-forming)
Comments: Also acts on dATP to form 3',5'-cyclic dAMP. Requires pyruvate. Activated by NAD+ in the presence of EC 2.4.2.31 NAD(P)+—arginine ADP-ribosyltransferase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9012-42-4
References:
1. Hirata, M. and Hayaishi, O. Adenyl cyclase of Brevibacterium liquefaciens. Biochim. Biophys Acta 149 (1967) 1-11. [PMID: 4295782]
Accepted name: guanylate cyclase
Reaction: GTP = 3',5'-cyclic GMP + diphosphate
For diagram of reaction click here
Other name(s): guanylyl cyclase; guanyl cyclase; GTP diphosphate-lyase (cyclizing)
Systematic name: GTP diphosphate-lyase (cyclizing; 3',5'-cyclic-GMP-forming)
Comments: Also acts on ITP and dGTP.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9054-75-5
References:
1. Garbers, D.L., Suddath, J.L. and Hardman, J.G. Enzymatic formation of inosine 3',5'-monophosphate and of 2'-deoxyguanosine 3',5'-monophosphate. Inosinate and deoxyguanylate cyclase activity. Biochim. Biophys. Acta 377 (1975) 174-185. [PMID: 235291]
2. Hardman, J.G. and Sutherland, E.W. Guanyl cyclase, an enzyme catalyzing the formation of guanosine 3',5'-monophosphate from guanosine triphosphate. J. Biol. Chem. 244 (1969) 6363-6370. [PMID: 4982201]
[EC 4.6.1.3 Transferred entry: now EC 4.2.3.4, 3-dehydroquinate synthase (EC 4.6.1.3 created 1978, deleted 2000)]
[EC 4.6.1.4 Transferred entry: now EC 4.2.3.5, chorismate synthase (EC 4.6.1.4 created 1978, modified 1983, deleted 2000)]
[EC 4.6.1.5 Transferred entry: now EC 4.2.3.7 pentalenene synthase (EC 4.6.1.5 created 1989, deleted 2000)]
Accepted name: cytidylate cyclase
Reaction: CTP = 3',5'-cyclic CMP + diphosphate
Other name(s): 3',5'-cyclic-CMP synthase; cytidylyl cyclase; cytidyl cyclase; CTP diphosphate-lyase (cyclizing); pycC (gene name) (ambiguous)
Systematic name: CTP diphosphate-lyase (cyclizing; 3',5'-cyclic-CMP-forming)
Comments: In bacteria and archaea the enzyme's product, cCMP, functions as a second messenger in bacterial immunity against viruses. The enzyme is synthesized following phage infection and activates immune effectors that execute an antiviral response.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 65357-82-6
References:
1. Cech, S.Y. and Ignarro, L.J. Cytidine 3',5'-monophosphate (cyclic CMP) formation by homogenates of mouse liver. Biochem. Biophys. Res. Commun. 80 (1978) 119-125. [PMID: 23778]
2. Newton, R.P., Salih, S.G., Hakeem, N.A., Kingston, E.E. and Beynon, J.H. 3',5'-Cyclic UMP, -cyclic IMP, -cyclic TMP and related enzymes in mammalian-tissues. Biochem. Soc. Trans. 13 (1985) 1134-1135.
3. Tal, N., Morehouse, B.R., Millman, A., Stokar-Avihail, A., Avraham, C., Fedorenko, T., Yirmiya, E., Herbst, E., Brandis, A., Mehlman, T., Oppenheimer-Shaanan, Y., Keszei, A.FA., Shao, S., Amitai, G., Kranzusch, P.J. and Sorek, R. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell 184 (2021) 5728Ð5739.e16. [PMID: 34644530]
[EC 4.6.1.7 Transferred entry: now EC 4.2.3.8, CASbene synthase (EC 4.6.1.7 created 1989, deleted 2000)]
[EC 4.6.1.8 Transferred entry: now EC 4.2.3.10, (–)-endo-fenchol synthase (EC 4.6.1.8 created 1992, deleted 2000)]
[EC 4.6.1.9 Transferred entry: now EC 4.2.3.11, sabinene-hydrate synthase (EC 4.6.1.9 created 1992, deleted 2000)]
[EC 4.6.1.10 Transferred entry: now EC 4.2.3.12, 6-pyruvoyltetrahydropterin synthase (EC 4.6.1.10 created 1999, deleted 2000)]
[EC 4.6.1.11 Transferred entry: now EC 4.2.3.13, trichodiene synthase (EC 4.6.1.11 created 1999, deleted 2000)]
Accepted name: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Reaction: 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
For diagram click here.
Other name(s): MECDP-synthase; 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol CMP-lyase (cyclizing)
Systematic name: 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol CMP-lyase (cyclizing; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate-forming)
Comments: The enzyme from Escherichia coli requires Mg2+ or Mn2+. Forms part of an alternative nonmevalonate pathway for terpenoid biosynthesis (for diagram, click here).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 287480-92-6
References:
1. Herz, S., Wungsintaweekul, J., Schuhr, C.A., Hecht, S., Lüttgen, H., Sagner, S., Fellermeier, M., Eisenreich, W., Zenk, M.H., Bacher, A. and Rohdich, F. Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erithritol 2-phosphate to 2-C-methyl-D-erithritol 2,4-cyclodiphosphate. Proc. Natl. Acad. Sci. USA 97 (2000) 2486-2490. [PMID: 10694574]
2. Takagi, M., Kuzuyama, T., Kaneda, K., Watanabe, H., Dairi, T. and Seto, H. Studies on the nonmevalonate pathway: Formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate from 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. Tetrahedron Lett. 41 (2000) 3395-3398.
Accepted name: phosphatidylinositol diacylglycerol-lyase
Reaction: 1-phosphatidyl-1D-myo-inositol = 1D-myo-inositol 1,2-cyclic phosphate + 1,2-diacyl-sn-glycerol
For diagram click here.
Other name(s): monophosphatidylinositol phosphodiesterase; phosphatidylinositol phospholipase C; 1-phosphatidylinositol phosphodiesterase; 1-phosphatidyl-D-myo-inositol inositolphosphohydrolase (cyclic-phosphate-forming); 1-phosphatidyl-1D-myo-inositol diacylglycerol-lyase (1,2-cyclic-phosphate-forming)
Systematic name: 1-phosphatidyl-1D-myo-inositol 1,2-diacyl-sn-glycerol-lyase (1D-myo-inositol-1,2-cyclic-phosphate-forming)
Comments: This enzyme is bacterial. Activity is also found in animals, but this activity is due to the presence of EC 3.1.4.11, phosphoinositide phospholipase C.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37288-19-0
References:
1. Allan, D. and Michell, R.H. Phosphatidylinositol cleavage catalysed by the soluble fraction from lymphocytes. Activity at pH5.5 and pH7.0. Biochem. J. 142 (1974) 591-597. [PMID: 4377210]
2. Friedel, R.O., Brown, J.D. and Durell, J. Monophosphatidyl inositol inositolphosphohydrolase in guinea-pig brain. Biochim. Biophys. Acta 144 (1967) 684-686. [PMID: 4294905]
3. Irvine, R.F. The enzymology of stimulated inositol lipid turnover. Cell Calcium 3 (1982) 295-309. [PMID: 6297738]
4. Michell, R.H. and Allan, D. Inositol cyclic phosphate as a product of phosphatidylinositol breakdown by phospholipase C (Bacillus cereus). FEBS Lett. 53 (1975) 302-304. [PMID: 236918]
5. Low, M.G. and Finean, J.B. Release of alkaline phosphatase fom membranes by a bacterial phosphatidylinositol phospholipase C. Biochem J. 167 (1977) 281-284. [PMID: 588258]
6. Henner, D.J., Yang, M., Chen, E., Helmikss, R. and Low, M.G. Sequence of the Bacillus thuringiensis phosphatidylinositol-specific phospholipase C. Nucleic Acids Res. 16 (1988) 10383 only. [PMID: 3194218]
Accepted name: glycosylphosphatidylinositol diacylglycerol-lyase
Reaction: 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol = 6-(α-D-glucosaminyl)-1D-myo-inositol 1,2-cyclic phosphate + 1,2-diacyl-sn-glycerol
For diagram click here.
Other name(s): (glycosyl)phosphatidylinositol-specific phospholipase C; GPI-PLC; GPI-specific phospholipase C; VSG-lipase; glycosyl inositol phospholipid anchor-hydrolyzing enzyme; glycosylphosphatidylinositol-phospholipase C; glycosylphosphatidylinositol-specific phospholipase C; variant-surface-glycoprotein phospholipase C; 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol diacylglycerol-lyase (1,2-cyclic-phosphate-forming)
Systematic name: 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol 1,2-diacyl-sn-glycerol-lyase [6-(α-D-glucosaminyl)-1D-myo-inositol 1,2-cyclic phosphate-forming]
Comments: This enzyme is also active when O-4 of the glucosamine is substituted by carrying the oligosaccharide that can link a protein to the structure. It therefore cleaves proteins from the lipid part of the glycosylphostphatidylinositol (GPI) anchors. In some cases, the long-chain acyl group at the sn-1 position of glycerol is replaced by an alkyl or alk-1-enyl group. In other cases, the diacylglycerol is replaced by ceramide (see Lip-1.4 and Lip-1.5 for definition). The only characterized enzyme with this specificity is from Trypanosoma brucei, where the acyl groups are myristoyl, but the function of the trypanosome enzyme is unknown. Substitution on O-2 of the inositol blocks action of this enzyme. It is not identical with EC 3.1.4.50, glycosylphosphatidylinositol phospholipase D.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 129070-68-4
References:
1. Hereld, D., Krakow, J.L., Bangs, J.D., Hart, G.W. and Englund, P.T. A phospholipase C from Trypanosoma brucei which selectively cleaves the glycolipid on the variant surface glycoprotein. J. Biol. Chem. 261 (1986) 13813-13819. [PMID: 3759991]
2. Carnall, N., Webb, H. and Carrington, M. Mutagenesis study of the glycosylphosphatidylinositol phospholipase C of Trypanosoma brucei. Mol. Biochem. Parasitol. 90 (1997) 423-432. [PMID: 9476790]
3. Armah, D.A. and Mensa-Wilmot, K. Tetramerization of glycosylphosphatidylinositol-specific phospholipase C from Trypanosoma brucei. J. Biol. Chem. 275 (2000) 19334-19342. [PMID: 10764777]
Accepted name: FAD-AMP lyase (cyclizing)
Reaction: FAD = AMP + riboflavin cyclic-4',5'-phosphate
Other name(s): FMN cyclase; FAD AMP-lyase (cyclic-FMN-forming)
Systematic name: FAD AMP-lyase (riboflavin-cyclic-4',5'-phosphate-forming)
Comments: Requires Mn2+ or Co2+. While FAD was the best substrate tested [2], the enzyme also splits ribonucleoside diphosphate-X compounds in which X is an acyclic or cyclic monosaccharide or derivative bearing an X-OH group that is able to attack internally the proximal phosphorus with the geometry necessary to form a P=X product; either a five-atom monocyclic phosphodiester or a cis-bicyclic phosphodiester-pyranose fusion. The reaction is strongly inhibited by ADP or ATP but is unaffected by the presence of the product, cFMN.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 208349-48-8
References:
1. Fraiz, F.J., Pinto, R.M., Costas, M.J., Avalos, M., Canales, J., Cabezas, A. and Cameselle, J.C. Enzymic formation of riboflavin 4',5'-cyclic phosphate from FAD: evidence for a specific low-Km FMN cyclase in rat liver. Biochem. J. 330 (1998) 881-888. [PMID: 9480905]
2. Cabezas, A., Pinto, R.M., Fraiz, F., Canales, J., Gonzalez-Santiago, S., and Cameselle, J.C. Purification, characterization, and substrate and inhibitor structure-activity studies of rat liver FAD-AMP lyase (cyclizing): preference for FAD and specificity for splitting ribonucleoside diphosphate-X into ribonucleotide and a five-atom cyclic phosphodiester of X, either a monocyclic compound or a cis-bicyclic phosphodiester-pyranose fusion. Biochemistry 40 (2001) 13710-13722. [PMID: 11695920]
Accepted name: tRNA-intron lyase
Reaction: pretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
Other name(s): transfer ribonucleate intron endoribonuclease; tRNA splicing endonuclease; splicing endonuclease; tRNATRPintron endonuclease; transfer splicing endonuclease
Systematic name: pretRNA lyase (intron-removing; 2',3'-cyclic-phosphate-forming)
Comments: The enzyme catalyses the final stage in the maturation of tRNA molecules.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Attardi, D.G., Margarit, I. and Tocchini-Valentini, G.P. Structural alterations in mutant precursors of the yeast tRNALeu3 gene which behave as defective substrates for a highly purified splicing endoribonuclease. EMBO J. 4 (1985) 3289-3297. [PMID: 3937725]
2. Peebles, C.L., Gegenheimer, P. and Abelson, J. Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease. Cell 32 (1983) 525-536. [PMID: 6186398]
3. Thompson, L.D., Brandon, L.D., Nieuwlandt, D.T. and Daniels, C.J. Transfer RNA intron processing in the halophilic archaebacteria. Can. J. Microbiol. 35 (1989) 36-42. [PMID: 2470486]
4. Thompson, L.D. and Daniels, C.J. A tRNA(Trp) intron endonuclease from Halobacterium volcanii. Unique substrate recognition properties. J. Biol. Chem. 263 (1988) 17951-17959. [PMID: 3192521]
Accepted name: cyclic pyranopterin monophosphate synthase
Reaction: (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate
For diagram of reaction click here.
Other name(s): MOCS1B (gene name); moaC (gene name); cnx3 (gene name)
Systematic name: (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate lyase (cyclic pyranopterin phosphate-forming)
Comments: The enzyme catalyses an early step in the biosynthesis of the molybdenum cofactor (MoCo). In bacteria and plants the reaction is catalysed by MoaC and Cnx3, respectively. In mammals the reaction is catalysed by the MOCS1B domain of the bifuctional MOCS1 protein, which also catalyses EC 4.1.99.22, GTP 3',8-cyclase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Rieder, C., Eisenreich, W., O'Brien, J., Richter, G., Götze, E., Boyle, P., Blanchard, S., Bacher, A. and Simon, H. Rearrangement reactions in the biosynthesis of molybdopterin - an NMR study with multiply 13C/15N labelled precursors. Eur. J. Biochem. 255 (1998) 24-36. [PMID: 9692897]
2. Wuebbens, M.M. and Rajagopalan, K.V. Investigation of the early steps of molybdopterin biosynthesis in Escherichia coli through the use of in vivo labeling studies. J. Biol. Chem. 270 (1995) 1082-1087. [PMID: 7836363]
3. Hover, B.M., Tonthat, N.K., Schumacher, M.A. and Yokoyama, K. Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl. Acad. Sci. USA 112 (2015) 6347-6352. [PMID: 25941396]
Accepted name: pancreatic ribonuclease
Reaction: (1) an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA] (overall reaction)
(1a) an [RNA] containing cytidine = an [RNA]-3'-cytidine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
(1b) an [RNA]-3'-cytidine-2',3'-cyclophosphate + H2O = an [RNA]-3'-cytidine-3'-phosphate
(2) an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
(2a) an [RNA] containing uridine = an [RNA]-3'-uridine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
(1b) an [RNA]-3'-uridine-2',3'-cyclophosphate + H2O = an [RNA]-3'-uridine-3'-phosphate
Other name(s): RNase; RNase I; RNase A; pancreatic RNase; ribonuclease I; endoribonuclease I; ribonucleic phosphatase; alkaline ribonuclease; ribonuclease; gene S glycoproteins; Ceratitis capitata alkaline ribonuclease; SLSG glycoproteins; gene S locus-specific glycoproteins; S-genotype-asssocd. glycoproteins; ribonucleate 3'-pyrimidino-oligonucleotidohydrolase
Systematic name: RNA lyase ([RNA]-3'-cytidine/uridine-3'-phosphate and 5'-hydroxy-ribonucleotide-3'-[RNA] producing)
Comments: Specifically cleaves at the 3'-side of pyrimidine (uracil or cytosine) phosphate bonds in RNA. The reaction takes place in two steps, with the 2',3'-cyclic phosphodiester intermediates released from the enzyme at the completion of the first step. Hydrolysis of these cyclic compounds occurs at a much slower rate through a reversal of the first step, in which the -OH group of water substitutes for the 2'-OH group of the ribose used in the first step, and does not take place until essentially all the susceptible 3',5'-phosphodiester bonds have been cyclised. The enzyme can act as an endo- or exo ribonuclease.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number:
References:
1. Anfinsen, C.B. and White, F.H., Jr. The ribonucleases: occurrence, structure, and properties. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2ndedn, vol.5, Academic Press, New York, 1961, pp. 95-122.
2. Beard, J.R. and Razzell, W.E. Purification of alkaline ribonuclease II from mitochondrial and soluble fractions of liver. J. Biol. Chem. 239 (1964) 4186-4193. [PMID: 14247667]
3. Cannistraro, V.J. and Kennell, D. Purification and characterization of ribonuclease M and mRNA degradation in Escherichia coli. Int. J. Biochem. 181 (1989) 363-370. [PMID: 2653829]
4. Cuchillo, C.M., Pares, X., Guasch, A., Barman, T., Travers, F. and Nogues, M.V. The role of 2',3'-cyclic phosphodiesters in the bovine pancreatic ribonuclease A catalysed cleavage of RNA: intermediates or products. FEBS Lett. 333 (1993) 207-210. [PMID: 7693511]
5. Loverix, S., Laus, G., Martins, J.C., Wyns, L. and Steyaert, J. Reconsidering the energetics of ribonuclease catalysed RNA hydrolysis. Eur. J. Biochem. 257 (1998) 286-290. [PMID: 9799130]
Accepted name: ribonuclease T2
Reaction: RNA + H2O = an [RNA fragment]-3'-nucleoside-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment] (overall reaction)
(1a) RNA = an [RNA fragment]-3'-nucleoside-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]
(1b) an [RNA fragment]-3'-nucleoside-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'-nucleoside-3'-phosphate
Other name(s): ribonuclease II; base-non-specific ribonuclease; nonbase-specific RNase; RNase (non-base specific); non-base specific ribonuclease; nonspecific RNase; RNase Ms; RNase M; RNase II; Escherichia coli ribonuclease II; ribonucleate nucleotido-2'-transferase (cyclizing); acid ribonuclease; RNAase CL; Escherichia coli ribonuclease I' ribonuclease PP2; ribonuclease N2; ribonuclease M; acid RNase; ribonnuclease (non-base specific); ribonuclease (non-base specific); RNase T2; ribonuclease PP3; ribonucleate 3'-oligonucleotide hydrolase; ribonuclease U4
Systematic name: [RNA] 5'-hydroxy-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'- nucleoside-2',3'-cyclophosphate-forming and hydrolysing)
Comments: A widely distributed family of related enzymes found in protozoans, plants, bacteria, animals and viruses that cleave ssRNA 3'-phosphate group with little base specificity. The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending with a 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses the cyclic products in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number:
References:
1. Garcia-Segura, J.M., Orozco, M.M., Fominaya, J.M. and Gavilanes, J.G. Purification, molecular and enzymic characterization of an acid RNase from the insect Ceratitis capitata. Eur. J. Biochem. 158 (1986) 367-372. [PMID: 3732273]
2. Heppel, L.A. Pig liver nuclei ribonuclease. In: Cantoni, G.L. and Davies, D.R. (Eds), Procedures in Nucleic Acid Research, Procedures in Nucleic Acid Research, New York, 1966, pp. 31-36.
3. Reddi, K.K. and Mauser, L.J. Studies on the formation of tobacco mosaic virus ribonucleic acid. VI. Mode of degradation of host ribonucleic acid to ribonucleosides and their conversion to ribonucleoside 5'-phosphates. Proc. Natl. Acad. Sci. USA 53 (1965) 607-613. [PMID: 14338240]
4. Uchida, I. and Egami, F. The specificity of ribonuclease T2. J. Biochem. (Tokyo) 61 (1967) 44-53. [PMID: 6048969]
5. Irie, M. and Ohgi, K. Ribonuclease T2. Methods Enzymol. 341 (2001) 42-55. [PMID: 11582795]
6. Luhtala, N. and Parker, R. T2 Family ribonucleases: ancient enzymes with diverse roles. Trends Biochem. Sci. 35 (2010) 253-259. [PMID: 20189811]
Accepted name: ribonuclease U2
Reaction: [RNA] containing adenosine + H2O = an [RNA fragment]-3'-adenosine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment] (overall reaction)
(1a) [RNA] containing adenosine = an [RNA fragment]-3'-adenosine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]
(1b) an [RNA fragment]-3'-adenosine-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'-adenosine -3'-phosphate
2 [RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment] (overall reaction)
(2a) [RNA] containing guanosine = an [RNA fragment]-3'-guanosine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]
(2b) an [RNA fragment]-3'-guanosine-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'- guanosine-3'-phosphate
Other name(s): purine specific endoribonuclease; ribonuclease U3; RNase U3; RNase U2; purine-specific ribonuclease; purine-specific RNase; Pleospora RNase; Trichoderma koningi RNase III; ribonuclease (purine)
Systematic name: [RNA]-purine 5'-hydroxy-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'-purine-nucleoside -2',3'-cyclophosphate-forming and hydrolysing)
Comments: The enzyme secreted by the fungus Ustilago sphaerogena cleaves at the 3'-phosphate group of purines, and catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending in Ap or Gp with 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Glitz, D.G. and Dekker, C.A. Studies on a ribonuclease from Ustilago sphaerogena. I. Purification and properties of the enzyme. Biochemistry 3 (1964) 1391-1399. [PMID: 14230791]
2. Glitz, D.G. and Dekker, C.A. Studies on a ribonuclease from Ustilago sphaerogena. II. Specificity of the enzyme. Biochemistry 3 (1964) 1399-1406. [PMID: 14230792]
3. Uchida, T. and Egami, F. Microbial ribonucleases with special reference to RNases T1, T 2, N 1, and U2. In: Boyer, P.D. (Ed.), The Enzymes, 3rdedn, vol.4, Academic Press, New York, 1971, pp. 205-250.
4. Martinez-Ruiz, A., Garcia-Ortega, L., Kao, R., Onaderra, M., Mancheno, J.M., Davies, J., Martinez del Pozo, A. and Gavilanes, J.G. Ribonuclease U2: cloning, production in Pichia pastoris and affinity chromatography purification of the active recombinant protein. FEMS Microbiol. Lett. 189 (2000) 165-169. [PMID: 10930732]
Accepted name: Enterobacter ribonuclease
Reaction: RNA containing adenosine-cytidine + H2O = an [RNA fragment]-3'-cytidine-3'-phosphate + a 5'-a hydroxy-adenosine -3'-[RNA fragment] (overall reaction)
(1a) RNA containing adenosine-cytidine = an [RNA fragment]-3'-cytidine-2',3'-cyclophosphate + a 5'-a hydroxy-adenosine -3'-[RNA fragment]
(1b) an [RNA fragment]-3'-cytidine-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'-cytidine-3'-phosphate
Systematic name: [RNA]-adenosine-cytidine 5'-hydroxy-adenosoine ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'-cytidine-2',3'-cyclophosphate-forming and hydrolysing)
Comments: Preference for cleavage at Cp-A bonds. Homopolymers of A, U or G are not hydrolysed. CpG bonds are hydrolysed less well and there is no detectable hydrolysis between two purines or two pyrimidines.The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending a with 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Levy, C.C. and Goldman, P. Residue specificity of a ribonuclease which hydrolyzes polycytidylic acid. J. Biol. Chem. 245 (1970) 3257-3262. [PMID: 5432809]
2. Marotta, C.A., Levy, C.C., Weissman, S.M. and Varricchio, F. Preferred sites of digestion of a ribonuclease from Enterobacter sp. in the sequence analysis of Bacillus stearothermophilus 5S ribonucleic acid. Biochemistry 12 (1973) 2901-2904. [PMID: 4719125]
Accepted name: Bacillus subtilis ribonuclease
Reaction: RNA = a 5'-hydroxy-ribonucleotide + n nucleoside-2',3'-cyclophosphates
Other name(s): Proteus mirabilis RNase; ribonucleate nucleotido-2'-transferase (cyclizing); bacterial RNA lyase; Bacillus subtilis intracellular ribonuclease
Systematic name: [RNA] 5'-hydroxy-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'- nucleoside -2',3'-cyclophosphate-forming)
Comments: This enzyme catalyses endonucleolytic cleavage to 2',3'-cyclic nucleotides. The cyclic products may be hydrolysed to the corresponding 3'-phosphates by 2',3'-cyclic-nucleotide 2'-phosphodiesterase (EC 3.1.4.16). The enzyme from B. subtilis is inhibited by ATP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Nishimura, H. and Maruo, B. Intracellular ribonuclease from Bacillus subtilis. Biochim. Biophys. Acta 40 (1960) 355-357. [PMID: 13854124]
2. Yamasaki, M. and Arima, K. Regulation of intracellular ribonuclease of Bacillus subtilis by ATP and ADP. Biochim. Biophys. Acta 139 (1967) 202-204. [PMID: 4962137]
3. Yamasaki, M. and Arima, K. Intracellular ribonuclease of Bacillus subtilis; specific inhibition by ATP and dATP. Biochem. Biophys. Res. Commun. 37 (1969) 430-436. [PMID: 4981632]
4. Center, M.S. and Behal, F.J. Studies on the ribonuclease activity of Proteus mirabilis. Biochim. Biophys. Acta 151 (1968) 698-699. [PMID: 4296400]
Accepted name: ribotoxin
Reaction: a 28S rRNA containing guanosine-adenosine pair + H2O = an [RNA fragment]-3'-adenosine-3'-phosphate + a 5'-a hydroxy-guanosine-3'-[RNA fragment] (overall reaction)
(1a) a 28S rRNA containing guanosine-adenosine pair = an [RNA fragment]-3'-adenosine-2',3'-cyclophosphate + a 5'-hydroxy-guanosine-3'-[RNA fragment]
(1b) an [RNA fragment]-3'-adenosine-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'-adenosine-3'-phosphate
Other name(s): α-sarcin; rRNA endonuclease (ambiguous)
Systematic name: [28S-rRNA]-guanosine-adenosine 5'-hydroxy-guanosine-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'-adenosine-2',3'-cyclophosphate-forming and hydrolysing)
Comments: Ribotoxins are rRNA endonucleases that catalyse the cleavage of the phosphodiester bond between guanosine and adenosine residues at one specific position in 28S rRNA. The enzyme secreted by Aspergillus giganteus specifically cleaves rat 28S rRNA between G4325 and A4326 and displays cytotoxic activity toward animal cells. It can also act on bacterial rRNAs. The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending with 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Chan, Y.L., Endo, Y. and Wool, I.G. The sequence of the nucleotides at the α-sarcin cleavage site in rat 28 S ribosomal ribonucleic acid. J. Biol. Chem 258 (1983) 12768-12770. [PMID: 6355092]
2. Lacadena, J., Martinez del Pozo, A., Lacadena, V., Martinez-Ruiz, A., Mancheno, J.M., Onaderra, M. and Gavilanes, J.G. The cytotoxin α-sarcin behaves as a cyclizing ribonuclease. FEBS Lett. 424 (1998) 46-48. [PMID: 9580156]
3. Citores, L., Iglesias, R., Ragucci, S., Di Maro, A. and Ferreras, J.M. Antifungal activity of α-sarcin against Penicillium digitatum: proposal of a new role for fungal ribotoxins. ACS Chem. Biol. 13 (2018) 1978-1982. [PMID: 29952541]
Accepted name: ribonuclease T1
Reaction: [RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment] (overall reaction)
(1a) [RNA] containing guanosine = [RNA fragment]-3'-guanosine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]
(1b) [RNA fragment]-3'-guanosine-2',3'-cyclophosphate + H2O = [RNA fragment]-3'-guanosine-3'-phosphate
Other name(s): barnase; bacterial ribonuclease Sa; guanyloribonuclease; Aspergillus oryzae ribonuclease; RNase N1; RNase N2; ribonuclease N3; ribonuclease U1; ribonuclease F1; ribonuclease Ch; ribonuclease PP1; ribonuclease SA; RNase F1; ribonuclease C2; binase; RNase Sa; guanyl-specific RNase; RNase G; RNase T1; ribonuclease guaninenucleotido-2'-transferase (cyclizing); ribonuclease N1
Systematic name: [RNA]-guanosine 5'-hydroxy-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'-guanosine-2',3'-cyclophosphate-forming and hydrolysing)
Comments: A family of related enzymes found in some fungi and bacteria. The enzyme is specific for cleavage at the 3'-phosphate group of guanosine in single stranded RNA, and catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending in Gp with 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Takahashi, K. The structure and function of ribonuclease T1. I. Chromatographic purification and properties of ribonuclease T1. J. Biochem. (Tokyo) 49 (1961) 1-8.
2. Kasai, K., Uchida, T., Egami, F., Yoshida, K. and Nomoto, M. Purification and crystallization of ribonuclease N1 from Neurospora crassa. J. Biochem. (Tokyo) 66 (1969) 389-396. [PMID: 5348588]
3. Loverix, S., Laus, G., Martins, J.C., Wyns, L. and Steyaert, J. Reconsidering the energetics of ribonuclease catalysed RNA hydrolysis. Eur. J. Biochem. 257 (1998) 286-290. [PMID: 9799130]
Accepted name: bacteriophage T4 restriction endoribonuclease RegB
Reaction: a [pre-mRNA]-containing guanosine-adenosine + H2O = a 5' hydroxy-guanosine-[pre-mRNA fragment] + a [pre-mRNA fragment]-3'-adenosine-3'-phosphate
(1a) a [pre-mRNA]-containing guanosine-adenosine + H2O = a 5' hydroxy-guanosine-[pre-mRNA fragment] + a [pre-mRNA fragment]-adenosine-2',3'-cyclophosphate
(1b) a [pre-mRNA fragment]- adenosine-2',3'-cyclophosphate + H2O = a [pre-mRNAfragment]-3'-adenosine-3'-phosphate
Other name(s): RegB
Systematic name: [pre-mRNA]-guanosine-adenosine 5'-hydroxy-guanosine-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'- adenosine -2',3'-cyclophosphate-forming and hydrolysing)
Comments: The enzyme from bacteriophage T4 cleaves early mRNAs between Ap and Gp at one specific specific GpGpApGp site, favouring their further transition to middle-phase mRNA. The activity is enhanced by Ribosomal S1 protein. The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending with 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Sanson, B., Hu, R.M., Troitskayadagger, E., Mathy, N. and Uzan, M. Endoribonuclease RegB from bacteriophage T4 is necessary for the degradation of early but not middle or late mRNAs. J. Mol. Biol. 297 (2000) 1063-1074. [PMID: 10764573]
2. Saida, F., Uzan, M. and Bontems, F. The phage T4 restriction endoribonuclease RegB: a cyclizing enzyme that requires two histidines to be fully active. Nucleic Acids Res. 31 (2003) 2751-2758. [PMID: 12771201]
3. Odaert, B., Saida, F., Aliprandi, P., Durand, S., Crechet, J.B., Guerois, R., Laalami, S., Uzan, M. and Bontems, F. Structural and functional studies of RegB, a new member of a family of sequence-specific ribonucleases involved in mRNA inactivation on the ribosome. J. Biol. Chem. 282 (2007) 2019-2028. [PMID: 17046813]
Accepted name: uridylate cyclase
Reaction: UTP = 3',5'-cyclic UMP + diphosphate
Glossary: 3',5'-cyclic UMP = cUMP
uridylate = CMP
Other name(s): pycC (gene name) (ambiguous)
Systematic name: UTP diphosphate-lyase (cyclizing; 3',5'-cyclic-UMP-forming)
Comments: The enzyme, found in bacteria and archaea, forms cUMP, which functions as a second messenger in bacterial immunity against viruses. The enzyme is synthesized following phage infection and activates immune effectors that execute an antiviral response.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number:
References:
1. Tal, N., Morehouse, B.R., Millman, A., Stokar-Avihail, A., Avraham, C., Fedorenko, T., Yirmiya, E., Herbst, E., Brandis, A., Mehlman, T., Oppenheimer-Shaanan, Y., Keszei, A.FA., Shao, S., Amitai, G., Kranzusch, P.J. and Sorek, R. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell 184 (2021) 5728-5739.e16. [PMID: 34644530]
Accepted name: α-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase
Reaction: α-D-ribose 1-methylphosphonate 5-phosphate + S-adenosyl-L-methionine + reduced electron acceptor = α-D-ribose 1,2-cyclic phosphate 5-phosphate + methane + L-methionine + 5'-deoxyadenosine + oxidized electron acceptor
For diagram of reaction click here.
Other name(s): phnJ (gene name)
Systematic name: α-D-ribose-1-methylphosphonate-5-phosphate C-P-lyase (methane forming)
Comments: This radical SAM (AdoMet) enzyme is part of the C-P lyase complex, which is responsible for processing phophonates into usable phosphate. Contains an [4Fe-4S] cluster. The enzyme from the bacterium Escherichia coli can act on additional α-D-ribose phosphonate substrates with different substituents attached to the phosphonate phosphorus (e.g. α-D-ribose-1-[N-(phosphonomethyl)glycine]-5-phosphate and α-D-ribose-1-(2-N-acetamidomethylphosphonate)-5-phosphate).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Kamat, S.S., Williams, H.J. and Raushel, F.M. Intermediates in the transformation of phosphonates to phosphate by bacteria. Nature 480 (2011) 570-573. [PMID: 22089136]
2. Jochimsen, B., Lolle, S., McSorley, F.R., Nabi, M., Stougaard, J., Zechel, D.L. and Hove-Jensen, B. Five phosphonate operon gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway. Proc. Natl. Acad. Sci. USA 108 (2011) 11393-11398. [PMID: 21705661]
3. Zhang, Q. and van der Donk, W.A. Answers to the carbon-phosphorus lyase conundrum. Chembiochem 13 (2012) 627-629. [PMID: 22334536]
Accepted name: L-piperazate synthase
Reaction: N5-hydroxy-L-ornithine = (3S)-1,2-diazinane-3-carboxylate + H2O
Glossary: (3S)-1,2-diazinane-3-carboxylate = (3S)-pyridazin-3-carboxylate = L-piperazate
Other name(s): ktzT (gene name)
Systematic name: (3S)-1,2-diazinane-3-carboxylate hydrolase (N5-hydroxy-L-ornithine-forming)
Comments: Contains a heme b cofactor. The enzyme, characterized from the bacterium Kutzneria sp. 744, is one of very few enzymes known to result in the formation of an N-N bond. (3S)-1,2-diazinane-3-carboxylate (piperazate) is known to be incorporated into assorted secondary products that are produced by nonribosomal peptide synthetase or nonribosomal peptide synthetase/polyketide synthase hybrid pathways, such as the kutznerides, padanamides, himastatins, and sanglifehrins.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Du, Y.L., He, H.Y., Higgins, M.A. and Ryan, K.S. A heme-dependent enzyme forms the nitrogen-nitrogen bond in piperazate. Nat. Chem. Biol. 13 (2017) 836-838. [PMID: 28628093]
Accepted name: aliphatic aldoxime dehydratase
Reaction: an aliphatic aldoxime = an aliphatic nitrile + H2O
Other name(s): OxdA; aliphatic aldoxime hydro-lyase
Systematic name: aliphatic aldoxime hydro-lyase (aliphatic-nitrile-forming)
Comments: The enzyme from Pseudomonas chlororaphis contains Ca2+ and protoheme IX, the iron of which must be in the form iron(II) for activity. The enzyme exhibits a strong preference for aliphatic aldoximes, such as butyraldoxime and acetaldoxime, over aromatic aldoximes, such as pyridine-2-aldoxime, which is a poor substrate. No activity was found with the aromatic aldoximes benzaldoxime and pyridine-4-aldoxime.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Oinuma, K.-I., Hashimoto, Y., Konishi, K., Goda, M., Noguchi, T., Higashibata, H. and Kobayashi, M. Novel aldoxime dehydratase involved in carbon-nitrogen triple bond synthesis of Pseudomonas chlororaphis B23: Sequencing, gene expression, purification and characterization. J. Biol. Chem. 278 (2003) 29600-29608. [PMID: 12773527]
2. Xie, S.X., Kato, Y., Komeda, H., Yoshida, S. and Asano, Y. A gene cluster responsible for alkylaldoxime metabolism coexisting with nitrile hydratase and amidase in Rhodococcus globerulus A-4. Biochemistry 42 (2003) 12056-12066. [PMID: 14556637]
3. Kato, Y., Yoshida, S., Xie, S.-X. and Asano, Y. Aldoxime dehydratase co-existing with nitrile hydratase and amidase in the iron-type nitrile hydratase-producer Rhodococcus sp. N-771. J. Biosci. Bioeng. 97 (2004) 250-259. [PMID: 16233624]
Accepted name: indoleacetaldoxime dehydratase
Reaction: (indol-3-yl)acetaldehyde oxime = (indol-3-yl)acetonitrile + H2O
For diagram of reaction, click here
Other name(s): indoleacetaldoxime hydro-lyase; 3-indoleacetaldoxime hydro-lyase; indole-3-acetaldoxime hydro-lyase; indole-3-acetaldehyde-oxime hydro-lyase; (indol-3-yl)acetaldehyde-oxime hydro-lyase
Systematic name: (indol-3-yl)acetaldehyde-oxime hydro-lyase [(indol-3-yl)acetonitrile-forming]
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Kumar, S.A. and Mahadevan, S. 3-Indoleacetaldoxime hydro-lyase: a pyridoxal-5'-phosphate activated enzyme. Arch. Biochem. Biophys. 103 (1963) 516-518. [PMID: 14099566]
2. Mahadevan, S. Conversion of 3-indoleacetoxime to 3-indoleacetonitrile by plants. Arch. Biochem. Biophys. 100 (1963) 557-558.
Accepted name: phenylacetaldoxime dehydratase
Reaction: (Z)-phenylacetaldehyde oxime = phenylacetonitrile + H2O
For diagram of reaction, click here
Other name(s): PAOx dehydratase; arylacetaldoxime dehydratase; OxdB; (Z)-phenylacetaldehyde-oxime hydro-lyase
Systematic name: (Z)-phenylacetaldehyde-oxime hydro-lyase (phenylacetonitrile-forming)
Comments: The enzyme from Bacillus sp. OxB-1 contains protoheme IX, the iron of which must be in the form iron(II) for activity. (Z)-Phenylacetaldoxime binds to ferric heme (the iron(III) form) via the oxygen atom whereas it binds to the active ferrous form via the nitrogen atom. In this way, the oxidation state of the heme controls the coordination stucture of the substrate—heme complex, which regulates enzyme activity [2]. The enzyme is active towards several (Z)-arylacetaldoximes and (E/Z)-alkylaldoximes as well as towards arylalkylaldoximes such as 3-phenylpropionaldoxime and 4-phenylbutyraldoxime. However, it is inactive with phenylacetaldoximes that have a substituent group at an α-site of an oxime group, for example, with (E/Z)-2-phenylpropionaldoxime and (E/Z)-mandelaldoxime. The activity of the enzyme is inhibited completely by the heavy-metal cations Cu+, Cu2+, Ag+ and Hg+ whereas Fe2+ and Sn2+ have an activatory effect.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Kato, Y., Nakamura, K., Sakiyama, H., Mayhew, S.G. and Asano, Y. Novel heme-containing lyase, phenylacetaldoxime dehydratase from Bacillus sp. strain OxB-1: purification, characterization, and molecular cloning of the gene. Biochemistry 39 (2000) 800-809. [PMID: 10651646]
2. Kobayashi, K., Yoshioka, S., Kato, Y., Asano, Y. and Aono, S. Regulation of aldoxime dehydratase activity by redox-dependent change in the coordination structure of the aldoxime-heme complex. J. Biol. Chem. 280 (2005) 5486-5490. [PMID: 15596434]
Accepted name: thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming)
Reaction: an N-(sulfonatooxy)alkanimidothioate = a nitrile + sulfate + sulfur
Glossary: an N-(sulfonatooxy)alkanimidothioate = a thiohydroximate-O-sulfate
Other name(s): NSP (gene name); nitrile-specifier protein
Systematic name: thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming)
Comments: The enzyme is involved in the breakdown of glucosinolates. It can act on both aliphatic and aromatic glucosinolates, and forms nitrile-containing products. cf. EC 4.8.1.6, N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming), and EC 4.8.1.7, phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Kissen, R. and Bones, A.M. Nitrile-specifier proteins involved in glucosinolate hydrolysis in Arabidopsis thaliana. J. Biol. Chem. 284 (2009) 12057-12070. [PMID: 19224919]
2. Burow, M., Losansky, A., Muller, R., Plock, A., Kliebenstein, D.J. and Wittstock, U. The genetic basis of constitutive and herbivore-induced ESP-independent nitrile formation in Arabidopsis. Plant Physiol. 149 (2009) 561-574. [PMID: 18987211]
Accepted name: N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming)
Reaction: N-(sulfonatooxy)alkenimidothioic acid with a terminal double bond = an epithionitrile + sulfate
Other name(s): ESP (gene name); epithionitrile-specifier protein; epithiospecifier protein
Systematic name: N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming)
Comments: The enzyme is involved in the breakdown of glucosinolates. It acts only on aliphatic N-(sulfonatooxy)alkenimidothioic acids produced from ω-alkenyl-glucosinolates, and forms epithionitrile-containing products. cf. EC 4.8.1.5, thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming), and EC 4.8.1.7, phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Lambrix, V., Reichelt, M., Mitchell-Olds, T., Kliebenstein, D.J. and Gershenzon, J. The Arabidopsis epithiospecifier protein promotes the hydrolysis of glucosinolates to nitriles and influences Trichoplusia ni herbivory. Plant Cell 13 (2001) 2793-2807. [PMID: 11752388]
2. Zabala M. de, T., Grant, M., Bones, A.M., Bennett, R., Lim, Y.S., Kissen, R. and Rossiter, J.T. Characterisation of recombinant epithiospecifier protein and its over-expression in Arabidopsis thaliana. Phytochemistry 66 (2005) 859-867. [PMID: 15845404]
Accepted name: phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase
Accepted name: phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase
Reaction: phenyl-N-(sulfonatooxy)methanimidothioate = benzylthiocyanate + sulfate
For diagram of reaction click here
Glossary: glucotropaeolin = 1-S-[(1Z)-2-phenyl-N-(sulfonatooxy)ethanimidoyl]-1-thio-β-D-glucopyranose
Other name(s): TFP (gene name) (ambiguous); thiocyanate-forming protein (ambiguous)
Systematic name: phenyl-N-(sulfonatooxy)methanimidothioate sulfate-lyase (benzylthiocyanate-forming)
Comments: The enzyme, characterized from the plant Lepidium sativum, is involved in the breakdown of the glucosinolate glucotropaeolin. Depending on the substrate, it can also form simple nitrile- and epithionitrile-containing products. cf. EC 4.8.1.5, thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming), and EC 4.8.1.6, N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Burow, M., Bergner, A., Gershenzon, J. and Wittstock, U. Glucosinolate hydrolysis in Lepidium sativum - identification of the thiocyanate-forming protein. Plant Mol. Biol. 63 (2007) 49-61. [PMID: 17139450]
Accepted name: N-(sulfonatooxy)prop-2-enimidothioate sulfolyase
Reaction: (1) N-(sulfonatooxy)prop-2-enimidothioate = prop-2-enylthiocyanate + sulfate
(2) N-(sulfonatooxy)prop-2-enimidothioate = 2-(thiiran-2-yl)acetonitrile + sulfate
Other name(s): TFP (gene name) (ambiguous); thiocyanate-forming protein (ambiguous)
Systematic name: N-(sulfonatooxy)prop-2-enimidothioate sulfate-lyase (prop2-enylthiocyanate-forming)
Comments: The enzyme, characterized from the plant Thlaspi arvense, is involved in the breakdown of the glucosinolate sinigrin. Depending on the substrate, it can also form simple nitrile-containing products. cf. EC 4.8.1.5, thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming) and EC 4.8.1.6, N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Kuchernig, J.C., Backenkohler, A., Lubbecke, M., Burow, M. and Wittstock, U. A thiocyanate-forming protein generates multiple products upon allylglucosinolate breakdown in Thlaspi arvense. Phytochemistry 72 (2011) 1699-1709. [PMID: 21783213]
2. Gumz, F., Krausze, J., Eisenschmidt, D., Backenkohler, A., Barleben, L., Brandt, W. and Wittstock, U. The crystal structure of the thiocyanate-forming protein from Thlaspi arvense, a kelch protein involved in glucosinolate breakdown. Plant Mol. Biol. 89 (2015) 67-81. [PMID: 26260516]
3. Eisenschmidt-Bonn, D., Schneegans, N., Backenkohler, A., Wittstock, U. and Brandt, W. Structural diversification during glucosinolate breakdown: mechanisms of thiocyanate, epithionitrile and simple nitrile formation. Plant J. 99 (2019) 329-343. [PMID: 30900313]
EC 4.98.1 Forming coordination complexes
Accepted name: protoporphyrin ferrochelatase
Reaction: protoheme + 2 H+ = protoporphyrin + Fe2+
For diagram of reaction click here
Other name(s): ferro-protoporphyrin chelatase; iron chelatase (ambiguous); heme synthetase (ambiguous); heme synthase (ambiguous); protoheme ferro-lyase; ferrochelatase (ambiguous)
Systematic name: protoheme ferro-lyase (protoporphyrin-forming)
Comments: The enzyme catalyses the terminal step in the heme biosynthesis pathways of eukaryotes and Gram-negative bacteria. The reaction is catalysed only in the reverse direction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Porra, R.J. and Jones, O.T. Studies on ferrochelatase. 1. Assay and properties of ferrochelatase from a pig-liver mitochondrial extract. Biochem. J. 87 (1963) 181-185. [PMID: 13972328]
2. Porra, R.J. and Jones, O.T. Studies on ferrochelatase. 2. An investigation of the role of ferrochelatase in the biosynthesis of various haem prosthetic groups. Biochem. J. 87 (1963) 186-192. [PMID: 13972329]
3. Bloomer, J.R., Hill, H.D., Morton, K.O., Anderson-Burnham, L.A. and Straka, J.G. The enzyme defect in bovine protoporphyria. Studies with purified ferrochelatase. J. Biol. Chem. 262 (1987) 667-671. [PMID: 3805002]
Accepted name: alkylmercury lyase
Reaction: an alkylmercury + H+ = an alkane + Hg2+
Other name(s): organomercury lyase; organomercurial lyase; alkylmercury mercuric-lyase
Systematic name: alkylmercury mercury(II)-lyase (alkane-forming)
Comments: Acts on CH3Hg+ and a number of other alkylmercury and arylmercury compounds, in the presence of cysteine or other thiols, liberating mercury as a mercaptide.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 72560-99-7
References:
1. Tezuka, T. and Tonomura, K. Purification and properties of an enzyme catalyzing the splitting of carbon-mercury linkages from mercury-resistant Pseudomonas K-62 strain. I. Splitting enzyme 1. J. Biochem. (Tokyo) 80 (1976) 79-87. [PMID: 9382]
Accepted name: sirohydrochlorin cobaltochelatase
Reaction: cobalt-sirohydrochlorin + 2 H+ = sirohydrochlorin + Co2+
For diagram of corrin and siroheme biosynthesis (part 2), click here
Other name(s): CbiK; CbiX; CbiXS; anaerobic cobalt chelatase; cobaltochelatase [ambiguous]; sirohydrochlorin cobalt-lyase
Systematic name: cobalt-sirohydrochlorin cobalt-lyase (sirohydrochlorin-forming)
Comments: This enzyme, which forms part of the anaerobic (early cobalt insertion) cobalamin biosynthesis pathway, is an ATP-independent type II chelatase. Two distinct forms are known - a primordial form named CbiX, which is most common in archaea, and a strictly bacterial form named CbiK. See EC 6.6.1.2, cobaltochelatase, for the cobaltochelatase that participates in the aerobic cobalamin biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1. Raux, E., Thermes, C., Heathcote, P., Rambach, A. and Warren, M.J. A role for Salmonella typhimurium cbiK in cobalamin (vitamin B12) and siroheme biosynthesis. J. Bacteriol. 179 (1997) 3202-3212. [PMID: 9150215]
2. Schubert, H.L., Raux, E., Wilson, K.S. and Warren, M.J. Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis. Biochemistry 38 (1999) 10660-10669. [PMID: 10451360]
3. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
4. Brindley, A.A., Raux, E., Leech, H.K., Schubert, H.L. and Warren, M.J. A story of chelatase evolution: Identification and characterisation of a small 13-15 kDa 'ancestral' cobaltochelatase (CbiXS) in the Archaea. J. Biol. Chem. 278 (2003) 22388-22395. [PMID: 12686546]
5. Frank, S., Brindley, A.A., Deery, E., Heathcote, P., Lawrence, A.D., Leech, H.K., Pickersgill, R.W. and Warren, M.J. Anaerobic synthesis of vitamin B12: characterization of the early steps in the pathway. Biochem Soc Trans. 33 (2005) 811-814. [PMID: 16042604]
6. Lobo, S.A., Brindley, A.A., Romao, C.V., Leech, H.K., Warren, M.J. and Saraiva, L.M. Two distinct roles for two functional cobaltochelatases (CbiK) in Desulfovibrio vulgaris hildenborough. Biochemistry 47 (2008) 5851-5857. [PMID: 18457416]
7. Lobo, S.A., Videira, M.A., Pacheco, I., Wass, M.N., Warren, M.J., Teixeira, M., Matias, P.M., Romao, C.V. and Saraiva, L.M. Desulfovibrio vulgaris CbiK(P) cobaltochelatase: evolution of a haem binding protein orchestrated by the incorporation of two histidine residues. Environ. Microbiol. 19 (2017) 106-118. [PMID: 27486032]
Accepted name: sirohydrochlorin ferrochelatase
Reaction: siroheme + 2 H+ = sirohydrochlorin + Fe2+
For diagram click here.
Other name(s): CysG; Met8P; SirB; sirohydrochlorin ferro-lyase (incorrect)
Systematic name: siroheme ferro-lyase (sirohydrochlorin-forming)
Comments: This enzyme catalyses the third of three steps leading to the formation of siroheme from uroporphyrinogen III. The first step involves the donation of two S-adenosyl-L-methionine-derived methyl groups to carbons 2 and 7 of uroporphyrinogen III to form precorrin-2 (EC 2.1.1.107, uroporphyrin-III C-methyltransferase) and the second step involves an NAD+-dependent dehydrogenation to form sirohydrochlorin from precorrin-2 (EC 1.3.1.76, precorrin-2 dehydrogenase). In Saccharomyces cerevisiae, the last two steps are carried out by a single bifunctional enzyme, Met8p. In some bacteria, steps 1-3 are catalysed by a single multifunctional protein called CysG, whereas in Bacillus megaterium, three separate enzymes carry out each of the steps, with SirB being responsible for the above reaction.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Schubert, H.L., Raux, E., Brindley, A.A., Leech, H.K., Wilson, K.S., Hill, C.P. and Warren, M.J. The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase. EMBO J. 21 (2002) 2068-2075. [PMID: 11980703]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
[EC 4.99.1.5 Transferred entry: aliphatic aldoxime dehydratase, now classified as EC 4.8.1.2, aliphatic aldoxime dehydratase (EC 4.99.1.5 created 2004, deleted 2021)]
[EC 4.99.1.6 Transferred entry: indoleacetaldoxime dehydratase, now classified as EC 4.8.1.3, indoleacetaldoxime dehydratase (EC 4.99.1.6 created 1965 as EC 4.2.1.29, transferred 2004 to EC 4.99.1.6, deleted 2021)]
[EC 4.99.1.7 Transferred entry: phenylacetaldoxime dehydratase, now classified as EC 4.8.1.4, phenylacetaldoxime dehydratase (EC 4.99.1.7 created 2005, deleted 2021)]
Accepted name: heme ligase
Reaction: 2 ferriprotoporphyrin IX = β-hematin
Other name(s): heme detoxification protein; HDP; hemozoin synthase
Systematic name: Fe3+:ferriprotoporphyrin IX ligase (β-hematin-forming)
Comments: This heme detoxifying enzyme is found in Plasmodium parasites and converts toxic heme to crystalline hemozoin. These organisms lack the mammalian heme oxygenase for elimination of heme.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Jani, D., Nagarkatti, R., Beatty, W., Angel, R., Slebodnick, C., Andersen, J., Kumar, S. and Rathore, D. HDP-a novel heme detoxification protein from the malaria parasite. PLoS Pathog. 4 (2008) e1000053. [PMID: 18437218]
Accepted name: coproporphyrin ferrochelatase
Reaction: Fe-coproporphyrin III + 2 H+ = coproporphyrin III + Fe2+
Glossary: Fe-coproporphyrin III = coproheme III
Other name(s): hemH (gene name)
Systematic name: protoheme ferro-lyase (protoporphyrin-forming)
Comments: The enzyme, present in Gram-positive bacteria, participates in heme biosynthesis. It can also catalyse the reaction of EC 4.99.1.1, protoporphyrin IX ferrochelatase, at a much lower level.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Hansson, M. and Hederstedt, L. Purification and characterisation of a water-soluble ferrochelatase from Bacillus subtilis. Eur. J. Biochem. 220 (1994) 201-208. [PMID: 8119288]
2. Al-Karadaghi, S., Hansson, M., Nikonov, S., Jonsson, B. and Hederstedt, L. Crystal structure of ferrochelatase: the terminal enzyme in heme biosynthesis. Structure 5 (1997) 1501-1510. [PMID: 9384565]
3. Hansson, M.D., Karlberg, T., Soderberg, C.A., Rajan, S., Warren, M.J., Al-Karadaghi, S., Rigby, S.E. and Hansson, M. Bacterial ferrochelatase turns human: Tyr13 determines the apparent metal specificity of Bacillus subtilis ferrochelatase. J. Biol. Inorg. Chem. 16 (2011) 235-242. [PMID: 21052751]
4. Dailey, H.A., Gerdes, S., Dailey, T.A., Burch, J.S. and Phillips, J.D. Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin. Proc. Natl. Acad. Sci. USA 112 (2015) 2210-2215. [PMID: 25646457]
Accepted name: magnesium dechelatase
Reaction: (1) chlorophyll a + 2 H+ = pheophytin a + Mg2+
(2) chlorophyllide a + 2 H+ = pheophorbide a + Mg2+
For diagram of reaction click here.
Other name(s): SGR (gene name); SGRL (gene name); Mg-dechelatase
Systematic name: chlorophyll a magnesium lyase
Comments: Inhibited by Ca2+, Mg2+ and especially Hg2+. SGR has very low activity with chlorophyllide a and none with chlorophyll b. It acts on chlorophyll a both in its free form and in protein complex. SGRL, on the other hand, is more active with chlorophyllide a than with chlorophyll a. The magnesium formed is scavenged by MCS (metal-chelating substance).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Tang, L., Okazawa, A., Fukusaki, E. and Kobayashi, A. Removal of magnesium by Mg-dechelatase is a major step in the chlorophyll-degrading pathway in Ginkgo biloba in the process of autumnal tints. Z. Naturforsch. C 55 (2000) 923-926. [PMID: 11204197]
2. Costa, M.A., Civello, P.M., Chaves, A.R. and Martínez, G.A. Characterization of Mg-dechelatase activity obtained from Fragaria x ananassa fruit. Plant Physiol. Biochem. 40 (2002) 111-118.
3. Wang, T., Quisenberry, S.S., Ni, X. and Tolmay, V. Enzymatic chlorophyll degradation in wheat near-isogenic lines elicited by cereal aphid (Homoptera: Aphididae) feeding. J. Econ. Entomol. 97 (2004) 661-667. [PMID: 15154496]
4. Suzuki, T., Kunieda, T., Murai, F., Morioka, S. and Shioi, Y. Mg-dechelation activity in radish cotyledons with artificial and native substrates, Mg-chlorophyllin a and chlorophyllide a. Plant Physiol. Biochem. 43 (2005) 459-464. [PMID: 15890522]
5. Kunieda, T., Amano, T. and Shioi, Y. Search for chlorophyll degradation enzyme, Mg-dechelatase, from extracts of Chenopodium album with native and artificial substrates. Plant Sci. 169 (2005) 177-183.
6. Shimoda, Y., Ito, H. and Tanaka, A. Arabidopsis STAY-GREEN, Mendel’s green cotyledon gene, encodes magnesium-dechelatase. Plant Cell 28 (2016) 2147-2160. [PMID: 27604697]
Accepted name: sirohydrochlorin nickelchelatase
Reaction: Ni-sirohydrochlorin + 2 H+ = sirohydrochlorin + Ni2+
For diagram of reaction click here.
Other name(s): cfbA (gene name)
Systematic name: Ni-sirohydrochlorin nickel-lyase (sirohydrochlorin-forming)
Comments: The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, participates in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F430, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase. It catalyses the insertion of the nickel ion into sirohydrochlorin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354 (2016) 339-342. [PMID: 27846569]
Accepted name: pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase
Reaction: Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide = pyridinium-3,5-bisthiocarboxylate mononucleotide + Ni2+
Other name(s): LarC; P2TMN nickel chelatase
Systematic name: Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide nickel-lyase (pyridinium-3,5-bisthiocarboxylate-mononucleotide forming)
Comments: This enzyme, found in Lactobacillus plantarum, is involved in the biosynthesis of a nickel-pincer cofactor. It catalyses the insertion of Ni2+ into the cofactor forming a covalent bond between a carbon atom and the nickel atom.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Desguin, B., Goffin, P., Viaene, E., Kleerebezem, M., Martin-Diaconescu, V., Maroney, M.J., Declercq, J.P., Soumillion, P. and Hols, P. Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Nat Commun 5 (2014) 3615. [PMID: 24710389]
2. Desguin, B., Soumillion, P., Hols, P. and Hausinger, R.P. Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion. Proc. Natl Acad. Sci. USA 113 (2016) 5598-5603. [PMID: 27114550]