An asterisk before "EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: ribitol-5-phosphate 2-dehydrogenase
Reaction: D-ribitol 5-phosphate + NAD(P)+ = D-ribulose 5-phosphate + NAD(P)H + H+
Other name(s): ribitol 5-phosphate dehydrogenase
Systematic name: D-ribitol-5-phosphate:NAD(P)+ 2-oxidoreductase
Comments: The enzyme, characterized from the bacterium Lactobacillus plantarum, can use both NAD+ and NADP+ as electron acceptor [cf. EC 1.1.1.405, ribitol-5-phosphate 2-dehydrogenase (NADP+)].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37250-67-2
References:
1. Glaser, L. Ribitol-5-phosphate dehydrogenase from Lactobacillus plantarum. Biochim. Biophys. Acta 67 (1963) 525-530. [PMID: 13948358]
Accepted name: tetrachlorobenzoquinone reductase
Reaction: 2,3,5,6-tetrachlorohydroquinone + NAD+ = 2,3,5,6-tetrachloro-1,4-benzoquinone + NADH + H+
Other name(s): pcpD (gene name); TCBQ reductase
Systematic name: 2,3,5,6-tetrachlorohydroquinone:NAD+ oxidoreductase
Comments: Contains FMN. The enzyme, characterized from the bacterium Sphingobium chlorophenolicum, participates in the degradation of pentachlorophenol.
References:
1. Chen, L. and Yang, J. Biochemical characterization of the tetrachlorobenzoquinone reductase involved in the biodegradation of pentachlorophenol. Int J Mol Sci 9 (2008) 198-212. [PMID: 19325743]
2. Yadid, I., Rudolph, J., Hlouchova, K. and Copley, S.D. Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol. Proc. Natl. Acad. Sci. USA 110 (2013) E2182-E2190. [PMID: 23676275]
Accepted name: ribitol-5-phosphate 2-dehydrogenase (NADP+)
Reaction: D-ribitol 5-phosphate + NADP+ = D-ribulose 5-phosphate + NADPH + H+
Other name(s): acs1 (gene name); bcs1 (gene name); tarJ (gene name); ribulose-5-phosphate reductase; ribulose-5-P reductase; D-ribulose 5-phosphate reductase
Systematic name: D-ribitol-5-phosphate:NADP+ 2-oxidoreductase
Comments: Requires Zn2+. The enzyme, characterized in bacteria, is specific for NADP. It is part of the synthesis pathway of CDP-ribitol. In Haemophilus influenzae it is part of a multifunctional enzyme also catalysing EC 2.7.7.40, D-ribitol-5-phosphate cytidylyltransferase. cf. EC 1.1.1.137, ribitol-5-phosphate 2-dehydrogenase.
References:
1. Zolli, M., Kobric, D.J. and Brown, E.D. Reduction precedes cytidylyl transfer without substrate channeling in distinct active sites of the bifunctional CDP-ribitol synthase from Haemophilus influenzae. Biochemistry 40 (2001) 5041-5048. [PMID: 11305920]
2. Pereira, M.P. and Brown, E.D. Bifunctional catalysis by CDP-ribitol synthase: convergent recruitment of reductase and cytidylyltransferase activities in Haemophilus influenzae and Staphylococcus aureus. Biochemistry 43 (2004) 11802-11812. [PMID: 15362865]
3. Pereira, M.P., D'Elia, M.A., Troczynska, J. and Brown, E.D. Duplication of teichoic acid biosynthetic genes in Staphylococcus aureus leads to functionally redundant poly(ribitol phosphate) polymerases. J. Bacteriol. 190 (2008) 5642-5649. [PMID: 18556787]
4. Baur, S., Marles-Wright, J., Buckenmaier, S., Lewis, R.J. and Vollmer, W. Synthesis of CDP-activated ribitol for teichoic acid precursors in Streptococcus pneumoniae. J. Bacteriol. 191 (2009) 1200-1210. [PMID: 19074383]
Accepted name: galactitol 2-dehydrogenase (L-tagatose-forming)
Reaction: galactitol + NAD+ = L-tagatose + NADH + H+
Other name(s): GatDH
Systematic name: galactitol:NAD+ 2-oxidoreductase (L-tagatose-forming)
Comments: The enzyme, characterized in the bacterium Rhodobacter sphaeroides, has a wide subtrate specificity. In addition to galactitol, it primarily oxidizes D-threitol and xylitol, and in addition to L-tagatose, it primarily reduces L-erythrulose, D-ribulose and L-glyceraldehyde. It is specific for NAD+. The enzyme also shows activity with D-tagatose (cf. EC 1.1.1.16, galactitol 2-dehydrogenase).
References:
1. Schneider, K.H., Jakel, G., Hoffmann, R. and Giffhorn, F. Enzyme evolution in Rhodobacter sphaeroides: selection of a mutant expressing a new galactitol dehydrogenase and biochemical characterization of the enzyme. Microbiology 141 (1995) 1865-1873. [PMID: 7551050]
2. Carius, Y., Christian, H., Faust, A., Zander, U., Klink, B.U., Kornberger, P., Kohring, G.W., Giffhorn, F. and Scheidig, A.J. Structural insight into substrate differentiation of the sugar-metabolizing enzyme galactitol dehydrogenase from Rhodobacter sphaeroides D. J. Biol. Chem. 285 (2010) 20006-20014. [PMID: 20410293]
Accepted name: D-altritol 5-dehydrogenase
Reaction: D-altritol + NAD+ = D-tagatose + NADH + H+
Systematic name: D-altritol:NAD+ 5-oxidoreductase
Comments: The enzyme, characterized in Agrobacterium fabrum C58, also has low activity with D-mannitol and D-arabinitol. It is part of a D-altritol degradation pathway.
References:
1. Wichelecki, D.J., Vetting, M.W., Chou, L., Al-Obaidi, N., Bouvier, J.T., Almo, S.C. and Gerlt, J.A. ATP-binding cassette (ABC) transport system solute-binding protein-guided identification of novel D-altritol and galactitol catabolic pathways in Agrobacterium tumefaciens C58. J. Biol. Chem. 290 (2015) 28963-28976. [PMID: 26472925]
Accepted name: D-lactate dehydrogenase (quinone)
Reaction: (R)-lactate + a quinone = pyruvate + a quinol
Other name(s): dld (gene name)
Systematic name: (R)-lactate:quinone 2-oxidoreductase
Comments: The enzyme is an FAD-dependent peripheral membrane dehydrogenase that participates in respiration. Electrons derived from D-lactate oxidation are transferred to the membrane soluble quinone pool.
References:
1. Kohn, L.D. and Kaback, H.R. Mechanisms of active transport in isolated bacterial membrane vesicles. XV. Purification and properties of the membrane-bound D-lactate dehydrogenase from Escherichia coli. J. Biol. Chem. 248 (1973) 7012-7017. [PMID: 4582730]
2. Futai, M. Membrane D-lactate dehydrogenase from Escherichia coli. Purification and properties. Biochemistry 12 (1973) 2468-2474. [PMID: 4575624]
3. Matsushita, K. and Kaback, H.R. D-lactate oxidation and generation of the proton electrochemical gradient in membrane vesicles from Escherichia coli GR19N and in proteoliposomes reconstituted with purified D-lactate dehydrogenase and cytochrome o oxidase. Biochemistry 25 (1986) 2321-2327. [PMID: 3013300]
4. Peersen, O.B., Pratt, E.A., Truong, H.T., Ho, C. and Rule, G.S. Site-specific incorporation of 5-fluorotryptophan as a probe of the structure and function of the membrane-bound D-lactate dehydrogenase of Escherichia coli: a 19F nuclear magnetic resonance study. Biochemistry 29 (1990) 3256-3262. [PMID: 2185834]
5. Dym, O., Pratt, E.A., Ho, C. and Eisenberg, D. The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme. Proc. Natl. Acad. Sci. USA 97 (2000) 9413-9418. [PMID: 10944213]
Accepted name: ribonucleoside-triphosphate reductase (formate)
Reaction: ribonucleoside 5'-triphosphate + formate = 2'-deoxyribonucleoside 5'-triphosphate + CO2 + H2O
Other name(s): nrdD (gene name); class III ribonucleoside-triphosphate reductase; anaerobic ribonucleotide reductase
Systematic name: ribonucleoside-5'-triphosphate:formate 2'-oxidoreductase
Comments: The enzyme, which is expressed in the bacterium Escherichia coli during anaerobic growth, contains an iron sulfur center. The active form of the enzyme contains an oxygen-sensitive glycyl radical that is generated by the activating enzyme NrdG via chemistry involving S-adenosylmethionine (SAM) and a [4Fe-4S] cluster. The glycyl radical is involved in generation of a transient thiyl radical on a cysteine residue, which attacks the substrate, forming a ribonucleotide 3'-radical, followed by water loss to form a ketyl radical. The ketyl radical gains an electron from a cysteine residue and a proton from formic acid, forming 3'-keto-deoxyribonucleotide and generating a thiosulfuranyl radical bridge between methionine and cysteine residues. Oxidation of formate by the thiosulfuranyl radical results in the release of CO2 and regeneration of the thiyl radical. cf. EC 1.17.4.1, ribonucleoside-diphosphate reductase and EC 1.17.4.2, ribonucleoside-triphosphate reductase (thioredoxin).
References:
1. Eliasson, R., Pontis, E., Fontecave, M., Gerez, C., Harder, J., Jornvall, H., Krook, M. and Reichard, P. Characterization of components of the anaerobic ribonucleotide reductase system from Escherichia coli. J. Biol. Chem. 267 (1992) 25541-25547. [PMID: 1460049]
2. Mulliez, E., Fontecave, M., Gaillard, J. and Reichard, P. An iron-sulfur center and a free radical in the active anaerobic ribonucleotide reductase of Escherichia coli. J. Biol. Chem. 268 (1993) 2296-2299. [PMID: 8381402]
3. Mulliez, E., Ollagnier, S., Fontecave, M., Eliasson, R. and Reichard, P. Formate is the hydrogen donor for the anaerobic ribonucleotide reductase from Escherichia coli. Proc. Natl. Acad. Sci. USA 92 (1995) 8759-8762. [PMID: 7568012]
4. Ollagnier, S., Mulliez, E., Schmidt, P.P., Eliasson, R., Gaillard, J., Deronzier, C., Bergman, T., Graslund, A., Reichard, P. and Fontecave, M. Activation of the anaerobic ribonucleotide reductase from Escherichia coli. The essential role of the iron-sulfur center for S-adenosylmethionine reduction. J. Biol. Chem. 272 (1997) 24216-24223. [PMID: 9305874]
5. Wei, Y., Mathies, G., Yokoyama, K., Chen, J., Griffin, R.G. and Stubbe, J. A chemically competent thiosulfuranyl radical on the Escherichia coli class III ribonucleotide reductase. J. Am. Chem. Soc. 136 (2014) 9001-9013. [PMID: 24827372]
Accepted name: (R)-2-hydroxyglutarate—pyruvate transhydrogenase
Reaction: (R)-2-hydroxyglutarate + pyruvate = 2-oxoglutarate + (R)-lactate
Other name(s): DLD3 (gene name)
Systematic name: (R)-2-hydroxyglutarate:pyruvate oxidoreductase [(R)-lactate-forming]
Comments: The enzyme, characterized in the yeast Saccharomyces cerevisiae, also functions as EC 1.1.2.4, D-lactate dehydrogenase (cytochrome), and is active with oxaloacetate as electron acceptor forming (R)-malate.
References:
1. Becker-Kettern, J., Paczia, N., Conrotte, J.F., Kay, D.P., Guignard, C., Jung, P.P. and Linster, C.L. Saccharomyces cerevisiae forms D-2-hydroxyglutarate and couples its degradation to D-lactate formation via a cytosolic transhydrogenase. J. Biol. Chem. 291 (2016) 6036-6058. [PMID: 26774271]
Accepted name: crotonobetainyl-CoA reductase
Reaction: γ-butyrobetainyl-CoA + electron-transfer flavoprotein = crotonobetainyl-CoA + reduced electron-transfer flavoprotein
Glossary: γ-butyrobetainyl-CoA = 4-(trimethylammonio)butanoyl-CoA
crotonobetainyl-CoA = (E)-4-(trimethylammonio)but-2-enoyl-CoA
Other name(s): caiA (gene name)
Systematic name: γ-butyrobetainyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase
Comments: The enzyme has been purified from the bacterium Escherichia coli O44 K74, in which it forms a complex with EC 2.8.3.21, L-carnitine CoA-transferase. The electron donor is believed to be an electron-transfer flavoprotein (ETF) encoded by the fixA and fixB genes.
References:
1. Roth, S., Jung, K., Jung, H., Hommel, R.K. and Kleber, H.P. Crotonobetaine reductase from Escherichia coli - a new inducible enzyme of anaerobic metabolization of L(–)-carnitine. Antonie Van Leeuwenhoek 65 (1994) 63-69. [PMID: 8060125]
2. Preusser, A., Wagner, U., Elssner, T. and Kleber, H.P. Crotonobetaine reductase from Escherichia coli consists of two proteins. Biochim. Biophys. Acta 1431 (1999) 166-178. [PMID: 10209289]
3. Elssner, T., Hennig, L., Frauendorf, H., Haferburg, D. and Kleber, H.P. Isolation, identification, and synthesis of γ-butyrobetainyl-CoA and crotonobetainyl-CoA, compounds involved in carnitine metabolism of E. coli. Biochemistry 39 (2000) 10761-10769. [PMID: 10978161]
4. Walt, A. and Kahn, M.L. The fixA and fixB genes are necessary for anaerobic carnitine reduction in Escherichia coli. J. Bacteriol. 184 (2002) 4044-4047. [PMID: 12081978]
Accepted name: menaquinone-9 β-reductase
Reaction: menaquinone-9 + reduced acceptor = β-dihydromenaquinone-9 + acceptor
Glossary: β-dihydromenaquinone-9 = MK-9(II-H2) = 2-methyl-3-[(2E,10E,14E,18E,22E,26E,30E,33E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,10,14,18,22,26,30,33-octaen-1-yl]naphthalene-1,4-dione
Other name(s): MenJ
Systematic name: menaquinone-9 oxidoreductase (β-dihydromenaquinone-9-forming)
Comments: The enzyme from the bacterium Mycobacterium tuberculosis reduces the β-isoprene unit of menaquinone-9, forming the predominant form of menaquinone found in mycobacteria. Contains FAD.
References:
1. Upadhyay, A., Fontes, F.L., Gonzalez-Juarrero, M., McNeil, M.R., Crans, D.C., Jackson, M. and Crick, D.C. Partial saturation of menaquinone in Mycobacterium tuberculosis: function and essentiality of a novel reductase, MenJ. ACS Cent. Sci. 1 (2015) 292-302. [PMID: 26436137]
Accepted name: 2,4-diaminopentanoate dehydrogenase
Reaction: (2R,4S)-2,4-diaminopentanoate + H2O + NAD(P)+ = (2R)-2-amino-4-oxopentanoate + NH3 + NAD(P)H + H+
Other name(s): 2,4-diaminopentanoic acid C4 dehydrogenase
Systematic name: (2R,4S)-2,4-diaminopentanoate:NAD(P)+ oxidoreductase (deaminating)
Comments: Also acts, more slowly, on 2,5-diaminohexanoate forming 2-amino-5-oxohexanoate, which then cyclizes non-enzymically to 1-pyrroline-2-methyl-5-carboxylate. It has equal activity with NAD+ and NADP+ [cf. EC 1.4.1.26, 2,4-diaminopentanoate dehydrogenase (NAD+)].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 39346-26-4
References:
1. Somack, R. and Costilow, R.N. 2,4-Diaminopentanoic acid C4 dehydrogenase. Purification and properties of the protein. J. Biol. Chem. 248 (1973) 385-388. [PMID: 4684685]
2. Stadtman, T.C. Lysine metabolism by clostridia. XIIB 2,4-Diaminohexanoate dehydrogenase (2,4-diaminopentanoate dehydrogenase). Adv. Enzymol. Relat. Areas Mol. Biol. 38 (1973) 441-445.
3. Tsuda, Y. and Friedmann, H.C. Ornithine metabolism by Clostridium sticklandii. Oxidation of ornithine to 2-amino-4-ketopentanoic acid via 2,4-diaminopentanoic acid; participation of B12 coenzyme, pyridoxal phosphate, and pyridine nucleotide. J. Biol. Chem. 245 (1970) 5914-5926. [PMID: 4394942]
Accepted name: L-arginine dehydrogenase
Reaction: L-arginine + H2O + NAD(P)+ = 5-guanidino-2-oxopentanoate + NH3 + NAD(P)H + H+
Other name(s): dauB (gene name); anabolic L-arginine dehydrogenase
Systematic name: L-arginine:NAD(P)+ oxidoreductase (deaminating)
Comments: The enzyme, which has been isolated from the bacterium Pseudomonas aeruginosa PAO1, forms with EC 1.4.99.6, D-arginine dehydrogenase, a two-enzyme complex involved in the racemization of D- and L-arginine.
References:
1. Li, C. and Lu, C.D. Arginine racemization by coupled catabolic and anabolic dehydrogenases. Proc. Natl. Acad. Sci. USA 106 (2009) 906-911. [PMID: 19139398]
Accepted name: 2,4-diaminopentanoate dehydrogenase (NAD+)
Reaction: (2R,4S)-2,4-diaminopentanoate + H2O + NAD+ = (2R)-2-amino-4-oxopentanoate + NH3 + NADH + H+
Other name(s): DAPDH (ambiguous)
Systematic name: (2R,4S)-2,4-diaminopentanoate:NADP+ oxidoreductase (deaminating)
Comments: The enzyme, characterized from an unknown bacterium in an environmental sample, has some activity with (2R,4R)-2,4-diaminopentanoate. It has very low activity with NADP+ (cf. EC 1.4.1.12, 2,4-diaminopentanoate dehydrogenase).
References:
1. Fonknechten, N., Perret, A., Perchat, N., Tricot, S., Lechaplais, C., Vallenet, D., Vergne, C., Zaparucha, A., Le Paslier, D., Weissenbach, J. and Salanoubat, M. A conserved gene cluster rules anaerobic oxidative degradation of L-ornithine. J. Bacteriol. 191 (2009) 3162-3167. [PMID: 19251850]
Accepted name: L-arginine oxidase
Reaction: L-arginine + H2O + O2 = 5-guanidino-2-oxopentanoate + NH3 + H2O2
Systematic name: L-arginine:oxygen oxidoreductase (deaminating)
Comments: Contains FAD. The enzyme from cyanobacteria can also act on other basic amino acids with lower activity. The enzyme from the bacterium Pseudomonas sp. TPU 7192 is highly specific.
References:
1. Miller, D.L. and Rodwell, V.W. Metabolism of basic amino acids in Pseudomonas putida. Intermediates in L-arginine catabolism. J. Biol. Chem. 246 (1971) 5053-5058. [PMID: 5570437]
2. Pistorius, E.K. and Voss, H. Some properties of a basic L-amino-acid oxidase from Anacystis nidulans. Biochim. Biophys. Acta 611 (1980) 227-240. [PMID: 6766743]
3. Gau, A.E., Heindl, A., Nodop, A., Kahmann, U. and Pistorius, E.K. L-amino acid oxidases with specificity for basic L-amino acids in cyanobacteria. Z. Naturforsch. C 62 (2007) 273-284. [PMID: 17542496]
4. Matsui, D., Terai, A. and Asano, Y. L-Arginine oxidase from Pseudomonas sp. TPU 7192: Characterization, gene cloning, heterologous expression, and application to L-arginine determination. Enzyme Microb. Technol. 82 (2016) 151-157. [PMID: 26672462]
Accepted name: D-arginine dehydrogenase
Reaction: D-arginine + acceptor + H2O = 5-guanidino-2-oxopentanoate + NH3 + reduced acceptor (overall reaction)
(1a) D-arginine + acceptor = iminoarginine + reduced acceptor
(1b) iminoarginine + H2O = 5-guanidino-2-oxopentanoate + NH3 (spontaneous)
Glossary: 5-guanidino-2-oxopentanoate = 2-ketoarginine
iminoarginine = 5-carbamimidamido-2-iminopentanoate
Other name(s): D-amino-acid:(acceptor) oxidoreductase (deaminating); D-amino-acid dehydrogenase; D-amino-acid:acceptor oxidoreductase (deaminating)
Systematic name: D-arginine:acceptor oxidoreductase (deaminating)
Comments: Contains a non-covalent FAD cofactor. The enzyme, which has been isolated from the bacterium Pseudomonas aeruginosa PAO1, forms with EC 1.4.1.25, L-arginine dehydrogenase, a two-enzyme complex involved in the racemization of D- and L-arginine. The enzyme has a broad substrate range and can act on most D-amino acids with the exception of D-glutamate and D-aspartate. However, activity is maximal with D-arginine and D-lysine. Not active on glycine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37205-44-0
References:
1. Tsukada, K. D-Amino acid dehydrogenases of Pseudomonas fluorescens. J. Biol. Chem. 241 (1966) 4522-4528. [PMID: 5925166]
2. Li, C. and Lu, C.D. Arginine racemization by coupled catabolic and anabolic dehydrogenases. Proc. Natl. Acad. Sci. USA 106 (2009) 906-911. [PMID: 19139398]
3. Fu, G., Yuan, H., Li, C., Lu, C.D., Gadda, G. and Weber, I.T. Conformational changes and substrate recognition in Pseudomonas aeruginosa D-arginine dehydrogenase. Biochemistry 49 (2010) 8535-8545. [PMID: 20809650]
4. Yuan, H., Fu, G., Brooks, P.T., Weber, I. and Gadda, G. Steady-state kinetic mechanism and reductive half-reaction of D-arginine dehydrogenase from Pseudomonas aeruginosa. Biochemistry 49 (2010) 9542-9550. [PMID: 20932054]
5. Fu, G., Yuan, H., Wang, S., Gadda, G. and Weber, I.T. Atomic-resolution structure of an N5 flavin adduct in D-arginine dehydrogenase. Biochemistry 50 (2011) 6292-6294. [PMID: 21707047]
6. Yuan, H., Xin, Y., Hamelberg, D. and Gadda, G. Insights on the mechanism of amine oxidation catalyzed by D-arginine dehydrogenase through pH and kinetic isotope effects. J. Am. Chem. Soc. 133 (2011) 18957-18965. [PMID: 21999550]
Accepted name: N-[(2S)-2-amino-2-carboxyethyl]-L-glutamate dehydrogenase
Reaction: N-[(2S)-2-amino-2-carboxyethyl]-L-glutamate + NAD+ + H2O = 2-oxoglutarate + L-2,3-diaminopropanoate + NADH + H+
Other name(s): SbnB
Systematic name: N-[(2S)-2-amino-2-carboxyethyl]-L-glutamate:NAD+ dehydrogenase (L-2,3-diaminopropanoate-forming)
Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of the siderophore staphyloferrin B.
References:
1. Beasley, F.C., Cheung, J. and Heinrichs, D.E. Mutation of L-2,3-diaminopropionic acid synthase genes blocks staphyloferrin B synthesis in Staphylococcus aureus. BMC Microbiol. 11 (2011) 199. [PMID: 21906287]
2. Kobylarz, M.J., Grigg, J.C., Takayama, S.J., Rai, D.K., Heinrichs, D.E. and Murphy, M.E. Synthesis of L-2,3-diaminopropionic acid, a siderophore and antibiotic precursor. Chem. Biol. 21 (2014) 379-388. [PMID: 24485762]
Accepted name: thiosulfate reductase (cytochrome)
Reaction: sulfite + hydrogen sulfide + 2 ferricytochrome c3 = thiosulfate + 2 ferrocytochrome c3
Systematic name: sulfite,hydrogen sulfide:ferricytochrome-c3 oxidoreductase (thiosulfate-forming)
Comments: The enzyme is found in sulfate-reducing bacteria. The source of the electrons is molecular hydrogen, via EC 1.12.2.1, cytochrome-c3 hydrogenase. The organisms utilize the sulfite that is produced for energy generation by EC 1.8.99.5, dissimilatory sulfite reductase.
References:
1. Ishimoto, M. and Koyama, J. On the role of a cytochrome in the thiosulfate reduction by sulfate-reducing bacterium. B. Chem. Soc. Jpn. 28 (1955) 231b-232.
2. Ishimoto, M., Toyama, J. Biochemical studies on sulfate reducing bacteria. VI. Separation of hydrogenase and thiosulfate reductase and partial purification of cytochrome and green pigment. J. Biochem. (Tokyo) 44 (1957) 233-242.
3. Nakatsukasa, W. and Akagi, J.M. Thiosulfate reductase isolated from Desulfotomaculum nigrificans. J. Bacteriol. 98 (1969) 429-433. [PMID: 5784203]
4. Haschke, R.H. and Campbell, L.L. Thiosulfate reductase of Desulfovibrio vulgaris. J. Bacteriol. 106 (1971) 603-607. [PMID: 5573735]
5. Hatchikian, E.C. Purification and properties of thiosulfate reductase from Desulfovibrio gigas. Arch. Microbiol. 105 (1975) 249-256. [PMID: 242299]
6. Aketagawa, J., Kobayashi, K. and Ishimoto, M. Purification and properties of thiosulfate reductase from Desulfovibrio vulgaris, Miyazaki F. J. Biochem. 97 (1985) 1025-1032. [PMID: 2993256]
Accepted name: glutathionyl-hydroquinone reductase
Reaction: glutathione + 2-(glutathione-S-yl)-hydroquinone = glutathione disulfide + hydroquinone
Other name(s): pcpF (gene name); yqjG (gene name)
Systematic name: 2-(glutathione-S-yl)-hydroquinone:glutathione oxidoreductase
Comments: This type of enzymes, which are found in bacteria, halobacteria, fungi, and plants, catalyse the glutathione-dependent reduction of glutathionyl-hydroquinones. The enzyme from the bacterium Sphingobium chlorophenolicum can act on halogenated substrates such as 2,6-dichloro-3-(glutathione-S-yl)-hydroquinone and 2,3,5-trichloro-6-(glutathione-S-yl)-hydroquinone. Substrates for these enzymes are often formed spontaneously by interaction of benzoquinones with glutathione.
References:
1. Huang, Y., Xun, R., Chen, G. and Xun, L. Maintenance role of a glutathionyl-hydroquinone lyase (PcpF) in pentachlorophenol degradation by Sphingobium chlorophenolicum ATCC 39723. J. Bacteriol. 190 (2008) 7595-7600. [PMID: 18820023]
2. Xun, L., Belchik, S.M., Xun, R., Huang, Y., Zhou, H., Sanchez, E., Kang, C. and Board, P.G. S-Glutathionyl-(chloro)hydroquinone reductases: a novel class of glutathione transferases. Biochem. J. 428 (2010) 419-427. [PMID: 20388120]
3. Lam, L.K., Zhang, Z., Board, P.G. and Xun, L. Reduction of benzoquinones to hydroquinones via spontaneous reaction with glutathione and enzymatic reaction by S-glutathionyl-hydroquinone reductases. Biochemistry 51 (2012) 5014-5021. [PMID: 22686328]
4. Green, A.R., Hayes, R.P., Xun, L. and Kang, C. Structural understanding of the glutathione-dependent reduction mechanism of glutathionyl-hydroquinone reductases. J. Biol. Chem. 287 (2012) 35838-35848. [PMID: 22955277]
Accepted name: anthocyanidin synthase
Reaction: a (2R,3S,4S)-leucoanthocyanidin + 2-oxoglutarate + O2 = an anthocyanidin + succinate + CO2 + 2 H2O (overall reaction)
(1a) a (2R,3S,4S)-leucoanthocyanidin + 2-oxoglutarate + O2 = a (4S)- 2,3-dehydroflavan-3,4-diol + succinate + CO2 + H2O
(1b) a (4S)- 2,3-dehydroflavan-3,4-diol = an anthocyanidin + H2O
For diagram of reaction click here
Glossary: taxifolin = 3,4-dihydroquercitin
Other name(s): leucocyanidin oxygenase; leucocyanidin,2-oxoglutarate:oxygen oxidoreductase; ANS (gene name)
Systematic name: (2R,3S,4S)-leucoanthocyanidin,2-oxoglutarate:oxygen oxidoreductase
Comments: The enzyme requires Fe(II) and ascorbate. It is involved in the pathway by which many flowering plants make anthocyanin flower pigments (glycosylated anthocyandins). The enzyme hydroxylates the C-3 carbon, followed by a trans diaxial elimination, forming a C-2,C-3 enol. The product loses a second water molecule to form anthocyanidins. When assayed in vitro, non-enzymic epimerization of the product can lead to formation of dihydroflavanols. Thus when the substrate is leucocyanidin, a mixture of (+)-taxifolin and (+)-epitaxifolin are formed. The enzyme can also oxidize the formed (+)-taxifolin to quercetin (cf. EC 1.14.11.23, flavonol synthase) [2,3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 180984-01-4
References:
1. Saito, K., Kobayashi, M., Gong, Z., Tanaka, Y. and Yamazaki, M. Direct evidence for anthocyanidin synthase as a 2-oxoglutarate-dependent oxygenase: molecular cloning and functional expression of cDNA from a red forma of Perilla frutescens. Plant J. 17 (1999) 181-190. [PMID: 10074715]
2. Turnbull, J.J., Sobey, W.J., Aplin, R.T., Hassan, A., Firmin, J.L., Schofield, C.J. and Prescott, A.G. Are anthocyanidins the immediate products of anthocyanidin synthase? Chem. Commun. (2000) 2473-2474.
3. Wilmouth, R.C., Turnbull, J.J., Welford, R.W., Clifton, I.J., Prescott, A.G. and Schofield, C.J. Structure and mechanism of anthocyanidin synthase from Arabidopsis thaliana. Structure 10 (2002) 93-103. [PMID: 11796114]
4. Turnbull, J.J., Nagle, M.J., Seibel, J.F., Welford, R.W., Grant, G.H. and Schofield, C.J. The C-4 stereochemistry of leucocyanidin substrates for anthocyanidin synthase affects product selectivity. Bioorg. Med. Chem. Lett. 13 (2003) 3853-3857. [PMID: 14552794]
5. Wellmann, F., Griesser, M., Schwab, W., Martens, S., Eisenreich, W., Matern, U. and Lukacin, R. Anthocyanidin synthase from Gerbera hybrida catalyzes the conversion of (+)-catechin to cyanidin and a novel procyanidin. FEBS Lett. 580 (2006) 1642-1648. [PMID: 16494872]
Accepted name: ectoine hydroxylase
Reaction: ectoine + 2-oxoglutarate + O2 = 5-hydroxyectoine + succinate + CO2
Glossary: ectoine = (4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate
5-hydroxyectoine = (4S,5S)-5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate
Other name(s): ectD (gene name); ectoine dioxygenase
Systematic name: ectoine,2-oxoglutarate:oxygen oxidoreductase (5-hydroxylating)
Comments: Requires Fe2+ and ascorbate. The enzyme, found in bacteria, is specific for ectoine.
References:
1. Bursy, J., Pierik, A.J., Pica, N. and Bremer, E. Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase. J. Biol. Chem. 282 (2007) 31147-31155. [PMID: 17636255]
2. Bursy, J., Kuhlmann, A.U., Pittelkow, M., Hartmann, H., Jebbar, M., Pierik, A.J. and Bremer, E. Synthesis and uptake of the compatible solutes ectoine and 5-hydroxyectoine by Streptomyces coelicolor A3(2) in response to salt and heat stresses. Appl. Environ. Microbiol. 74 (2008) 7286-7296. [PMID: 18849444]
3. Reuter, K., Pittelkow, M., Bursy, J., Heine, A., Craan, T. and Bremer, E. Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD. PLoS One 5 (2010) e10647. [PMID: 20498719]
Accepted name: L-proline cis-4-hydroxylase
Reaction: L-proline + 2-oxoglutarate + O2 = cis-4-hydroxy-L-proline + succinate + CO2
Systematic name: L-proline,2-oxoglutarate:oxygen oxidoreductase (cis-4-hydroxylating)
Comments: Requires Fe2+ and ascorbate. The enzyme, isolated from Rhizobium species, only produces cis-4-hydroxy-L-proline (cf. EC 1.14.11.57, L-proline trans-4-hydroxylase).
References:
1. Hara, R. and Kino, K. Characterization of novel 2-oxoglutarate dependent dioxygenases converting L-proline to cis-4-hydroxy-L-proline. Biochem. Biophys. Res. Commun. 379 (2009) 882-886. [PMID: 19133227]
Accepted name: L-proline trans-4-hydroxylase
Reaction: L-proline + 2-oxoglutarate + O2 = trans-4-hydroxy-L-proline + succinate + CO2
Systematic name: L-proline,2-oxoglutarate:oxygen oxidoreductase (trans-4-hydroxylating)
Comments: Requires Fe2+ and ascorbate. The enzyme, isolated from multiple bacterial species, only produces trans-4-hydroxy-L-proline (cf. EC 1.14.11.56, L-proline cis-4-hydroxylase).
References:
1. Lawrence, C.C., Sobey, W.J., Field, R.A., Baldwin, J.E. and Schofield, C.J. Purification and initial characterization of proline 4-hydroxylase from Streptomyces griseoviridus P8648: a 2-oxoacid, ferrous-dependent dioxygenase involved in etamycin biosynthesis. Biochem. J. 313 (1996) 185-191. [PMID: 8546682]
2. Shibasaki, T., Mori, H., Chiba, S. and Ozaki, A. Microbial proline 4-hydroxylase screening and gene cloning. Appl. Environ. Microbiol. 65 (1999) 4028-4031. [PMID: 10473412]
Accepted name: pentachlorophenol monooxygenase
Reaction: (1) pentachlorophenol + NADPH + H+ + O2 = 2,3,5,6-tetrachloro-1,4-benzoquinone + NADP+ + chloride + H2O
(2) 2,3,5,6-tetrachlorophenol + NADPH + H+ + O2 = 2,3,5,6-tetrachlorohydroquinone + NADP+ + H2O
Other name(s): pcpB (gene name); pentachlorophenol dechlorinase; pentachlorophenol dehalogenase; pentachlorophenol 4-monooxygenase; PCP hydroxylase; pentachlorophenol hydroxylase; PCB 4-monooxygenase; PCB4MO
Systematic name: pentachlorophenol,NADPH:oxygen oxidoreductase (hydroxylating, dechlorinating)
Comments: A flavoprotein (FAD). The enzyme displaces a diverse range of substituents from the 4-position of polyhalogenated phenols but requires that a halogen substituent be present at the 2-position [2]. If C-4 carries a halogen substituent, reaction 1 is catalysed; if C-4 is unsubstituted, reaction 2 is catalysed.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 136111-57-4
References:
1. Schenk, T., Müller, R., Mörsberger, F., Otto, M.K. and Lingens, F. Enzymatic dehalogenation of pentachlorophenol by extracts from Arthrobacter sp. strain ATCC 33790. J. Bacteriol. 171 (1989) 5487-5491. [PMID: 2793827]
2. Xun, L., Topp, E. and Orser, C.S. Diverse substrate range of a Flavobacterium pentachlorophenol hydroxylase and reaction stoichiometries. J. Bacteriol. 174 (1992) 2898-2902. [PMID: 1569020]
3. Xun, L., Topp, E. and Orser, C.S. Confirmation of oxidative dehalogenation of pentachlorophenol by a Flavobacterium pentachlorophenol hydroxylase. J. Bacteriol. 174 (1992) 5745-5747. [PMID: 1512208]
4. Lange, C.C., Schneider, B.J. and Orser, C.S. Verification of the role of PCP 4-monooxygenase in chlorine elimination from pentachlorophenol by Flavobacterium sp. strain ATCC 39723. Biochem. Biophys. Res. Commun. 219 (1996) 146-149. [PMID: 8619798]
5. Nakamura, T., Motoyama, T., Hirono, S. and Yamaguchi, I. Identification, characterization, and site-directed mutagenesis of recombinant pentachlorophenol 4-monooxygenase. Biochim. Biophys. Acta 1700 (2004) 151-159. [PMID: 15262224]
6. Chen, L. and Yang, J. Biochemical characterization of the tetrachlorobenzoquinone reductase involved in the biodegradation of pentachlorophenol. Int J Mol Sci 9 (2008) 198-212. [PMID: 19325743]
7. Hlouchova, K., Rudolph, J., Pietari, J.M., Behlen, L.S. and Copley, S.D. Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum. Biochemistry 51 (2012) 3848-3860. [PMID: 22482720]
8. Rudolph, J., Erbse, A.H., Behlen, L.S. and Copley, S.D. A radical intermediate in the conversion of pentachlorophenol to tetrachlorohydroquinone by Sphingobium chlorophenolicum. Biochemistry 53 (2014) 6539-6549. [PMID: 25238136]
Accepted name: magnesium-protoporphyrin IX monomethyl ester (oxidative) cyclase
Reaction: magnesium-protoporphyrin IX 13-monomethyl ester + 3 NADPH + 3 H+ + 3 O2 = 3,8-divinyl protochlorophyllide a + 3 NADP+ + 5 H2O (overall reaction)
(1a) magnesium-protoporphyrin IX 13-monomethyl ester + NADPH + H+ + O2 = 131-hydroxy-magnesium-protoporphyrin IX 13-monomethyl ester + NADP+ + H2O
(1b) 131-hydroxy-magnesium-protoporphyrin IX 13-monomethyl ester + NADPH + H+ + O2 = 131-oxo-magnesium-protoporphyrin IX 13-monomethyl ester + NADP+ + 2 H2O
(1c) 131-oxo-magnesium-protoporphyrin IX 13-monomethyl ester + NADPH + H+ + O2 = 3,8-divinyl protochlorophyllide a + NADP+ + 2 H2O
For diagram of reaction click here.
Other name(s): Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase
Systematic name: magnesium-protoporphyrin-IX 13-monomethyl ester,NADPH:oxygen oxidoreductase (hydroxylating)
Comments: Requires Fe(II) for activity. The enzyme participates in the biosynthesis of chlorophyllide a in aerobic organisms. The same transformation is achieved in anaerobic organisms by EC 1.21.98.3, anaerobic magnesium-protoporphyrin IX monomethyl ester cyclase. Some facultative phototrophic bacteria, such as Rubrivivax gelatinosus, possess both enzymes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 92353-62-3
References:
1. Walker, C.J., Mansfield, K.E., Rezzano, I.N., Hanamoto, C.M., Smith, K.M. and Castelfranco, P.A. The magnesium-protoporphyrin IX (oxidative) cyclase system. Studies on the mechanism and specificity of the reaction sequence. Biochem. J. 255 (1988) 685-692. [PMID: 3202840]
2. Bollivar, D.W. and Beale, S.I. The chlorophyll biosynthetic enzyme Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase (characterization and partial purification from Chlamydomonas reinhardtii and Synechocystis sp. PCC 6803). Plant Physiol. 112 (1996) 105-114. [PMID: 12226378]
3. Pinta, V., Picaud, M., Reiss-Husson, F. and Astier, C. Rubrivivax gelatinosus acsF (previously orf358) codes for a conserved, putative binuclear-iron-cluster-containing protein involved in aerobic oxidative cyclization of Mg-protoporphyrin IX monomethylester. J. Bacteriol. 184 (2002) 746-753. [PMID: 11790744]
4. Tottey, S., Block, M.A., Allen, M., Westergren, T., Albrieux, C., Scheller, H.V., Merchant, S. and Jensen, P.E. Arabidopsis CHL27, located in both envelope and thylakoid membranes, is required for the synthesis of protochlorophyllide. Proc. Natl. Acad. Sci. USA 100 (2003) 16119-16124. [PMID: 14673103]
[EC 1.14.13.117 Transferred entry: isoleucine N-monooxygenase, Now EC 1.14.14.39, isoleucine N-monooxygenase (EC 1.14.13.117 created 2010, deleted 2017)]
[EC 1.14.13.118 Transferred entry: valine N-monooxygenase. Now EC 1.14.14.38, valine N-monooxygenase (EC 1.14.13.118 created 2010, deleted 2017)]
[EC 1.14.13.124 Transferred entry: phenylalanine N-monooxygenase, now classified as EC 1.14.14.40, phenylalanine N-monooxygenase (EC 1.14.13.124 created 2011, deleted 2017)]
Accepted name: valine N-monooxygenase
Reaction: L-valine + 2 O2 + 2 [reduced NADPH—hemoprotein reductase] = (E)-2-methylpropanal oxime + 2 [oxidized NADPH—hemoprotein reductase] + CO2 + 3 H2O (overall reaction)
(1a) L-valine + O2 + [reduced NADPH—hemoprotein reductase] = N-hydroxy-L-valine + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) N-hydroxy-L-valine + O2 + [reduced NADPH—hemoprotein reductase] = N,N-dihydroxy-L-valine + [oxidized NADPH—hemoprotein reductase] + H2O
(1c) N,N-dihydroxy-L-valine = (E)-2-methylpropanal oxime + CO2 + H2O
Other name(s): CYP79D1; CYP79D2
Systematic name: L-valine,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (N-hydroxylating)
Comments: A cytochrome P-450 (heme-thiolate) protein. This enzyme catalyses two successive N-hydroxylations of L-valine, the committed step in the biosynthesis of the cyanogenic glucoside linamarin in Manihot esculenta (cassava). The product of the two hydroxylations, N,N-dihydroxy-L-valine, is labile and undergoes dehydration and decarboxylation that produce the (E) isomer of the oxime. It is still not known whether the decarboxylation is spontaneous or catalysed by the enzyme. The enzyme can also accept L-isoleucine as substrate, with a lower activity. It is different from EC 1.14.14.39, isoleucine N-monooxygenase, which prefers L-isoleucine.
References:
1. Andersen, M.D., Busk, P.K., Svendsen, I. and Møller, B.L. Cytochromes P-450 from cassava (Manihot esculenta Crantz) catalyzing the first steps in the biosynthesis of the cyanogenic glucosides linamarin and lotaustralin. Cloning, functional expression in Pichia pastoris, and substrate specificity of the isolated recombinant enzymes. J. Biol. Chem. 275 (2000) 1966-1975. [PMID: 10636899]
2. Forslund, K., Morant, M., Jørgensen, B., Olsen, C.E., Asamizu, E., Sato, S., Tabata, S. and Bak, S. Biosynthesis of the nitrile glucosides rhodiocyanoside A and D and the cyanogenic glucosides lotaustralin and linamarin in Lotus japonicus. Plant Physiol. 135 (2004) 71-84. [PMID: 15122013]
Accepted name: isoleucine N-monooxygenase
Reaction: L-isoleucine + 2 O2 + 2 [reduced NADPH—hemoprotein reductase] = (1E,2S)-2-methylbutanal oxime + 2 [oxidized NADPH—hemoprotein reductase] + CO2 + 3 H2O (overall reaction)
(1a) L-isoleucine + O2 + [reduced NADPH—hemoprotein reductase] = N-hydroxy-L-isoleucine + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) N-hydroxy-L-isoleucine + O2 + [reduced NADPH—hemoprotein reductase] = N,N-dihydroxy-L-isoleucine + [oxidized NADPH—hemoprotein reductase] + H2O
(1c) N,N-dihydroxy-L-isoleucine = (1E,2S)-2-methylbutanal oxime + CO2 + H2O (spontaneous)
Other name(s): CYP79D3 (gene name); CYP79D4 (gene name)
Systematic name: L-isoleucine,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (N-hydroxylating)
Comments: This cytochrome P-450 (heme-thiolate) enzyme, found in plants, catalyses two successive N-hydroxylations of L-isoleucine, the committed step in the biosynthesis of the cyanogenic glucoside lotaustralin. The product of the two hydroxylations, N,N-dihydroxy-L-isoleucine, is labile and undergoes dehydration followed by decarboxylation, producing the oxime. It is still not known whether the decarboxylation is spontaneous or catalysed by the enzyme. The enzyme can also accept L-valine, but with a lower activity. cf. EC 1.14.14.38, valine N-monooxygenase.
References:
1. Andersen, M.D., Busk, P.K., Svendsen, I. and Møller, B.L. Cytochromes P-450 from cassava (Manihot esculenta Crantz) catalyzing the first steps in the biosynthesis of the cyanogenic glucosides linamarin and lotaustralin. Cloning, functional expression in Pichia pastoris, and substrate specificity of the isolated recombinant enzymes. J. Biol. Chem. 275 (2000) 1966-1975. [PMID: 10636899]
2. Forslund, K., Morant, M., Jørgensen, B., Olsen, C.E., Asamizu, E., Sato, S., Tabata, S. and Bak, S. Biosynthesis of the nitrile glucosides rhodiocyanoside A and D and the cyanogenic glucosides lotaustralin and linamarin in Lotus japonicus. Plant Physiol. 135 (2004) 71-84. [PMID: 15122013]
Accepted name: phenylalanine N-monooxygenase
Reaction: L-phenylalanine + 2 O2 + 2 [reduced NADPH—hemoprotein reductase] = (E)-phenylacetaldoxime + 2 [oxidized NADPH—hemoprotein reductase] + CO2 + 3 H2O (overall reaction)
(1a) L-phenylalanine + O2 + [reduced NADPH—hemoprotein reductase] = N-hydroxy-L-phenylalanine + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) N-hydroxy-L-phenylalanine + O2 + [reduced NADPH—hemoprotein reductase] = N,N-dihydroxy-L-phenylalanine + [oxidized NADPH—hemoprotein reductase] + H2O
(1c) N,N-dihydroxy-L-phenylalanine = (E)-phenylacetaldoxime + CO2 + H2O
Other name(s): phenylalanine N-hydroxylase; CYP79A2 (gene name); CYP79D16 (gene name)
Systematic name: L-phenylalanine,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (N-hydroxylating)
Comments: This cytochrome P-450 (heme-thiolate) enzyme, found in plants, catalyses two successive N-hydroxylations of L-phenylalanine, a committed step in the biosynthesis of benzylglucosinolate and the cyanogenic glucosides (R)-prunasin and (R)-amygdalin. The product of the two hydroxylations, N,N-dihydroxy-L-phenylalanine, is labile and undergoes dehydration followed by decarboxylation, producing an oxime. It is still not known whether the decarboxylation is spontaneous or catalysed by the enzyme.
References:
1. Wittstock, U. and Halkier, B.A. Cytochrome P450 CYP79A2 from Arabidopsis thaliana L. Catalyzes the conversion of L-phenylalanine to phenylacetaldoxime in the biosynthesis of benzylglucosinolate. J. Biol. Chem. 275 (2000) 14659-14666. [PMID: 10799553]
2. Yamaguchi, T., Yamamoto, K. and Asano, Y. Identification and characterization of CYP79D16 and CYP71AN24 catalyzing the first and second steps in L-phenylalanine-derived cyanogenic glycoside biosynthesis in the Japanese apricot, Prunus mume Sieb. et Zucc. Plant Mol. Biol. 86 (2014) 215-223. [PMID: 25015725]
Accepted name: (E)-2-methylbutanal oxime monooxygenase
Reaction: (1) (E)-2-methylbutanal oxime + [reduced NADPH—hemoprotein reductase] + O2 = 2-hydroxy-2-methylbutanenitrile + [oxidized NADPH—hemoprotein reductase] + 2 H2O (overall reaction)
(1a) (E)-2-methylbutanal oxime = (Z)-2-methylbutanal oxime
(1b) (Z)-2-methylbutanal oxime = 2-methylbutanenitrile + H2O
(1c) 2-methylbutanenitrile + [reduced NADPH—hemoprotein reductase] + O2 = 2-hydroxy-2-methylbutanenitrile + [oxidized NADPH—hemoprotein reductase] + H2O
(2) (E)-2-methylpropanal oxime + [reduced NADPH—hemoprotein reductase] + O2 = 2-hydroxy-2-methylpropanenitrile + [oxidized NADPH—hemoprotein reductase] + 2 H2O (overall reaction)
(2a) (E)-2-methylpropanal oxime = (Z)-2-methylpropanal oxime
(2b) (Z)-2-methylpropanal oxime = 2-methylpropanenitrile + H2O
(2c) 2-methylpropanenitrile + [reduced NADPH—hemoprotein reductase] + O2 = 2-hydroxy-2-methylpropanenitrile + [oxidized NADPH—hemoprotein reductase] + H2O
Other name(s): CYP71E7 (gene name)
Systematic name: (E)-2-methylbutanal oxime,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase
Comments: This cytochrome P-450 (heme thiolate) enzyme is involved in the biosynthesis of the cyanogenic glucosides lotaustralin and linamarin. It catalyses three different activities - isomerization of its substrate, the (E) isomer, to the (Z) isomer, dehydration, and C-hydroxylation.
References:
1. Jørgensen, K., Morant, A.V., Morant, M., Jensen, N.B., Olsen, C.E., Kannangara, R., Motawia, M.S., Møller, B.L. and Bak, S. Biosynthesis of the cyanogenic glucosides linamarin and lotaustralin in cassava: isolation, biochemical characterization, and expression pattern of CYP71E7, the oxime-metabolizing cytochrome P450 enzyme. Plant Physiol. 155 (2011) 282-292. [PMID: 21045121]
Accepted name: homomethionine N-monooxygenase
Reaction: an L-polyhomomethionine + 2 O2 + 2 [reduced NADPH—hemoprotein reductase] = an ω-(methylthio)-(E)-alkanal oxime + CO2 + 3 H2O + 2 [oxidized NADPH—hemoprotein reductase] (overall reaction)
(1a) an L-polyhomomethionine + O2 + [reduced NADPH—hemoprotein reductase] = an L-N-hydroxypolyhomomethionine + H2O + [oxidized NADPH—hemoprotein reductase]
(1b) an L-N-hydroxypolyhomomethionine + O2 + [reduced NADPH—hemoprotein reductase] = an L-N,N-dihydroxypolyhomomethionine + H2O + [oxidized NADPH—hemoprotein reductase]
(1c) an L-N,N-dihydroxypolyhomomethionine = ω-(methylthio)-(E)-alkanal oxime + CO2 + H2O
Other name(s): CYP79F1 (gene name); CYP79F2 (gene name)
Systematic name: L-homomethionine,[NADPH—hemoprotein reductase]:oxygen oxidoreductase
Comments: This plant cytochrome P-450 (heme thiolate) enzyme is involved in methionine-derived aliphatic glucosinolates biosynthesis. It catalyses two successive N-hydroxylations, which are followed by dehydration and decarboxylation. CYP79F1 from Arabidopsis thaliana can metabolize homo-, di-, tri-, tetra-, penta-, and hexahomomethionine to their corresponding aldoximes, while CYP79F2 from the same plant can only metabolize penta- and hexahomomethionine.
References:
1. Hansen, C.H., Wittstock, U., Olsen, C.E., Hick, A.J., Pickett, J.A. and Halkier, B.A. Cytochrome p450 CYP79F1 from Arabidopsis catalyzes the conversion of dihomomethionine and trihomomethionine to the corresponding aldoximes in the biosynthesis of aliphatic glucosinolates. J. Biol. Chem. 276 (2001) 11078-11085. [PMID: 11133994]
2. Chen, S., Glawischnig, E., Jørgensen, K., Naur, P., Jorgensen, B., Olsen, C.E., Hansen, C.H., Rasmussen, H., Pickett, J.A. and Halkier, B.A. CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis. Plant J. 33 (2003) 923-937. [PMID: 12609033]
Accepted name: (methylthio)alkanaldoxime N-monooxygenase
Reaction: an (E)-ω-(methylthio)alkanal oxime + O2 + glutathione + [reduced NADPH—hemoprotein reductase] = an (E)-1-(glutathione-S-yl)-ω-(methylthio)alkylhydroximate + 2 H2O + [oxidized NADPH—hemoprotein reductase] (overall reaction)
(1a) an (E)-ω-(methylthio)alkanal oxime + O2 + [reduced NADPH—hemoprotein reductase] = a 1-aci-nitro-ω-(methylthio)alkane + H2O + [oxidized NADPH—hemoprotein reductase]
(1b) a 1-aci-nitro-ω-(methylthio)alkane + glutathione = an (E)-1-(glutathione-S-yl)-ω-(methylthio)alkylhydroximate + H2O
Other name(s): CYP83A1 (gene name)
Systematic name: (E)-ω-(methylthio)alkananaldoxime,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (N-hydroxylating)
Comments: This cytochrome P-450 (heme thiolate) enzyme is involved in the biosynthesis of glucosinolates in plants. The enzyme catalyses an N-hydroxylation of the E isomer of n-(methylthio)aldoximes, forming an aci-nitro intermediate that reacts non-enzymically with glutathione to produce an N-alkyl-thiohydroximate adduct, the committed precursor of glucosinolates. In the absence of a thiol compound, the enzyme is suicidal, probably due to interaction of the reactive aci-nitro intermediate with active site residues.
References:
1. Bak, S., Tax, F.E., Feldmann, K.A., Galbraith, D.W. and Feyereisen, R. CYP83B1, a cytochrome P450 at the metabolic branch point in auxin and indole glucosinolate biosynthesis in Arabidopsis. Plant Cell 13 (2001) 101-111. [PMID: 11158532]
2. Naur, P., Petersen, B.L., Mikkelsen, M.D., Bak, S., Rasmussen, H., Olsen, C.E. and Halkier, B.A. CYP83A1 and CYP83B1, two nonredundant cytochrome P450 enzymes metabolizing oximes in the biosynthesis of glucosinolates in Arabidopsis. Plant Physiol. 133 (2003) 63-72. [PMID: 12970475]
3. Clausen, M., Kannangara, R.M., Olsen, C.E., Blomstedt, C.K., Gleadow, R.M., Jørgensen, K., Bak, S., Motawie, M.S. and Møller, B.L. The bifurcation of the cyanogenic glucoside and glucosinolate biosynthetic pathways. Plant J. 84 (2015) 558-573. [PMID: 26361733]
Accepted name: heme oxygenase (staphylobilin-producing)
Reaction: (1) protoheme + 5 reduced acceptor + 4 O2 = 5-oxo-δ-bilirubin + Fe2+ + formaldehyde + 5 acceptor + 4 H2O
(2) protoheme + 5 reduced acceptor + 4 O2 = 15-oxo-β-bilirubin + Fe2+ + formaldehyde + 5 acceptor + 4 H2O
Glossary: staphylobilins = 5-oxo-δ-bilirubin and 15-oxo-β-bilirubin
Other name(s): haem oxygenase (ambiguous); heme oxygenase (decyclizing) (ambiguous); heme oxidase (ambiguous); haem oxidase (ambiguous); heme oxygenase (ambiguous); isdG (gene name); isdI (gene name)
Systematic name: protoheme,hydrogen-donor:oxygen oxidoreductase (δ/β-methene-oxidizing, hydroxylating)
Comments: This enzyme, which is found in some pathogenic bacteria, is involved in an iron acquisition system that catabolizes the host's hemoglobin. The two enzymes from the bacterium Staphylococcus aureus, encoded by the isdG and isdI genes, produce 67.5 % and 56.2 % 5-oxo-δ-bilirubin, respectively.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Reniere, M.L., Ukpabi, G.N., Harry, S.R., Stec, D.F., Krull, R., Wright, D.W., Bachmann, B.O., Murphy, M.E. and Skaar, E.P. The IsdG-family of haem oxygenases degrades haem to a novel chromophore. Mol. Microbiol. 75 (2010) 1529-1538. [PMID: 20180905]
2. Matsui, T., Nambu, S., Ono, Y., Goulding, C.W., Tsumoto, K. and Ikeda-Saito, M. Heme degradation by Staphylococcus aureus IsdG and IsdI liberates formaldehyde rather than carbon monoxide. Biochemistry 52 (2013) 3025-3027. [PMID: 23600533]
Accepted name: lytic chitin monoxygenase
Reaction: [(1→4)-N-acetyl-β-D-glucosaminyl]n+m + reduced acceptor + O2 = [(1→4)-N-acetyl-β-D-glucosaminyl]m-1-(1→4)-N-acetyl-2-deoxy-2-amino-D-glucono-1,5-lactone + [(1→4)-N-acetyl-β-D-glucosaminyl]n + acceptor + H2O
Other name(s): LPMO (ambiguous); CBP21; chitin oxidohydrolase
Systematic name: chitin, hydrogen-donor:oxygen oxidoreductase (N-acetyl-β-D-glucosaminyl C1-hydroxylating/C4-dehdrogenating)
Comments: The enzyme cleaves chitin in an oxidative manner, releasing fragments of chitin with an N-acetylamino-D-glucono-1,5-lactone at the reducing end. The initially formed lactone at the reducing end of the shortened chitin chain quickly hydrolyses spontaneously to the aldonic acid. In vitro ascorbate can serve as reducing agent. The enzyme contains copper at the active site.
References:
1. Vaaje-Kolstad, G., Westereng, B., Horn, S.J., Liu, Z., Zhai, H., Sorlie, M. and Eijsink, V.G. An oxidative enzyme boosting the enzymatic conversion of recalcitrant polysaccharides. Science 330 (2010) 219-222. [PMID: 20929773]
2. Vaaje-Kolstad, G., Bohle, L.A., Gaseidnes, S., Dalhus, B., Bjoras, M., Mathiesen, G. and Eijsink, V.G. Characterization of the chitinolytic machinery of Enterococcus faecalis V583 and high-resolution structure of its oxidative CBM33 enzyme. J. Mol. Biol. 416 (2012) 239-254. [PMID: 22210154]
3. Gudmundsson, M., Kim, S., Wu, M., Ishida, T., Momeni, M.H., Vaaje-Kolstad, G., Lundberg, D., Royant, A., Stahlberg, J., Eijsink, V.G., Beckham, G.T. and Sandgren, M. Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-ray photoreduction. J. Biol. Chem. 289 (2014) 18782-18792. [PMID: 24828494]
4. Zhang, H., Zhao, Y., Cao, H., Mou, G. and Yin, H. Expression and characterization of a lytic polysaccharide monooxygenase from Bacillus thuringiensis. Int. J. Biol. Macromol. 79 (2015) 72-75. [PMID: 25936286]
Accepted name: ribonucleoside-diphosphate reductase
Reaction: 2'-deoxyribonucleoside 5'-diphosphate + thioredoxin disulfide + H2O = ribonucleoside 5'-diphosphate + thioredoxin
Other name(s): ribonucleotide reductase (ambiguous); CDP reductase; ribonucleoside diphosphate reductase; UDP reductase; ADP reductase; nucleoside diphosphate reductase; ribonucleoside 5'-diphosphate reductase; ribonucleotide diphosphate reductase; 2'-deoxyribonucleoside-diphosphate:oxidized-thioredoxin 2'-oxidoreductase; RR; nrdB (gene name); nrdF (gene name); nrdJ (gene name)
Systematic name: 2'-deoxyribonucleoside-5'-diphosphate:thioredoxin-disulfide 2'-oxidoreductase
Comments: This enzyme is responsible for the de novo conversion of ribonucleoside diphosphates into deoxyribonucleoside diphosphates, which are essential for DNA synthesis and repair. There are three types of this enzyme differing in their cofactors. Class Ia enzymes contain a diferric-tyrosyl radical, class Ib enzymes contain a dimanganese-tyrosyl radical, and class II enzymes contain adenosylcobalamin. In all cases the cofactors are involved in generation of a transient thiyl radical on a cysteine residue, which attacks the substrate, forming a ribonucleotide 3'-radical, followed by water loss to form a ketyl radical. The ketyl radical is reduced to 3'-keto-deoxynucleotide concomitant with formation of a disulfide anion radical between two cysteine residues. A proton-coupled electron-transfer from the disulfide radical to the substrate generates a 3'-deoxynucleotide radical, and the final product is formed when the hydrogen atom that was initially removed from the 3'-position of the nucleotide by the thiyl radical is returned to the same position. The disulfide bridge is reduced by the action of thioredoxin. cf. EC 1.1.98.6, ribonucleoside-triphosphate reductase (formate) and EC 1.17.4.2, ribonucleoside-triphosphate reductase (thioredoxin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9047-64-7
References:
1. Larsson, A. and Reichard, P. Enzymatic synthesis of deoxyribonucleotides. IX. Allosteric effects in the reduction of pyrimidine ribonucleotides by the ribonucleoside diphosphate reductase system of Escherichia coli. J. Biol. Chem. 241 (1966) 2533-2539. [PMID: 5330119]
2. Larsson, A. and Reichard, P. Enzymatic synthesis of deoxyribonucleotides. X. Reduction of purine ribonucleotides; allosteric behavior and substrate specificity of the enzyme system from Escherichia coli B. J. Biol. Chem. 241 (1966) 2540-2549. [PMID: 5330120]
3. Moore, E.C. and Hurlbert, R.B. Regulation of mammalian deoxyribonucleotide biosynthesis by nucleotides as activators and inhibitors. J. Biol. Chem. 241 (1966) 4802-4809. [PMID: 5926184]
4. Larsson, A. Ribonucleotide reductase from regenerating rat liver. II. Substrate phosphorylation level and effect of deoxyadenosine triphosphate. Biochim. Biophys. Acta 324 (1973) 447-451. [PMID: 4543472]
5. Lammers, M. and Follmann, H. The ribonucleotide reductases - a unique group of metalloenzymes essential for cell-proliferation. Struct. Bonding 54 (1983) 27-91.
6. Stubbe, J., Ator, M. and Krenitsky, T. Mechanism of ribonucleoside diphosphate reductase from Escherichia coli. Evidence for 3'-C--H bond cleavage. J. Biol. Chem. 258 (1983) 1625-1631. [PMID: 6337142]
7. Lenz, R. and Giese, B. Studies on the Mechanism of Ribonucleotide Reductases. J. Am. Chem. Soc. 119 (1997) 2784-2794.
8. Lawrence, C.C., Bennati, M., Obias, H.V., Bar, G., Griffin, R.G. and Stubbe, J. High-field EPR detection of a disulfide radical anion in the reduction of cytidine 5'-diphosphate by the E441Q R1 mutant of Escherichia coli ribonucleotide reductase. Proc. Natl. Acad. Sci. USA 96 (1999) 8979-8984. [PMID: 10430881]
9. Qiu, W., Zhou, B., Darwish, D., Shao, J. and Yen, Y. Characterization of enzymatic properties of human ribonucleotide reductase holoenzyme reconstituted in vitro from hRRM1, hRRM2, and p53R2 subunits. Biochem. Biophys. Res. Commun. 340 (2006) 428-434. [PMID: 16376858]
Accepted name: ribonucleoside-triphosphate reductase (thioredoxin)
Reaction: 2'-deoxyribonucleoside 5'-triphosphate + thioredoxin disulfide + H2O = ribonucleoside 5'-triphosphate + thioredoxin
Other name(s): ribonucleotide reductase (ambiguous); 2'-deoxyribonucleoside-triphosphate:oxidized-thioredoxin 2'-oxidoreductase
Systematic name: 2'-deoxyribonucleoside-5'-triphosphate:thioredoxin-disulfide 2'-oxidoreductase
Comments: The enzyme, characterized from the bacterium Lactobacillus leichmannii, is similar to class II ribonucleoside-diphosphate reductase (cf. EC 1.17.4.1). However, it is specific for the triphosphate versions of its substrates. The enzyme contains an adenosylcobalamin cofactor that is involved in generation of a transient thiyl radical on a cysteine residue. This radical attacks the substrate, forming a ribonucleotide 3'-radical, followed by water loss to form a ketyl radical. The ketyl radical is reduced to 3'-keto-deoxynucleotide concomitant with formation of a disulfide anion radical between two cysteine residues. A proton-coupled electron-transfer from the disulfide radical to the substrate generates a 3'-deoxynucleotide radical, and the final product is formed when the hydrogen atom that was initially removed from the 3'-position of the nucleotide by the thiyl radical is returned to the same position. The disulfide bridge is reduced by the action of thioredoxin. cf. EC 1.1.98.6, ribonucleoside-triphosphate reductase (formate).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9068-66-0
References:
1. Blakley, R.L. Cobamides and ribonucleotide reduction. I. Cobamide stimulation of ribonucleotide reduction in extracts of Lactobacillus leichmannii. J. Biol. Chem. 240 (1965) 2173-2180. [PMID: 14299643]
2. Goulian, M. and Beck, W.S. Purification and properties of cobamide-dependent ribonucleotide reductase from Lactobacillus leichmannii. J. Biol. Chem. 241 (1966) 4233-4242. [PMID: 5924645]
3. Stubbe, J., Ackles, D., Segal, R. and Blakley, R.L. On the mechanism of ribonucleoside triphosphate reductase from Lactobacillus leichmannii. Evidence for 3' C--H bond cleavage. J. Biol. Chem. 256 (1981) 4843-4846. [PMID: 7014560]
4. Ashley, G.W., Harris, G. and Stubbe, J. The mechanism of Lactobacillus leichmannii ribonucleotide reductase. Evidence for 3' carbon-hydrogen bond cleavage and a unique role for coenzyme B12. J. Biol. Chem. 261 (1986) 3958-3964. [PMID: 3512563]
5. Lawrence, C.C. and Stubbe, J. The function of adenosylcobalamin in the mechanism of ribonucleoside triphosphate reductase from Lactobacillus leichmannii. Curr. Opin. Chem. Biol. 2 (1998) 650-655. [PMID: 9818192]
6. Licht, S.S., Booker, S. and Stubbe, J. Studies on the catalysis of carbon-cobalt bond homolysis by ribonucleoside triphosphate reductase: evidence for concerted carbon-cobalt bond homolysis and thiyl radical formation. Biochemistry 38 (1999) 1221-1233. [PMID: 9930982]
Accepted name: tetrachloroethene reductive dehalogenase
Reaction: trichloroethene + chloride + acceptor = tetrachloroethene + reduced acceptor
Glossary: methyl viologen = 1,1'-dimethyl-4,4'-bipyridinium
Other name(s): tetrachloroethene reductase
Systematic name: acceptor:trichloroethene oxidoreductase (chlorinating)
Comments: This enzyme allows the common pollutant tetrachloroethene to support bacterial growth and is responsible for disposal of a number of chlorinated hydrocarbons. The reaction occurs in the reverse direction. The enzyme also reduces trichloroethene to dichloroethene. Although the physiological reductant is unknown, the supply of reductant in some organisms involves menaquinol, which is reduced by molecular hydrogen via the action of EC 1.12.5.1, hydrogen:quinone oxidoreductase. The enzyme contains a corrinoid and two iron-sulfur clusters. Methyl viologen can act as electron donor in vitro.
References:
1. Holliger, C, Wohlfarth, G. and Diekert, G. Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol. Rev. 22 (1998) 383-398.
2. Glod, G., Angst, W., Holliger, C. and Schwarzenbach, R.P. Corrinoid-mediated reduction of tetrachloroethene, trichloroethene, and trichlorofluoroethene in homogeneous aqueous solution: Reaction kinetics and reaction mechanisms. Environ. Sci. Technol. 31 (1997) 253-260.
3. Neumann, A., Wohlfarth, G. and Diekert, G. Purification and characterization of tetrachloroethene reductive dehalogenase from Dehalospirillum multivorans. J. Biol. Chem. 271 (1996) 16515-16519. [PMID: 8663199]
4. Schumacher, W., Holliger, C., Zehnder, A.J.B. and Hagen, W.R. Redox chemistry of cobalamin and iron-sulfur cofactors in the tetrachloroethene reductase of Dehalobacter restrictus. FEBS Lett. 409 (1997) 421-425. [PMID: 9224702]
5. Schumacher, W. and Holliger, C. The proton/electron ratio of the menaquinone-dependent electron transport from dihydrogen to tetrachloroethene in "Dehalobacter restrictus". J. Bacteriol. 178 (1996) 2328-2333. [PMID: 8636034]
[EC 1.97.1.8 Transferred entry: tetrachloroethene reductive dehalogenase. Now EC 1.21.99.5, tetrachloroethene reductive dehalogenase (EC 1.97.1.8 created 2001, deleted 2017)]
Accepted name: reticuline N-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + (S)-reticuline = S-adenosyl-L-homocysteine + (S)-tembetarine
(2) S-adenosyl-L-methionine + (S)-corytuberine = S-adenosyl-L-homocysteine + magnoflorine
For diagram of reaction click here
Other name(s): RNMT
Systematic name: S-adenosyl-L-methionine:(S)-reticuline N-methyltransferase
Comments: The enzyme from opium poppy (Papaver somniferum) can also methylate (R)-reticuline, tetrahydropapaverine, (S)-glaucine and (S)-bulbocapnine. It is involved in the biosynthesis of the quaternary benzylisoquinoline alkaloid magnoflorine.
References:
1. Morris, J.S. and Facchini, P.J. Isolation and characterization of reticuline N-methyltransferase involved in biosynthesis of the aporphine alkaloid magnoflorine in opium poppy. J. Biol. Chem. 291 (2016) 23416-23427. [PMID: 27634038]
Accepted name: desmethylxanthohumol 6'-O-methyltransferase
Reaction: S-adenosyl-L-methionine + desmethylxanthohumol = S-adenosyl-L-homocysteine + xanthohumol
For diagram of reaction click here.
Glossary: desmethylxanthohumol = (2E)-3-(4-hydroxyphenyl)-1-[2,4,6-trihydroxy-3-(3-methylbut-2-en-1-yl)phenyl]prop-2-en-1-one
xanthohumol = (2E)-1-[2,4-dihydroxy-6-methoxy-3-(3-methylbut-2-en-1-yl)phenyl]-3-(4-hydroxyphenyl)prop-2-en-1-one
Other name(s): OMT1 (ambiguous)
Systematic name: S-adenosyl-L-methionine:desmethylxanthohumol 6'-O-methyltransferase
Comments: Found in hops (Humulus lupulus). The enzyme can also methylate xanthogalenol.
References:
1. Nagel, J., Culley, L.K., Lu, Y., Liu, E., Matthews, P.D., Stevens, J.F. and Page, J.E. EST analysis of hop glandular trichomes identifies an O-methyltransferase that catalyzes the biosynthesis of xanthohumol. Plant Cell 20 (2008) 186-200. [PMID: 18223037]
Accepted name: xanthohumol 4'-O-methyltransferase
Reaction: S-adenosyl-L-methionine + xanthohumol = S-adenosyl-L-homocysteine + 4'-O-methylxanthohumol
For diagram of reaction click here.
Glossary: xanthohumol = (2E)-1-[2,4-dihydroxy-6-methoxy-3-(3-methylbut-2-en-1-yl)phenyl]-3-(4-hydroxyphenyl)prop-2-en-1-one
Other name(s): OMT2 (ambiguous)
Systematic name: S-adenosyl-L-methionine:xanthohumol 4'-O-methyltransferase
Comments: The enzyme from hops (Humulus lupulus) has a broad substrate specificity. The best substrates in vitro are resveratrol, desmethylxanthohumol, naringenin chalcone and isoliquiritigenin.
References:
1. Nagel, J., Culley, L.K., Lu, Y., Liu, E., Matthews, P.D., Stevens, J.F. and Page, J.E. EST analysis of hop glandular trichomes identifies an O-methyltransferase that catalyzes the biosynthesis of xanthohumol. Plant Cell 20 (2008) 186-200. [PMID: 18223037]
Accepted name: histone acetyltransferase
Reaction: acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N6-acetyl-L-lysine
Other name(s): nucleosome-histone acetyltransferase; histone acetokinase; histone acetylase; histone transacetylase; lysine acetyltransferase; protein lysine acetyltransferase; acetyl-CoA:histone acetyltransferase
Systematic name: acetyl-CoA:[protein]-L-lysine acetyltransferase
Comments: A group of enzymes acetylating histones. Several of the enzymes can also acetylate lysines in other proteins [3,4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9054-51-7
References:
1. Gallwitz, D. and Sures, I. Histone acetylation. Purification and properties of three histone-specific acetyltransferases from rat thymus nuclei. Biochim. Biophys. Acta 263 (1972) 315-328. [PMID: 5031160]
2. Makowski, A.M., Dutnall, R.N. and Annunziato, A.T. Effects of acetylation of histone H4 at lysines 8 and 16 on activity of the Hat1 histone acetyltransferase. J. Biol. Chem. 276 (2001) 43499-43502. [PMID: 11585814]
3. Lee, K.K. and Workman, J.L. Histone acetyltransferase complexes: one size doesn’t fit all. Nat. Rev. Mol. Cell. Biol. 8 (2007) 284-295. [PMID: 17380162]
4. Thao, S. and Escalante-Semerena, J.C. Biochemical and thermodynamic analyses of Salmonella enterica Pat, a multidomain, multimeric Nε-lysine acetyltransferase involved in carbon and energy metabolism. MBio 2 (2011) E216. [PMID: 22010215]
5. Wu, H., Moshkina, N., Min, J., Zeng, H., Joshua, J., Zhou, M.M. and Plotnikov, A.N. Structural basis for substrate specificity and catalysis of human histone acetyltransferase 1. Proc. Natl. Acad. Sci. USA 109 (2012) 8925-8930. [PMID: 22615379]
6. Das, C., Roy, S., Namjoshi, S., Malarkey, C.S., Jones, D.N., Kutateladze, T.G., Churchill, M.E. and Tyler, J.K. Binding of the histone chaperone ASF1 to the CBP bromodomain promotes histone acetylation. Proc. Natl. Acad. Sci. USA 111 (2014) E1072-E1081. [PMID: 24616510]
Accepted name: 2-heptyl-4(1H)-quinolone synthase
Reaction: octanoyl-CoA + 2-aminobenzoylacetate = 2-heptyl-4(1H)-quinolone + CoA + CO2 + H2O (overall reaction)
(1a) octanoyl-CoA + L-cysteinyl-[PqsC protein] = S-octanoyl-L-cysteinyl-[PqsC protein] + CoA
(1b) S-octanoyl-L-cysteinyl-[PqsC protein] + 2-aminobenzoylacetate = 1-(2-aminophenyl)decane-1,3-dione + CO2 + L-cysteinyl-[PqsC protein]
(1c) 1-(2-aminophenyl)decane-1,3-dione = 2-heptyl-4(1H)-quinolone + H2O
Glossary: 4-hydroxy-2(1H)-quinolone = 2,4-dihydroxyquinoline
2-heptyl-4(1H)-quinolone = 2-heptyl-4-hydroxyquinoline
anthraniloyl-CoA = 2-aminobenzoyl-CoA
Other name(s): pqsBC (gene names); malonyl-CoA:anthraniloyl-CoA C-acetyltransferase (decarboxylating)
Systematic name: octanoyl-CoA:2-aminobenzoylacetate octanoyltransferase
Comments: The enzyme, characterized from the bacterium Pseudomonas aeruginosa, is a heterodimeric complex. The PqsC subunit acquires an octanoyl group from octanoyl-CoA and attaches it to an internal cysteine residue. Together with the PqsB subunit, the proteins catalyse the coupling of the octanoyl group with 2-aminobenzoylacetate, leading to decarboxylation and dehydration events that result in closure of the quinoline ring.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Dulcey, C.E., Dekimpe, V., Fauvelle, D.A., Milot, S., Groleau, M.C., Doucet, N., Rahme, L.G., Lepine, F. and Deziel, E. The end of an old hypothesis: the Pseudomonas signaling molecules 4-hydroxy-2-alkylquinolines derive from fatty acids, not 3-ketofatty acids. Chem. Biol. 20 (2013) 1481-1491. [PMID: 24239007]
2. Drees, S.L., Li, C., Prasetya, F., Saleem, M., Dreveny, I., Williams, P., Hennecke, U., Emsley, J. and Fetzner, S. PqsBC, a condensing enzyme in the biosynthesis of the Pseudomonas aeruginosa quinolone Signal: crystal structure, inhibition, and reaction mechanism. J. Biol. Chem. 291 (2016) 6610-6624. [PMID: 26811339]
Accepted name: 4-hydroxyphenylalkanoate synthase
Reaction: (1) 4-hydroxybenzoyl-[4-hydroxyphenylalkanoate synthase] + 8 malonyl-CoA + 16 NADPH + 16 H+ = 17-(4-hydroxyphenyl)heptadecanoyl-[4-hydroxyphenylalkanoate synthase] + 8 CO2 + 8 CoA + 16 NADP+ + 8 H2O
(2) 4-hydroxybenzoyl-[4-hydroxyphenylalkanoate synthase] + 9 malonyl-CoA + 18 NADPH + 18 H+ + holo-[4-hydroxyphenylalkanoate synthase] = 19-(4-hydroxyphenyl)nonadecanoyl-[4-hydroxyphenylalkanoate synthase] + 9 CO2 + 9 CoA + 18 NADP+ + 9 H2O
Other name(s): msl7 (gene name); Pks15/1
Systematic name: malonyl-CoA:4-hydroxybenzoyl-[4-hydroxyphenylalkanoate synthase] malonyltransferase (4-hydroxyphenylalkanoate-forming)
Comments: The enzyme is part of the biosynthetic pathway of phenolphthiocerol, a lipid that serves as a virulence factor of pathogenic mycobacteria. It catalyses the elongation of 4-hydroxybenzoate that is loaded on its acyl-carrier domain to form 4-hydroxyphenylalkanoate intermediates. The enzyme adds either 8 or 9 malonyl-CoA units, resulting in formation of 17-(4-hydroxyphenyl)heptadecanoate or 19-(4-hydroxyphenyl)nonadecanoate, respectively. As the enzyme lacks a thioesterase domain [1], the product remains loaded on the acyl-carrier domain at the end of catalysis, and has to be hydrolysed by an as-yet unknown mechanism.
References:
1. Sirakova, T.D., Thirumala, A.K., Dubey, V.S., Sprecher, H. and Kolattukudy, P.E. The Mycobacterium tuberculosis pks2 gene encodes the synthase for the hepta- and octamethyl-branched fatty acids required for sulfolipid synthesis. J. Biol. Chem. 276 (2001) 16833-16839. [PMID: 11278910]
2. Constant, P., Perez, E., Malaga, W., Laneelle, M.A., Saurel, O., Daffe, M. and Guilhot, C. Role of the pks15/1 gene in the biosynthesis of phenolglycolipids in the Mycobacterium tuberculosis complex. Evidence that all strains synthesize glycosylated p-hydroxybenzoic methyl esters and that strains devoid of phenolglycolipids harbor a frameshift mutation in the pks15/1 gene. J. Biol. Chem. 277 (2002) 38148-38158. [PMID: 12138124]
3. Simeone, R., Leger, M., Constant, P., Malaga, W., Marrakchi, H., Daffe, M., Guilhot, C. and Chalut, C. Delineation of the roles of FadD22, FadD26 and FadD29 in the biosynthesis of phthiocerol dimycocerosates and related compounds in Mycobacterium tuberculosis. FEBS J. 277 (2010) 2715-2725. [PMID: 20553505]
Accepted name: anthraniloyl-CoA anthraniloyltransferase
Reaction: anthraniloyl-CoA + malonyl-CoA = 2-aminobenzoylacetyl-CoA + CoA + CO2 (overall reaction)
(1a) anthraniloyl-CoA + L-cysteinyl-[PqsD protein] = S-anthraniloyl-L-cysteinyl-[PqsD protein] + CoA
(1b) S-anthraniloyl-L-cysteinyl-[PqsD protein] + malonyl-CoA = 2-aminobenzoylacetyl-CoA + CO2 + L-cysteinyl-[PqsD protein]
Glossary: anthraniloyl-CoA = 2-aminobenzoyl-CoA
Other name(s): pqsD (gene name)
Systematic name: anthraniloyl-CoA:malonyl-CoA anthraniloyltransferase
Comments: The enzyme, characterized from the bacterium Pseudomonas aeruginosa, participates in the synthesis of the secondary metabolites 2-heptyl-3-hydroxy-4(1H)-quinolone and 4-hydroxy-2(1H)-quinolone. The enzyme transfers an anthraniloyl group from anthraniloyl-CoA to an internal L-cysteine residue, followed by its transfer to malonyl-CoA to produce a short-lived product that can cyclize spontaneously to form 4-hydroxy-2(1H)-quinolone. However, when EC 3.1.2.32, 2-aminobenzoylacetyl-CoA thiesterase, is present, it removes the CoA moiety from the product, forming the stable 2-aminobenzoylacetate.
References:
1. Bera, A.K., Atanasova, V., Robinson, H., Eisenstein, E., Coleman, J.P., Pesci, E.C. and Parsons, J.F. Structure of PqsD, a Pseudomonas quinolone signal biosynthetic enzyme, in complex with anthranilate. Biochemistry 48 (2009) 8644-8655. [PMID: 19694421]
2. Dulcey, C.E., Dekimpe, V., Fauvelle, D.A., Milot, S., Groleau, M.C., Doucet, N., Rahme, L.G., Lepine, F. and Deziel, E. The end of an old hypothesis: the Pseudomonas signaling molecules 4-hydroxy-2-alkylquinolines derive from fatty acids, not 3-ketofatty acids. Chem. Biol. 20 (2013) 1481-1491. [PMID: 24239007]
3. Drees, S.L. and Fetzner, S. PqsE of Pseudomonas aeruginosa acts as pathway-specific thioesterase in the biosynthesis of alkylquinolone signaling molecules. Chem. Biol. 22 (2015) 611-618. [PMID: 25960261]
Accepted name: 2-amino-4-oxopentanoate thiolase
Reaction: acetyl-CoA + D-alanine = CoA + (2R)-2-amino-4-oxopentanoate
Other name(s): AKPT; AKP thiolase; 2-amino-4-ketopentanoate thiolase
Systematic name: acetyl-CoA:D-alanine acetyltransferase
Comments: A pyridoxal 5'-phosphate enzyme. The enzyme, characterized from the bacterium Clostridium sticklandii, is part of a degradation pathway of ornithine. It is specific for acetyl-CoA and D-alanine.
References:
1. Jeng, I.M., Somack, R. and Barker, H.A. Ornithine degradation in Clostridium sticklandii; pyridoxal phosphate and coenzyme A dependent thiolytic cleavage of 2-amino-4-ketopentanoate to alanine and acetyl coenzyme A. Biochemistry 13 (1974) 2898-2903. [PMID: 4407783]
2. Fonknechten, N., Perret, A., Perchat, N., Tricot, S., Lechaplais, C., Vallenet, D., Vergne, C., Zaparucha, A., Le Paslier, D., Weissenbach, J. and Salanoubat, M. A conserved gene cluster rules anaerobic oxidative degradation of L-ornithine. J. Bacteriol. 191 (2009) 3162-3167. [PMID: 19251850]
Accepted name: 2-phosphinomethylmalate synthase
Reaction: acetyl-CoA + H2O + 3-(hydroxyphosphinoyl)pyruvate = phosphinomethylmalate + CoA
Other name(s): pmmS (gene name)
Systematic name: acetyl-CoA:phosphinopyruvate C-acetyltransferase (thioester-hydrolysing, phosphinomethylmalate-forming)
Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus, participates in the pathway for bialaphos biosynthesis. It requires a divalent metal ion and can also act on oxaloacetate.
References:
1. Shimotohno, K.W., Seto, H., Otake, N., Imai, S. and Murakami, T. Studies on the biosynthesis of bialaphos (SF-1293). 8. Purification and characterization of 2-phosphinomethylmalic acid synthase from Streptomyces hygroscopicus SF-1293. J. Antibiot. (Tokyo) 41 (1988) 1057-1065. [PMID: 3170341]
2. Shimotohno, K.W., Imai, S., Murakami, T. and Seto, H. Purification and characterization of citrate synthase from Streptomyces hygroscopicus SF-1293 and comparison of its properties with those of 2-phosphinomethylmalic acid synthase. Agric. Biol. Chem. 54 (1990) 463-470. [PMID: 1368511]
Accepted name: type 1 galactoside α-(1,2)-fucosyltransferase
Reaction: GDP-β-L-fucose + β-D-galactosyl-(1→3)-N-acetyl-β-D-glucosaminyl-R = GDP + α-L-fucosyl-(1→2)-β-D-galactosyl-(1→3)-N-acetyl-β-D-glucosaminyl-R
For diagram of reaction click here.
Other name(s): galactoside 2-α-L-fucosyltransferase (ambiguous); blood group H α-2-fucosyltransferase (ambiguous); guanosine diphosphofucose-galactoside 2-L-fucosyltransferase; α-(1→2)-L-fucosyltransferase (ambiguous); α-2-fucosyltransferase (ambiguous); α-2-L-fucosyltransferase (ambiguous); blood-group substance H-dependent fucosyltransferase (ambiguous); guanosine diphosphofucose-glycoprotein 2-α-fucosyltransferase (ambiguous); guanosine diphosphofucose-β-D-galactosyl-α-2-L-fucosyltransferase (ambiguous); guanosine diphosphofucose-galactosylacetylglucosaminylgalactosylglucosylceramide α-L-fucosyltransferase (ambiguous); guanosine diphosphofucose-glycoprotein 2-α-L-fucosyltransferase (ambiguous); secretor-type β-galactoside α1→2fucosyltransferase; β-galactoside α1→2fucosyltransferase (ambiguous); GDP-β-L-fucose:β-D-galactosyl-R 2-α-L-fucosyltransferase (ambiguous); FUT2 (gene name); GDP-β-L-fucose:β-D-galactosyl-(1→3)-N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide 2-α-L-fucosyltransferase
Systematic name: GDP-β-L-fucose:β-D-galactosyl-(1→3)-N-acetyl-β-D-glucosaminyl-R α-(1,2)-L-fucosyltransferase (configuration-inverting)
Comments: The enzyme acts on a glycoconjugates where R (see reaction) is a glycoprotein or glycosphingolipid. The recognized moiety of the substrate is known as a type 1 histo-blood group antigen precursor disaccharide, and the action of the enzyme produces an H type 1 antigen. In humans the main enzyme performing this reaction is encoded by the FUT2 gene (also known as the Secretor gene), which is also able to act on type 2 substrates (see EC 2.4.1.344). The enzyme from the bacterium Helicobacter pylori cannot act on type 2 substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 56093-23-3
References:
1. Beyer, T.A. and Hill, R.L. Enzymatic properties of the β-galactoside α1→2 fucosyltransferase from porcine submaxillary gland. J. Biol. Chem. 255 (1980) 5373-5379. [PMID: 7372640]
2. Beyer, T.A., Sadler, J.E. and Hill, R.L. Purification to homogeneity of H blood group β-galactoside α1→2 fucosyltransferase from porcine submaxillary gland. J. Biol. Chem. 255 (1980) 5364-5372. [PMID: 6246105]
3. Kumazaki, T. and Yoshida, A. Biochemical evidence that secretor gene, Se, is a structural gene encoding a specific fucosyltransferase. Proc. Natl. Acad. Sci. USA 81 (1984) 4193-4197. [PMID: 6588382]
4. Koda, Y., Soejima, M., Wang, B. and Kimura, H. Structure and expression of the gene encoding secretor-type galactoside 2-α-L-fucosyltransferase (FUT2). Eur. J. Biochem. 246 (1997) 750-755. [PMID: 9219535]
5. Wang, G., Boulton, P.G., Chan, N.W., Palcic, M.M. and Taylor, D.E. Novel Helicobacter pylori α1,2-fucosyltransferase, a key enzyme in the synthesis of Lewis antigens. Microbiology 145 (1999) 3245-3253. [PMID: 10589734]
Accepted name: rhamnopyranosyl-N-acetylglucosaminyl-diphospho-decaprenol β-1,4/1,5-galactofuranosyltransferase
Reaction: 2 UDP-α-D-galactofuranose + α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol = 2 UDP + β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol (overall reaction)
(1a) UDP-α-D-galactofuranose + α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol = UDP + β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol
(1b) UDP-α-D-galactofuranose + β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol = UDP + β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol
For diagram of reaction click here.
Other name(s): arabinogalactan galactofuranosyl transferase 1; GlfT1
Systematic name: UDP-α-D-galactofuranose:α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol 4-β/4-β-galactofuranosyltransferase (configuration-inverting)
Comments: Isolated from the bacteria Mycobacterium tuberculosis and M. smegmatis, the enzyme has dual β-(1→4) and β-(1→5) transferase action. Involved in the formation of the cell wall in mycobacteria.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Mikusová, K., Belánová, M., Korduláková, J., Honda, K., McNeil, M.R., Mahapatra, S., Crick, D.C. and Brennan, P.J. Identification of a novel galactosyl transferase involved in biosynthesis of the mycobacterial cell wall. J. Bacteriol. 188 (2006) 6592-6598. [PMID: 16952951]
2. Belánová, M., Dianisková, P., Brennan, P.J., Completo, G.C., Rose, N.L., Lowary, T.L. and Mikusová, K. Galactosyl transferases in mycobacterial cell wall synthesis. J. Bacteriol. 190 (2008) 1141-1145. [PMID: 18055597]
Accepted name: UDP-Gal:α-D-GlcNAc-diphosphoundecaprenol β-1,3-galactosyltransferase
Reaction: UDP-α-D-galactose + N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + β-D-Gal-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
Other name(s): WbbD; WbbD β3Gal-transferase; UDP-Gal:GlcNAc-R β1,3-galactosyltransferase; UDP-Gal:GlcNAcα-pyrophosphate-R β1,3-galactosyltransferase; UDP-Gal:GlcNAc-R galactosyltransferase
Systematic name: UDP-α-D-galactose:N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-β-galactosyltransferase (configuration-inverting)
Comments: The enzyme is involved in the the biosynthesis of the O-antigen repeating unit of Escherichia coli O7:K1 (VW187). Requires Mn2+. cf. EC 2.4.1.343, UDP-Gal:α-D-GlcNAc-diphosphoundecaprenol α-1,3-galactosyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Riley, J.G., Menggad, M., Montoya-Peleaz, P.J., Szarek, W.A., Marolda, C.L., Valvano, M.A., Schutzbach, J.S. and Brockhausen, I. The wbbD gene of E. coli strain VW187 (O7:K1) encodes a UDP-Gal: GlcNAcα-pyrophosphate-R β1,3-galactosyltransferase involved in the biosynthesis of O7-specific lipopolysaccharide. Glycobiology 15 (2005) 605-613. [PMID: 15625181]
2. Brockhausen, I., Riley, J.G., Joynt, M., Yang, X. and Szarek, W.A. Acceptor substrate specificity of UDP-Gal: GlcNAc-R β1,3-galactosyltransferase (WbbD) from Escherichia coli O7:K1. Glycoconj. J. 25 (2008) 663-673. [PMID: 18536883]
Accepted name: UDP-Gal:α-D-GlcNAc-diphosphoundecaprenol α-1,3-galactosyltransferase
Reaction: UDP-α-D-galactose + N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + α-D-Gal-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
Other name(s): wclR (gene name)
Systematic name: UDP-α-D-galactose:N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-α-galactosyltransferase (configuration-retaining)
Comments: The enzyme is involved in the the biosynthesis of the O-antigen repeating unit of Escherichia coli O3. Requires a divalent metal ion (Mn2+, Mg2+ or Fe2+). cf. EC 2.4.1.303, UDP-Gal:α-D-GlcNAc-diphosphoundecaprenol β-1,3-galactosyltransferase.
References:
1. Chen, C., Liu, B., Xu, Y., Utkina, N., Zhou, D., Danilov, L., Torgov, V., Veselovsky, V. and Feng, L. Biochemical characterization of the novel α-1, 3-galactosyltransferase WclR from Escherichia coli O3. Carbohydr. Res. 430 (2016) 36-43. [PMID: 27196310]
Accepted name: type 2 galactoside α-(1,2)-fucosyltransferase
Reaction: GDP-β-L-fucose + β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-R = GDP + α-L-fucosyl-(1→2)-β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-R
Other name(s): blood group H α-2-fucosyltransferase (ambiguous); guanosine diphosphofucose-galactoside 2-L-fucosyltransferase (ambiguous); α-(1→2)-L-fucosyltransferase (ambiguous); α-2-fucosyltransferase (ambiguous); α-2-L-fucosyltransferase (ambiguous); blood-group substance H-dependent fucosyltransferase (ambiguous); guanosine diphosphofucose-glycoprotein 2-α-fucosyltransferase (ambiguous); guanosine diphosphofucose-lactose fucosyltransferase; GDP fucose-lactose fucosyltransferase; guanosine diphospho-L-fucose-lactose fucosyltransferase; guanosine diphosphofucose-β-D-galactosyl-α-2-L-fucosyltransferase (ambiguous); guanosine diphosphofucose-galactosylacetylglucosaminylgalactosylglucosylceramide α-L-fucosyltransferase (ambiguous); guanosine diphosphofucose-glycoprotein 2-α-L-fucosyltransferase (ambiguous); H-gene-encoded β-galactoside α(1→2)fucosyltransferase; β-galactoside α(1→2)fucosyltransferase (ambiguous); GDP-L-fucose:lactose fucosyltransferase; GDP-β-L-fucose:β-D-galactosyl-R 2-α-L-fucosyltransferase (ambiguous); FUT1 (gene name); FUT2 (gene name)
Systematic name: GDP-β-L-fucose:β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-R α-(1,2)-L-fucosyltransferase (configuration-inverting)
Comments: The enzyme acts on a glycoconjugates where R (see reaction) is a glycoprotein or glycosphingolipid. The recognized moiety of the substrate is known as a type 2 histo-blood group antigen precursor disaccharide, and the action of the enzyme produces an H type 2 antigen. Humans possess two enzymes able to catalyse this reaction, encoded by the FUT1 and FUT2 genes (also known as the H and Secretor genes, respectively), but only FUT1 is expressed in red blood cells. cf. EC 2.4.1.69, type 1 galactoside α-(1,2)-fucosyltransferase.
References:
1. Basu, S., Basu, M. and Chien, J.L. Enzymatic synthesis of a blood group H-related glycosphingolipid by an α-fucosyltransferase from bovine spleen. J. Biol. Chem. 250 (1975) 2956-2962. [PMID: 804484]
2. Grollman, A.P. GDP-L-fucose:lactose fucosyltransferase from mammary gland. Methods Enzymol. 8 (1966) 351-353.
3. Ernst, L.K., Rajan, V.P., Larsen, R.D., Ruff, M.M. and Lowe, J.B. Stable expression of blood group H determinants and GDP-L-fucose: β-D-galactoside 2-α-L-fucosyltransferase in mouse cells after transfection with human DNA. J. Biol. Chem. 264 (1989) 3436-3447. [PMID: 2464598]
4. Larsen, R.D., Ernst, L.K., Nair, R.P. and Lowe, J.B. Molecular cloning, sequence, and expression of a human GDP-L-fucose:β-D-galactoside 2-α-L-fucosyltransferase cDNA that can form the H blood group antigen. Proc. Natl. Acad. Sci. USA 87 (1990) 6674-6678. [PMID: 2118655]
Accepted name: β-galactoside α-(2,6)-sialyltransferase
Reaction: CMP-N-acetyl-β-neuraminate + β-D-galactosyl-R = CMP + N-acetyl-α-neuraminyl-(2→6)-β-D-galactosyl-R
Other name(s): ST6Gal-I; CMP-N-acetylneuraminate:β-D-galactosyl-1,4-N-acetyl-β-D-glucosamine α-2,6-N-acetylneuraminyltransferase; lactosylceramide α-2,6-N-sialyltransferase; CMP-N-acetylneuraminate:β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosamine α-(2→6)-N-acetylneuraminyltransferase; β-galactoside α-2,6-sialyltransferase
Systematic name: CMP-N-acetyl-β-neuraminate:β-D-galactoside α-(2→6)-N-acetylneuraminyltransferase (configuration-inverting)
Comments: The enzyme acts on the terminal non-reducing β-D-galactosyl residue of the oligosaccharide moiety of glycoproteins and glycolipids.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9075-81-4
References:
1. Spiro, M.H. and Spiro, R.G. Glycoprotein biosynthesis: studies on thyroglobulin. Thyroid sialyltransferase. J. Biol. Chem. 243 (1968) 6520-6528. [PMID: 5726897]
2. Hickman, J., Ashwell, G., Morell, A.G., van der Hamer, C.J.A. and Scheinberg, I.H. Physical and chemical studies on ceruloplasmin. 8. Preparation of N-acetylneuraminic acid-1-14C-labeled ceruloplasmin. J. Biol. Chem. 245 (1970) 759-766. [PMID: 4313609]
3. Bartholomew, B.A., Jourdian, G.W. and Roseman, S. The sialic acids. XV. Transfer of sialic acid to glycoproteins by a sialyltransferase from colostrum. J. Biol. Chem. 248 (1973) 5751-5762. [PMID: 4723915]
4. Paulson, J.C., Beranek, W.E. and Hill, R.L. Purification of a sialyltransferase from bovine colostrum by affinity chromatography on CDP-agarose. J. Biol. Chem. 252 (1977) 2356-2362. [PMID: 849932]
5. Schachter, H., Narasimhan, S., Gleeson, P. and Vella, G. Glycosyltransferases involved in elongation of N-glycosidically linked oligosaccharides of the complex or N-acetyllactosamine type. Methods Enzymol. 98 (1983) 98-134. [PMID: 6366476]
6. Albarracin, I., Lassaga, F.E. and Caputto, R. Purification and characterization of an endogenous inhibitor of the sialyltransferase CMP-N-acetylneuraminate: lactosylceramide α2,6-N-acetylneuraminyltransferase (EC 2.4.99.-). Biochem. J. 254 (1988) 559-565. [PMID: 2460092]
Accepted name: N-acetyllactosaminide α-2,3-sialyltransferase
Reaction: CMP-N-acetyl-β-neuraminate + β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-R = CMP + N-acetyl-α-neuraminyl-(2→3)-β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-R
Other name(s): cytidine monophosphoacetylneuraminate-β-galactosyl(1→4)acetylglucosaminide α2→3-sialyltransferase; α2→3 sialyltransferase (ambiguous); SiaT (ambiguous); CMP-N-acetylneuraminate:β-D-galactosyl-1,4-N-acetyl-D-glucosaminyl-glycoprotein α-2,3-N-acetylneuraminyltransferase; neolactotetraosylceramide α-2,3-sialyltransferase; CMP-N-acetylneuraminate:β-D-galactosyl-(1→4)-N-acetyl-D-glucosaminyl-glycoprotein α-(2→3)-N-acetylneuraminyltransferase
Systematic name: CMP-N-acetyl-β-neuraminate:β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-R (2→3)-N-acetyl-α-neuraminyltransferase (configuration-inverting)
Comments: The enzyme recognizes the sequence β-D-galactosyl-(1→4)-N-acetyl-D-glucosaminyl (known as type 2 histo-blood group precursor disaccharide) in non-reducing termini of glycan moieties in glycoproteins and glycolipids. The enzyme from chicken brain was shown to act on neolactotetraosylceramide, producing ganglioside LM1 [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 77537-85-0
References:
1. Van den Eijnden, D.H. and Schiphorst, W.E.C.M. Detection of β-galactosyl(1→4)N-acetylglucosaminide α(2→3)-sialyltransferase activity in fetal calf liver and other tissues. J. Biol. Chem. 256 (1981) 3159-3162. [PMID: 7204397]
2. Basu, M., Basu, S., Stoffyn, A. and Stoffyn, P. Biosynthesis in vitro of sialyl(α2-3)neolactotetraosylceramide by a sialyltransferase from embryonic chicken brain. J. Biol. Chem. 257 (1982) 12765-12769. [PMID: 7130178]
[EC 2.4.99.10 Transferred entry: neolactotetraosylceramide α-2,3-sialyltransferase. Now included in EC 2.4.99.6, N-acetyllactosaminide α-2,3-sialyltransferase (EC 2.4.99.10 created 1986, deleted 2017)]
Accepted name: 2-acylphloroglucinol 4-prenyltransferase
Reaction: dimethylallyl diphosphate + a 2-acylphloroglucinol = diphosphate + a 2-acyl-4-prenylphloroglucinol
For diagram of reaction click here or click here.
Glossary: naringenin chalcone = 2',4,4',6'-tetrahydroxychalcone = 3-(4-hydroxyphemyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
phlorisovalerophenone = 3-methyl-1-(2,4,6-trihydroxyphenyl)butan-1-one
Other name(s): PT-1 (gene name); PT1L (gene name); aromatic prenyltransferase (ambiguous)
Systematic name: dimethylallyl-diphosphate:2-acylphloroglucinol 4-dimethylallyltransferase
Comments: The enzyme, characterized from hop (Humulus lupulus), acts on phlorisovalerophenone, phlormethylbutanophenone, and phlorisobutanophenone during the synthesis of bitter acids. It also acts with much lower activity on naringenin chalcone. Forms a complex with EC 2.5.1.137, 2-acyl-4-prenylphloroglucinol 6-prenyltransferase, which catalyses additional prenylation reactions. Requires Mg2+.
References:
1. Tsurumaru, Y., Sasaki, K., Miyawaki, T., Uto, Y., Momma, T., Umemoto, N., Momose, M. and Yazaki, K. HlPT-1, a membrane-bound prenyltransferase responsible for the biosynthesis of bitter acids in hops. Biochem. Biophys. Res. Commun. 417 (2012) 393-398. [PMID: 22166201]
2. Li, H., Ban, Z., Qin, H., Ma, L., King, A.J. and Wang, G. A heteromeric membrane-bound prenyltransferase complex from hop catalyzes three sequential aromatic prenylations in the bitter acid pathway. Plant Physiol. 167 (2015) 650-659. [PMID: 25564559]
Accepted name: 2-acyl-4-prenylphloroglucinol 6-prenyltransferase
Reaction: (1) dimethylallyl diphosphate + a 2-acyl-4-prenylphloroglucinol = diphosphate + a 2-acyl-4,6-bisprenylphloroglucinol
(2) dimethylallyl diphosphate + a 2-acyl-4,6-bisprenylphloroglucinol = diphosphate + a a 2-acyl-4,6,6-trisprenylcyclohexa-2,4-dien-1-one
For diagram of reaction click here.
Glossary: a 2-acyl-4,6,6-triprenylphloroglucinol = a β bitter acid
Other name(s): PT2 (gene name); aromatic prenyltransferase (ambiguous)
Systematic name: dimethylallyl-diphosphate:2-acyl-4-prenylphloroglucinol 6-dimethylallyltransferase
Comments: The enzyme, characterized from hop (Humulus lupulus), catalyses two successive prenylations of a 2-acyl-4-prenylphloroglucinol during the synthesis of bitter acids. Forms a complex with EC 2.5.1.136, 2-acylphloroglucinol 4-prenyltransferase, which catalyses the initial prenylation of the substrates. Requires Mg2+.
References:
1. Li, H., Ban, Z., Qin, H., Ma, L., King, A.J. and Wang, G. A heteromeric membrane-bound prenyltransferase complex from hop catalyzes three sequential aromatic prenylations in the bitter acid pathway. Plant Physiol. 167 (2015) 650-659. [PMID: 25564559]
Accepted name: coumarin 8-geranyltransferase
Reaction: (1) geranyl diphosphate + umbelliferone = diphosphate + 8-geranylumbelliferone
(2) geranyl diphosphate + esculetin = diphosphate + 8-geranylesculetin
Glossary: esculetin = 6,7-dihydroxy-1-benzopyran-2-one
umbelliferone = 7-hydroxy-1-benzopyran-2-one
Other name(s): ClPT1
Systematic name: geranyl-diphosphate:umbelliferone 8-geranyltransferase
Comments: The enzyme, characterized from the plant Citrus limon, is specific for geranyl diphosphate as a prenyl donor. It also has low activity with the coumarins 5,7-dihydroxycoumarin and 5-methoxy-7-hydroxycoumarin.
References:
1. Munakata, R., Inoue, T., Koeduka, T., Karamat, F., Olry, A., Sugiyama, A., Takanashi, K., Dugrand, A., Froelicher, Y., Tanaka, R., Uto, Y., Hori, H., Azuma, J., Hehn, A., Bourgaud, F. and Yazaki, K. Molecular cloning and characterization of a geranyl diphosphate-specific aromatic prenyltransferase from lemon. Plant Physiol. 166 (2014) 80-90. [PMID: 25077796]
Accepted name: umbelliferone 6-dimethylallyltransferase
Reaction: dimethylallyl diphosphate + umbelliferone = diphosphate + demethylsuberosin
For diagram of reaction click here.
Glossary: demethylsuberosin = 7-hydroxy-6-prenyl-1-benzopyran-2-one
osthenol = 7-hydroxy-8-prenyl-1-benzopyran-2-one
Other name(s): PcPT
Systematic name: dimethylallyl-diphosphate:umbelliferone 6-dimethylallyltransferase
Comments: The enzyme from parsley (Petroselinum crispum) is specific for umbelliferone and dimethylallyl diphosphate. A minor product is osthenol, which is produced by transfer of the dimethylallyl group to C-8 of umbelliferone.
References:
1. Hamerski, D., Schmitt, D. and Matern, U. Induction of two prenyltransferases for the accumulation of coumarin phytoalexins in elicitor-treated Ammi majus cell suspension cultures. Phytochemistry 29 (1990) 1131-1135. [PMID: 1366425]
2. Karamat, F., Olry, A., Munakata, R., Koeduka, T., Sugiyama, A., Paris, C., Hehn, A., Bourgaud, F. and Yazaki, K. A coumarin-specific prenyltransferase catalyzes the crucial biosynthetic reaction for furanocoumarin formation in parsley. Plant J. 77 (2014) 627-638. [PMID: 24354545]
Accepted name: 3-aminobutanoyl-CoA transaminase
Reaction: 3-aminobutanoyl-CoA + 2-oxoglutarate = acetoacetyl-CoA + L-glutamate
Other name(s): kat (gene name); acyl-CoA β-transaminase
Systematic name: 3-aminobutanoyl-CoA:2-oxoglutarate aminotransferase
Comments: The enzyme, found in bacteria, is part of a L-lysine degradation pathway. The enzyme is also active with other β-amino compounds such as 3-amino-5-methylhexanoyl-CoA and 3-amino-3-phenylpropanoyl-CoA.
References:
1. Perret, A., Lechaplais, C., Tricot, S., Perchat, N., Vergne, C., Pelle, C., Bastard, K., Kreimeyer, A., Vallenet, D., Zaparucha, A., Weissenbach, J. and Salanoubat, M. A novel acyl-CoA β-transaminase characterized from a metagenome. PLoS One 6 (2011) e22918. [PMID: 21826218]
Accepted name: (S)-ureidoglycine—glyoxylate transaminase
Reaction: (S)-ureidoglycine + glyoxylate = N-carbamoyl-2-oxoglycine + glycine
Other name(s): (S)-ureidoglycine—glyoxylate aminotransferase; UGXT; PucG
Systematic name: (S)-ureidoglycine:glyoxylate aminotransferase
Comments: A pyridoxal 5'-phosphate protein. The protein, found in bacteria, can use other amino-group acceptors, but is specific for (S)-ureidoglycine.
References:
1. Ramazzina, I., Costa, R., Cendron, L., Berni, R., Peracchi, A., Zanotti, G. and Percudani, R. An aminotransferase branch point connects purine catabolism to amino acid recycling. Nat. Chem. Biol. 6 (2010) 801-806. [PMID: 20852637]
Accepted name: farnesol kinase
Reaction: CTP + (2E,6E)-farnesol = CDP + (2E,6E)-farnesyl phosphate
For diagram of reaction click here.
Other name(s): FOLK (gene name)
Systematic name: CTP:(2E,6E)-farnesol phosphotransferase
Comments: The enzyme, found in plants and animals, can also use other nucleotide triphosphates as phosphate donor, albeit less efficiently. The plant enzyme can also use geraniol and geranylgeraniol as substrates with lower activity, but not farnesyl phosphate (cf. EC 2.7.4.32, farnesyl phosphate kinase) [2].
References:
1. Bentinger, M., Grunler, J., Peterson, E., Swiezewska, E. and Dallner, G. Phosphorylation of farnesol in rat liver microsomes: properties of farnesol kinase and farnesyl phosphate kinase. Arch. Biochem. Biophys. 353 (1998) 191-198. [PMID: 9606952]
2. Fitzpatrick, A.H., Bhandari, J. and Crowell, D.N. Farnesol kinase is involved in farnesol metabolism, ABA signaling and flower development in Arabidopsis. Plant J. 66 (2011) 1078-1088. [PMID: 21395888]
Accepted name: farnesyl phosphate kinase
Reaction: CTP + (2E,6E)-farnesyl phosphate = CDP + (2E,6E)-farnesyl diphosphate
For diagram of reaction click here.
Systematic name: CTP:(2E,6E)-farnesyl-phosphate phosphotransferase
Comments: The enzyme, found in plants and animals, is specific for CTP as phosphate donor. It does not use farnesol as substrate (cf. EC 2.7.1.216, farnesol kinase).
References:
1. Bentinger, M., Grunler, J., Peterson, E., Swiezewska, E. and Dallner, G. Phosphorylation of farnesol in rat liver microsomes: properties of farnesol kinase and farnesyl phosphate kinase. Arch. Biochem. Biophys. 353 (1998) 191-198. [PMID: 9606952]
2. Fitzpatrick, A.H., Bhandari, J. and Crowell, D.N. Farnesol kinase is involved in farnesol metabolism, ABA signaling and flower development in Arabidopsis. Plant J. 66 (2011) 1078-1088. [PMID: 21395888]
Accepted name: 4-hydroxybenzoate adenylyltransferase
Reaction: ATP + 4-hydroxybenzoate = diphosphate + 4-hydroxybenzoyl adenylate
Other name(s): fadD22 (gene name); 4-hydroxybenzoate adenylase
Systematic name: ATP:4-hydroxybenzoate adenylyltransferase
Comments: This mycobacterial enzyme participates in the biosynthesis of phenolphthiocerols. Following the substrate's activation by adenylation, it is transferred to an acyl-carrier protein domain within the enzyme, from which it is transferred to EC 2.3.1.261, 4-hydroxyphenylalkanoate synthase.
References:
1. Simeone, R., Leger, M., Constant, P., Malaga, W., Marrakchi, H., Daffe, M., Guilhot, C. and Chalut, C. Delineation of the roles of FadD22, FadD26 and FadD29 in the biosynthesis of phthiocerol dimycocerosates and related compounds in Mycobacterium tuberculosis. FEBS J. 277 (2010) 2715-2725. [PMID: 20553505]
2. Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040-1050. [PMID: 25561717]
Accepted name: teichoic acid poly(glycerol phosphate) polymerase
Reaction: n CDP-glycerol + 4-O-[(2R)-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = n CMP + 4-O-{poly[(2R)-glycerophospho]-(2R)-glycerophospho}-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): teichoic-acid synthase; cytidine diphosphoglycerol glycerophosphotransferase; poly(glycerol phosphate) polymerase; teichoic acid glycerol transferase; glycerophosphate synthetase; CGPTase; CDP-glycerol glycerophosphotransferase (ambiguous); Tag polymerase; CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase; tagF (gene name); tarF (gene name) (ambiguous)
Systematic name: CDP-glycerol:4-O-[(2R)-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol glycerophosphotransferase
Comments: Involved in the biosynthesis of poly glycerol phosphate teichoic acids in bacterial cell walls. This enzyme adds 30-50 glycerol units to the linker molecule, but only after it has been primed with the first glycerol unit by EC 2.7.8.44, teichoic acid poly(glycerol phosphate) primase. cf. EC 2.7.8.45, teichoic acid glycerol-phosphate transferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9076-71-5
References:
1. Burger, M.M. and Glaser, L. The synthesis of teichoic acids. I. Polyglycerophosphate. J. Biol. Chem. 239 (1964) 3168-3177. [PMID: 14245357]
2. Schertzer, J.W. and Brown, E.D. Purified, recombinant TagF protein from Bacillus subtilis 168 catalyzes the polymerization of glycerol phosphate onto a membrane acceptor in vitro. J. Biol. Chem. 278 (2003) 18002-18007. [PMID: 12637499]
3. Schertzer, J.W., Bhavsar, A.P. and Brown, E.D. Two conserved histidine residues are critical to the function of the TagF-like family of enzymes. J. Biol. Chem. 280 (2005) 36683-36690. [PMID: 16141206]
4. Pereira, M.P., Schertzer, J.W., D'Elia, M.A., Koteva, K.P., Hughes, D.W., Wright, G.D. and Brown, E.D. The wall teichoic acid polymerase TagF efficiently synthesizes poly(glycerol phosphate) on the TagB product lipid III. Chembiochem 9 (2008) 1385-1390. [PMID: 18465758]
5. Sewell, E.W., Pereira, M.P. and Brown, E.D. The wall teichoic acid polymerase TagF is non-processive in vitro and amenable to study using steady state kinetic analysis. J. Biol. Chem. 284 (2009) 21132-21138. [PMID: 19520862]
6. Lovering, A.L., Lin, L.Y., Sewell, E.W., Spreter, T., Brown, E.D. and Strynadka, N.C. Structure of the bacterial teichoic acid polymerase TagF provides insights into membrane association and catalysis. Nat. Struct. Mol. Biol. 17 (2010) 582-589. [PMID: 20400947]
7. Brown, S., Meredith, T., Swoboda, J. and Walker, S. Staphylococcus aureus and Bacillus subtilis W23 make polyribitol wall teichoic acids using different enzymatic pathways. Chem. Biol. 17 (2010) 1101-1110. [PMID: 21035733]
Accepted name: CDP-ribitol ribitolphosphotransferase
Reaction: n CDP-ribitol + 4-O-di[(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = n CMP + 4-O-(D-ribitylphospho)n-di[(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): teichoic-acid synthase (ambiguous); polyribitol phosphate synthetase (ambiguous); teichoate synthetase (ambiguous); poly(ribitol phosphate) synthetase (ambiguous); polyribitol phosphate polymerase (ambiguous); teichoate synthase (ambiguous); CDP-ribitol:poly(ribitol phosphate) ribitolphosphotransferase
Systematic name: CDP-ribitol:4-O-di[(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol ribitolphosphotransferase
Comments: Involved in the biosynthesis of poly ribitol phosphate teichoic acids in the cell wall of the bacterium Staphylococcus aureus. This enzyme adds around 40 ribitol units to the linker molecule.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9076-71-5
References:
1. Ishimoto, N. and Strominger, J.L. Polyribitol phosphate synthetase of Staphylococcus aureus. J. Biol. Chem. 241 (1966) 639-650. [PMID: 5908130]
2. Brown, S., Zhang, Y.H. and Walker, S. A revised pathway proposed for Staphylococcus aureus wall teichoic acid biosynthesis based on in vitro reconstitution of the intracellular steps. Chem. Biol. 15 (2008) 12-21. [PMID: 18215769]
3. Pereira, M.P., D'Elia, M.A., Troczynska, J. and Brown, E.D. Duplication of teichoic acid biosynthetic genes in Staphylococcus aureus leads to functionally redundant poly(ribitol phosphate) polymerases. J. Bacteriol. 190 (2008) 5642-5649. [PMID: 18556787]
4. Brown, S., Meredith, T., Swoboda, J. and Walker, S. Staphylococcus aureus and Bacillus subtilis W23 make polyribitol wall teichoic acids using different enzymatic pathways. Chem. Biol. 17 (2010) 1101-1110. [PMID: 21035733]
Accepted name: teichoic acid glycerol-phosphate transferase
Reaction: CDP-glycerol + 4-O-[(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = CDP + 4-O-di[(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): tarF (gene name) (ambiguous); teichoic acid glycerol-phosphate primase
Systematic name: CDP-glycerol:4-O-[(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol glycerophosphotransferase
Comments: Involved in the biosynthesis of teichoic acid linkage units in the cell walls of some bacteria such as Staphylococcus aureus. This enzyme adds a second glycerol unit to the disaccharide linker of the teichoic acid. cf. EC 2.7.8.12, teichoic acid poly(glycerol phosphate) polymerase.
References:
1. Brown, S., Zhang, Y.H. and Walker, S. A revised pathway proposed for Staphylococcus aureus wall teichoic acid biosynthesis based on in vitro reconstitution of the intracellular steps. Chem. Biol. 15 (2008) 12-21. [PMID: 18215769]
2. Brown, S., Meredith, T., Swoboda, J. and Walker, S. Staphylococcus aureus and Bacillus subtilis W23 make polyribitol wall teichoic acids using different enzymatic pathways. Chem. Biol. 17 (2010) 1101-1110. [PMID: 21035733]
Accepted name: teichoic acid ribitol-phosphate primase
Reaction: CDP-ribitol + 4-O-[(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = CMP + 4-O-[1-D-ribitylphospho-(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): Tar primase; tarK (gene name)
Systematic name: CDP-ribitol:4-O-[(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol ribitylphosphotransferase
Comments: Involved in the biosynthesis of teichoic acid linkage units in the cell wall of Bacillus subtilis W23. This enzyme adds the first ribitol unit to the disaccharide linker of the teichoic acid.
References:
1. Brown, S., Meredith, T., Swoboda, J. and Walker, S. Staphylococcus aureus and Bacillus subtilis W23 make polyribitol wall teichoic acids using different enzymatic pathways. Chem. Biol. 17 (2010) 1101-1110. [PMID: 21035733]
Accepted name: teichoic acid ribitol-phosphate polymerase
Reaction: n CDP-ribitol + 4-O-[1-D-ribitylphospho-(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = n CMP + 4-O-[(1-D-ribitylphospho)n-(1-D-ribitylphospho)-(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): Tar polymerase (ambiguous); tarL (gene name) (ambiguous)
Systematic name: CDP-ribitol:4-O-[1-D-ribitylphospho-(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol ribitolphosphotransferase
Comments: Involved in the biosynthesis of teichoic acid linkage units in the cell wall of Bacillus subtilis W23. This enzyme adds the 25-35 ribitol units to the linker molecule.
References:
1. Brown, S., Meredith, T., Swoboda, J. and Walker, S. Staphylococcus aureus and Bacillus subtilis W23 make polyribitol wall teichoic acids using different enzymatic pathways. Chem. Biol. 17 (2010) 1101-1110. [PMID: 21035733]
Accepted name: adenosine-5'-diphospho-5'-[DNA] diphosphatase
Reaction: (1) adenosine-5'-diphospho-5'-[DNA] + H2O = AMP + phospho-5'-[DNA]
(2) adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O = AMP + 5'-phospho-(ribonucleotide)-[DNA]
Other name(s): aprataxin; 5'-App5'-DNA adenylate hydrolase; APTX (gene name); HNT3 (gene name)
Systematic name: adenosine-5'-diphospho-5'-[DNA] hydrolase (adenosine 5'-phosphate-forming)
Comments: Aprataxin is a DNA-binding protein involved in different types of DNA break repair. The enzyme acts (among other activities) on abortive DNA ligation intermediates that contain an adenylate covalently linked to the 5'-phosphate DNA terminus. It also acts when the adenylate is covalently linked to the 5'-phosphate of a ribonucleotide linked to a DNA strand, which is the result of abortive ligase activty on products of EC 3.1.26.4, ribonuclease H, an enzyme that cleaves RNA-DNA hybrids on the 5' side of the ribonucleotide found in the 5'-RNA-DNA-3' junction. Aprataxin binds the adenylate group to a histidine residue within the active site, followed by its hydrolysis from the nucleic acid and eventual release, leaving a 5'-phosphate terminus that can be efficiently rejoined. The enzyme also possesses the activities of EC 3.1.11.8, guaosine-5'-diphospho-5'-[DNA] diphosphatase, and EC 3.1.12.2, DNA-3'-diphospho-5'-guanosine diphosphatase.
References:
1. Ahel, I., Rass, U., El-Khamisy, S.F., Katyal, S., Clements, P.M., McKinnon, P.J., Caldecott, K.W. and West, S.C. The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates. Nature 443 (2006) 713-716. [PMID: 16964241]
2. Tumbale, P., Williams, J.S., Schellenberg, M.J., Kunkel, T.A. and Williams, R.S. Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity. Nature 506 (2014) 111-115. [PMID: 24362567]
Accepted name: guaosine-5'-diphospho-5'-[DNA] diphosphatase
Reaction: guaosine-5'-diphospho-5'-[DNA] + H2O = phospho-5'-[DNA] + GMP
Other name(s): aprataxin; pp5'G5'DNA diphosphatase; pp5'G5'-DNA guanylate hydrolase; APTX (gene name); HNT3 (gene name)
Systematic name: guaosine-5'-diphospho-5'-[DNA] hydrolase (guanosine 5'-phosphate-forming)
Comments: Aprataxin is a DNA-binding protein that catalyses (among other activities) the 5' decapping of Gpp-DNA (formed by homologs of RtcB3 from the bacterium Myxococcus xanthus).The enzyme binds the guanylate group to a histidine residue at its active site, forming a covalent enzyme-nucleotide phosphate intermediate, followed by the hydrolysis of the guanylate from the nucleic acid and eventual release. The enzyme forms a 5'-phospho terminus that can be efficiently joined by "classical" ligases. The enzyme also possesses the activitiy of EC 3.1.11.7, adenosine-5'-diphospho-5'-[DNA] diphosphatase and EC 3.1.12.2, DNA-3'-diphospho-5'-guanosine diphosphatase.
References:
1. Maughan, W.P. and Shuman, S. Characterization of 3'-phosphate RNA ligase paralogs RtcB1, RtcB2, and RtcB3 from Myxococcus xanthus highlights DNA and RNA 5'-phosphate capping activity of RtcB3. J. Bacteriol. 197 (2015) 3616-3624. [PMID: 26350128]
Accepted name: DNA-3'-diphospho-5'-guanosine diphosphatase
Reaction: [DNA]-3'-diphospho-5'-guanosine + H2O = [DNA]-3'-phosphate + GMP
Other name(s): aprataxin; DNA-3'pp5'G guanylate hydrolase; APTX (gene name); HNT3 (gene name)
Systematic name: [DNA]-3'-diphospho-5'-guanosine hydrolase (guanosine 5'-phosphate-forming)
Comments: Aprataxin is a DNA-binding protein that catalyses (among other activities) the 3' decapping of DNA-ppG (formed by EC 6.5.1.8, 3'-phosphate/5'-hydroxy nucleic acid ligase) [1]. The enzyme binds the guanylate group to a histidine residue at its active site, forming a covalent enzyme-nucleotide phosphate intermediate, followed by the hydrolysis of the guanylate from the nucleic acid and its eventual release. The enzyme also possesses the activity of EC 3.1.11.7, adenosine-5'-diphospho-5'-[DNA] diphosphatase, and EC 3.1.11.8, guaosine-5'-diphospho-5'-[DNA] diphosphatase.
References:
1. Das, U., Chauleau, M., Ordonez, H. and Shuman, S. Impact of DNA3'pp5'G capping on repair reactions at DNA 3' ends. Proc. Natl. Acad. Sci. USA 111 (2014) 11317-11322. [PMID: 25049385]
2. Chauleau, M., Jacewicz, A. and Shuman, S. DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition. Nucleic Acids Res. 43 (2015) 6075-6083. [PMID: 26007660]
Accepted name: chitinase
Reaction: Random endo-hydrolysis of N-acetyl-β-D-glucosaminide (1→4)-β-linkages in chitin and chitodextrins
Glossary: chitin = [(1→4)-β-D-GlcpNAc]n = (1→4)-2-acetamido-2-deoxy-β-D-glucan
Other name(s): ChiC; chitodextrinase (ambiguous); 1,4-β-poly-N-acetylglucosaminidase; poly-β-glucosaminidase; β-1,4-poly-N-acetyl glucosamidinase; poly[1,4-(N-acetyl-β-D-glucosaminide)] glycanohydrolase
Systematic name: (1→4)-2-acetamido-2-deoxy-β-D-glucan glycanohydrolase
Comments: The enzyme binds to chitin and randomly cleaves glycosidic linkages in chitin and chitodextrins in a non-processive mode, generating chitooligosaccharides and free ends on which exo-chitinases and exo-chitodextrinases can act. Activity is greatly stimulated in the presence of EC 1.14.99.53, lytic chitin monoxygenase, which attacks the crystalline structure of chitin and makes the polymer more accesible to the chitinase. cf. EC 3.2.1.202, endo-chitodextrinase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9001-06-3
References:
1. Zechmeister, L. and Tóth, G. Chromatographic adsorption of the enzymes of emulsin which act on chitins. Enzymologia 7 (1939) 165-169.
2. Tracey, M.V. Chitinase in some basidiomycetes. Biochem. J. 61 (1955) 579-586. [PMID: 13276340]
3. Fischer, E.H. and Stein, E.A. Cleavage of O- and S-glycosidic bonds (survey). In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 4, Academic Press, New York, 1960, pp. 301-312.
4. Connell, T.D., Metzger, D.J., Lynch, J. and Folster, J.P. Endochitinase is transported to the extracellular milieu by the eps-encoded general secretory pathway of Vibrio cholerae. J. Bacteriol. 180 (1998) 5591-5600. [PMID: 9791107]
5. Francetic, O., Badaut, C., Rimsky, S. and Pugsley, A.P. The ChiA (YheB) protein of Escherichia coli K-12 is an endochitinase whose gene is negatively controlled by the nucleoid-structuring protein H-NS. Mol. Microbiol. 35 (2000) 1506-1517. [PMID: 10760150]
6. Zverlov, V.V., Fuchs, K.P. and Schwarz, W.H. Chi18A, the endochitinase in the cellulosome of the thermophilic, cellulolytic bacterium Clostridium thermocellum. Appl. Environ. Microbiol. 68 (2002) 3176-3179. [PMID: 12039789]
7. Rottloff, S., Stieber, R., Maischak, H., Turini, F.G., Heubl, G. and Mithofer, A. Functional characterization of a class III acid endochitinase from the traps of the carnivorous pitcher plant genus, Nepenthes. J. Exp. Bot. 62 (2011) 4639-4647. [PMID: 21633084]
Accepted name: exo-chitinase (non-reducing end)
Reaction: Hydrolysis of N,N'-diacetylchitobiose from the non-reducing end of chitin and chitodextrins.
Other name(s): chiB (gene name)
Systematic name: (1→4)-2-acetamido-2-deoxy-β-D-glucan diacetylchitobiohydrolase (non-reducing end)
Comments: The enzyme hydrolyses the second glycosidic (1→4) linkage from non-reducing ends of chitin and chitodextrin molecules, liberating N,N'-diacetylchitobiose disaccharides. cf. EC 3.2.1.201, exo-chitinase (reducing end).
References:
1. Tanaka, T., Fukui, T. and Imanaka, T. Different cleavage specificities of the dual catalytic domains in chitinase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Biol. Chem. 276 (2001) 35629-35635. [PMID: 11468293]
2. Hult, E.L., Katouno, F., Uchiyama, T., Watanabe, T. and Sugiyama, J. Molecular directionality in crystalline β-chitin: hydrolysis by chitinases A and B from Serratia marcescens 2170. Biochem. J. 388 (2005) 851-856. [PMID: 15717865]
3. Ohnuma, T., Numata, T., Osawa, T., Mizuhara, M., Lampela, O., Juffer, A.H., Skriver, K. and Fukamizo, T. A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis. Planta 234 (2011) 123-137. [PMID: 21390509]
4. Gutierrez-Roman, M.I., Dunn, M.F., Tinoco-Valencia, R., Holguin-Melendez, F., Huerta-Palacios, G. and Guillen-Navarro, K. Potentiation of the synergistic activities of chitinases ChiA, ChiB and ChiC from Serratia marcescens CFFSUR-B2 by chitobiase (Chb) and chitin binding protein (CBP). World J Microbiol Biotechnol 30 (2014) 33-42. [PMID: 23824666]
Accepted name: exo-chitinase (reducing end)
Reaction: Hydrolysis of N,N'-diacetylchitobiose from the reducing end of chitin and chitodextrins.
Other name(s): chiA (gene name)
Systematic name: (1→4)-2-acetamido-2-deoxy-β-D-glucan diacetylchitobiohydrolase (reducing end)
Comments: The enzyme hydrolyses the second glycosidic (1→4) linkage from reducing ends of chitin and chitodextrin molecules, liberating N,N'-diacetylchitobiose disaccharides.cf. EC 3.2.1.200, exo-chitinase (non-reducing end).
References:
1. Hult, E.L., Katouno, F., Uchiyama, T., Watanabe, T. and Sugiyama, J. Molecular directionality in crystalline β-chitin: hydrolysis by chitinases A and B from Serratia marcescens 2170. Biochem. J. 388 (2005) 851-856. [PMID: 15717865]
2. Nakagawa, Y.S., Eijsink, V.G., Totani, K. and Vaaje-Kolstad, G. Conversion of α-chitin substrates with varying particle size and crystallinity reveals substrate preferences of the chitinases and lytic polysaccharide monooxygenase of Serratia marcescens. J. Agric. Food Chem. 61 (2013) 11061-11066. [PMID: 24168426]
3. Gutierrez-Roman, M.I., Dunn, M.F., Tinoco-Valencia, R., Holguin-Melendez, F., Huerta-Palacios, G. and Guillen-Navarro, K. Potentiation of the synergistic activities of chitinases ChiA, ChiB and ChiC from Serratia marcescens CFFSUR-B2 by chitobiase (Chb) and chitin binding protein (CBP). World J Microbiol Biotechnol 30 (2014) 33-42. [PMID: 23824666]
4. Brurberg, M.B., Nes, I.F. and Eijsink, V.G. Comparative studies of chitinases A and B from Serratia marcescens. Microbiology 142 (1996) 1581-1589. [PMID: 8757722]
Accepted name: endo-chitodextinase
Reaction: Hydrolysis of chitodextrins, releasing N,N'-diacetylchitobiose and small amounts of N,N',N''-triacetylchitotriose.
Other name(s): endo I (gene name); chitodextrinase (ambiguous); endolytic chitodextrinase; periplasmic chitodextrinase
Systematic name: (1→4)-2-acetamido-2-deoxy-β-D-glucan diacetylchitobiohydrolase (endo-cleaving)
Comments: The enzyme, characterized from the bacterium Vibrio furnissii, is an endo-cleaving chitodextrinase that participates in the the chitin catabolic pathway found in members of the Vibrionaceae. Unlike EC 3.2.1.14, chitinase, it has no activity on chitin. The smallest substrate is a tetrasaccharide, and the final products are N,N'-diacetylchitobiose and small amounts of N,N',N''-triacetylchitotriose. cf. EC 3.2.1.200, exo-chitinase (non-reducing end), and EC 3.2.1.201, exo-chitinase (reducing end).
References:
1. Bassler, B.L., Yu, C., Lee, Y.C. and Roseman, S. Chitin utilization by marine bacteria. Degradation and catabolism of chitin oligosaccharides by Vibrio furnissii. J. Biol. Chem. 266 (1991) 24276-24286. [PMID: 1761533]
2. Keyhani, N.O. and Roseman, S. The chitin catabolic cascade in the marine bacterium Vibrio furnissii. Molecular cloning, isolation, and characterization of a periplasmic chitodextrinase. J. Biol. Chem. 271 (1996) 33414-33424. [PMID: 8969204]
Accepted name: N2-acetyl-L-2,4-diaminobutanoate deacetylase
Reaction: N2-acetyl-L-2,4-diaminobutanoate + H2O = L-2,4-diaminobutanoate + acetate
Other name(s): doeB (gene name)
Systematic name: N2-acetyl-L-2,4-diaminobutanoate amidohydrolase
Comments: The enzyme, found in bacteria, has no activity with N4-acetyl-L-2,4-diaminobutanoate (cf. EC 3.5.4.44, ectoine hydrolase).
References:
1. Schwibbert, K., Marin-Sanguino, A., Bagyan, I., Heidrich, G., Lentzen, G., Seitz, H., Rampp, M., Schuster, S.C., Klenk, H.P., Pfeiffer, F., Oesterhelt, D. and Kunte, H.J. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. Environ. Microbiol. 13 (2011) 1973-1994. [PMID: 20849449]
Accepted name: oxamate amidohydrolase
Reaction: oxamate + H2O = oxalate + ammonia
Other name(s): HpxW
Systematic name: oxamate amidohydrolase
Comments: The enzyme has been characterized from the bacterium Klebsiella pneumoniae.
References:
1. Hicks, K.A. and Ealick, S.E. Biochemical and structural characterization of Klebsiella pneumoniae oxamate amidohydrolase in the uric acid degradation pathway. Acta Crystallogr D Struct Biol 72 (2016) 808-816. [PMID: 27303801]
Accepted name: jasmonoyl-L-amino acid hydrolase
Reaction: a jasmonoyl-L-amino acid + H2O = jasmonate + an L-amino acid
Glossary: tuberonic acid = 12-hydroxyjasmonate = {(1R,2R)-3-oxo-2-[(2Z)-5-hydroxypent-2-enyl]cyclopentyl}acetate
jasmonate = {(1R,2R)-3-oxo-2-[(2Z)-pent-2-enyl]cyclopentyl}acetate
Other name(s): IAR3 (gene name); ILL4 (gene name); ILL6 (gene name)
Systematic name: jasmonoyl-L amino acid amidohydrolase
Comments: This entry includes a family of enzymes that recyle jasmonoyl-amino acid conjugates back to jasmonates. The enzymes from Arabidopsis thaliana have been shown to also act on 12-hydroxyjasmonoyl-L-isoleucine, generating tuberonic acid.
References:
1. Widemann, E., Miesch, L., Lugan, R., Holder, E., Heinrich, C., Aubert, Y., Miesch, M., Pinot, F. and Heitz, T. The amidohydrolases IAR3 and ILL6 contribute to jasmonoyl-isoleucine hormone turnover and generate 12-hydroxyjasmonic acid upon wounding in Arabidopsis leaves. J. Biol. Chem. 288 (2013) 31701-31714. [PMID: 24052260]
Accepted name: ectoine hydrolase
Reaction: ectoine + H2O = N2-acetyl-L-2,4-diaminobutanoate
Glossary: ectoine = (4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate
Other name(s): doeA (gene name)
Systematic name: ectoine aminohydrolase
Comments: The enzyme, found in some halophilic bacteria, is involved in the degradation of the compatible solute ectoine. The enzyme, which belongs to peptidase family M24, only acts in the direction of ectoine hydrolysis. It also produces smaller amounts of N4-acetyl-L-2,4-diaminobutanoate, which is recycled back to ectoine by EC 4.2.1.108, ectoine synthase.
References:
1. Schwibbert, K., Marin-Sanguino, A., Bagyan, I., Heidrich, G., Lentzen, G., Seitz, H., Rampp, M., Schuster, S.C., Klenk, H.P., Pfeiffer, F., Oesterhelt, D. and Kunte, H.J. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. Environ. Microbiol. 13 (2011) 1973-1994. [PMID: 20849449]
Accepted name: melamine deaminase
Reaction: (1) melamine + H2O = ammeline + NH3
(2) ammeline + H2O = ammelide + NH3
Glossary: melamine = 2,4,6-triamino-1,3,5-triazine
ammeline = 4,6-diamino-1,3,5-triazin-2-ol
ammelide = 6-amino-1,3,5-triazine-2,4-diol
Other name(s): triA (gene name)
Systematic name: melamine aminohydrolase
Comments: The enzyme, isolated from the bacterium Acidovorax citrulli, performs the deamination of melamine 15-fold faster than the deamination of ammeline. It also has activity with 2-chloro-4,6-diamino-s-triazine, but has no activity toward halo-substituted triazine ring compounds such as atrazine (cf. EC 3.8.1.8, atrazine chlorohydrolase).
References:
1. Seffernick, J.L., Souza, M.L., Sadowsky, M.J. and Wackett, L.P. Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different. J. Bacteriol. 183 (2001) 2405-2410. [PMID: 11274097]
Accepted name: cAMP deaminase
Reaction: 3',5'-cyclic AMP + H2O = 3',5'-cyclic IMP + NH3
Other name(s): cyclic adenylate deaminase; CadD
Systematic name: 3',5'-cyclic AMP aminohydrolase
Comments: Requires Zn2+. The enzyme, isolated from the bacterium Leptospira interrogans, is specific for cAMP.
References:
1. Goble, A.M., Feng, Y., Raushel, F.M. and Cronan, J.E. Discovery of a cAMP deaminase that quenches cyclic AMP-dependent regulation. ACS Chem. Biol. 8 (2013) 2622-2629. [PMID: 24074367]
Accepted name: ectoine synthase
Reaction: N4-acetyl-L-2,4-diaminobutanoate = L-ectoine + H2O
For diagram of reaction click here.
Glossary: ectoine = (4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate
Other name(s): ectC (gene name); N-acetyldiaminobutyrate dehydratase; N-acetyldiaminobutanoate dehydratase; L-ectoine synthase; 4-N-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming)
Systematic name: N4-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming)
Comments: Ectoine is an osmoprotectant that is found in halophilic eubacteria. This enzyme is part of the ectoine biosynthesis pathway and only acts in the direction of ectoine formation. cf. EC 3.5.4.44, ectoine hydrolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Peters, P., Galinski, E.A. and Truper, H.G. The biosynthesis of ectoine. FEMS Microbiol. Lett. 71 (1990) 157-162.
2. Ono, H., Sawada, K., Khunajakr, N., Tao, T., Yamamoto, M., Hiramoto, M., Shinmyo, A., Takano, M. and Murooka, Y. Characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, Halomonas elongata. J. Bacteriol. 181 (1999) 91-99. [PMID: 9864317]
3. Kuhlmann, A.U. and Bremer, E. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl. Environ. Microbiol. 68 (2002) 772-783. [PMID: 11823218]
4. Louis, P. and Galinski, E.A. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143 (1997) 1141-1149. [PMID: 9141677]
5. Schwibbert, K., Marin-Sanguino, A., Bagyan, I., Heidrich, G., Lentzen, G., Seitz, H., Rampp, M., Schuster, S.C., Klenk, H.P., Pfeiffer, F., Oesterhelt, D. and Kunte, H.J. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. Environ. Microbiol. 13 (2011) 1973-1994. [PMID: 20849449]
Accepted name: cis-L-3-hydroxyproline dehydratase
Reaction: cis-3-hydroxy-L-proline = 1-pyrroline-2-carboxylate + H2O
Glossary: 1-pyrroline-2-carboxylate = 4,5-dihydro-3H-pyrrole-2-carboxylate
Other name(s): cis-L-3-hydroxyproline hydro-lyase; c3LHypD
Systematic name: cis-3-hydroxy-L-proline hydro-lyase (1-pyrroline-2-carboxylate-forming)
References:
1. Zhang, X., Kumar, R., Vetting, M.W., Zhao, S., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. A unique cis-3-hydroxy-L-proline dehydratase in the enolase superfamily. J. Am. Chem. Soc. 137 (2015) 1388-1391. [PMID: 25608448]
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.
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: 4-hydroxyproline betaine 2-epimerase
Reaction: (1) trans-4-hydroxy-L-proline betaine = cis-4-hydroxy-D-proline betaine
(2) L-proline betaine = D-proline betaine
Other name(s): hpbD (gene name); Hyp-B 2-epimerase; (4R)-4-hydroxyproline betaine 2-epimerase
Systematic name: 4-hydroxyproline betaine 2-epimerase
Comments: The enzyme, characterized from the bacteria Pelagibaca bermudensis and Paracoccus denitrificans, specifically catalyses racemization of trans-4-hydroxy-L-proline betaine and L-proline betaine at the C-2 position.
References:
1. Zhao, S., Kumar, R., Sakai, A., Vetting, M.W., Wood, B.M., Brown, S., Bonanno, J.B., Hillerich, B.S., Seidel, R.D., Babbitt, P.C., Almo, S.C., Sweedler, J.V., Gerlt, J.A., Cronan, J.E. and Jacobson, M.P. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature 502 (2013) 698-702. [PMID: 24056934]
2. Kumar, R., Zhao, S., Vetting, M.W., Wood, B.M., Sakai, A., Cho, K., Solbiati, J., Almo, S.C., Sweedler, J.V., Jacobson, M.P., Gerlt, J.A. and Cronan, J.E. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio 5 (2014) e00933. [PMID: 24520058]
Accepted name: tagaturonate epimerase
Reaction: D-tagaturonate = D-fructuronate
Other name(s): fructuronate epimerase; tagaturonate/fructuronate epimerase; UxaE
Systematic name: D-tagaturonate 3-epimerase
Comments: The enzyme, present in bacteria, is involved in a degradation pathway of D-galacturonate.
References:
1. Rodionova, I.A., Scott, D.A., Grishin, N.V., Osterman, A.L. and Rodionov, D.A. Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. Environ Microbiol 14 (2012) 2920-2934. [PMID: 22925190]
Accepted name: D-tagatose 6-phosphate 4-epimerase
Reaction: D-tagatose 6-phosphate = D-fructose 6-phosphate
Systematic name: D-tagatose 6-phosphate 4-epimerase
Comments: The enzyme from Agrobacterium fabrum C58 is part of D-altritol and galactitol degradation pathways.
References:
1. Wichelecki, D.J., Vetting, M.W., Chou, L., Al-Obaidi, N., Bouvier, J.T., Almo, S.C. and Gerlt, J.A. ATP-binding cassette (ABC) transport system solute-binding protein-guided identification of novel D-altritol and galactitol catabolic pathways in Agrobacterium tumefaciens C58. J. Biol. Chem. 290 (2015) 28963-28976. [PMID: 26472925]
[EC 5.3.3.20 Transferred entry: 2-hydroxyisobutanoyl-CoA mutase. Now EC 5.4.99.64, 2-hydroxyisobutanoyl-CoA mutase (EC 5.3.3.20 created 2016, deleted 2017)]
Accepted name: 2-hydroxyisobutanoyl-CoA mutase
Reaction: 2-hydroxy-2-methylpropanoyl-CoA = (S)-3-hydroxybutanoyl-CoA
Glossary: 2-hydroxy-2-methylpropanoyl-CoA = 2-hydroxyisobutanoyl-CoA
Other name(s): hcmAB (gene names)
Systematic name: 2-hydroxy-2-methylpropanoyl mutase
Comments: The enzyme, characterized from the bacterium Aquincola tertiaricarbonis, uses radical chemistry to rearrange the positions of both a methyl group and a hydroxyl group. It consists of two subunits, the smaller one containing a cobalamin cofactor. It plays a central role in the degradation of assorted substrates containing a tert-butyl moiety.
References:
1. Yaneva, N., Schuster, J., Schafer, F., Lede, V., Przybylski, D., Paproth, T., Harms, H., Muller, R.H. and Rohwerder, T. Bacterial acyl-CoA mutase specifically catalyzes coenzyme B12-dependent isomerization of 2-hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA. J. Biol. Chem. 287 (2012) 15502-15511. [PMID: 22433853]
2. Kurteva-Yaneva, N., Zahn, M., Weichler, M.T., Starke, R., Harms, H., Muller, R.H., Strater, N. and Rohwerder, T. Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase. J. Biol. Chem. 290 (2015) 9727-9737. [PMID: 25720495]
Accepted name: carnitine-CoA ligase
Reaction: ATP + L-carnitine + CoA = AMP + diphosphate + L-carnitinyl-CoA
Glossary: carnitine = 3-hydroxy-4-(trimethylammonio)butanoate
crotonobetaine = (E)-4-(trimethylammonio)but-2-enoate
γ-butyrobetaine = 4-(trimethylammonio)butanoate
Other name(s): caiC (gene name)
Systematic name: L-carnitine:CoA ligase (AMP-forming)
Comments: The enzyme, originally characterized from the bacterium Escherichia coli, can catalyse the transfer of CoA to L-carnitine, crotonobetaine and γ-butyrobetaine. In vitro the enzyme also exhibits the activity of EC 2.8.3.21, L-carnitine CoA-transferase.
References:
1. Eichler, K., Bourgis, F., Buchet, A., Kleber, H.P. and Mandrand-Berthelot, M.A. Molecular characterization of the cai operon necessary for carnitine metabolism in Escherichia coli. Mol. Microbiol. 13 (1994) 775-786. [PMID: 7815937]
2. Bernal, V., Arense, P., Blatz, V., Mandrand-Berthelot, M.A., Canovas, M. and Iborra, J.L. Role of betaine:CoA ligase (CaiC) in the activation of betaines and the transfer of coenzyme A in Escherichia coli. J. Appl. Microbiol. 105 (2008) 42-50. [PMID: 18266698]
Accepted name: 3'-phosphate/5'-hydroxy nucleic acid ligase
Reaction: (1) (ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP = (ribonucleotide)n+m + GMP + diphosphate (overall reaction)
(1a) GTP + [RNA ligase]-L-histidine = 5'-guanosyl [RNA ligase]-Nτ-phosphono-L-histidine + diphosphate
(1b) 5'-guanosyl [RNA ligase]-Nτ-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate = (ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
(1c) (ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m = (ribonucleotide)n+m + GMP
(2) (ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O = (ribonucleotide)n+m + GMP + diphosphate (overall reaction)
(2a) (ribonucleotide)n-2',3'-cyclophosphate + H2O = (ribonucleotide)n-3'-phosphate
(2b) GTP + [RNA ligase]-L-histidine = 5'-guanosyl [RNA ligase]-Nτ-phosphono-L-histidine + diphosphate
(2c) 5'-guanosyl [RNA ligase]-Nτ-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate = (ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
(2d) (ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m = (ribonucleotide)n+m + GMP
Other name(s): rtcB (gene name)
Systematic name: poly(ribonucleotide)-3'-phosphate:5'-hydroxy-poly(ribonucleotide) ligase (GMP-forming)
Comments: The enzyme is a GTP- and Mn2+-dependent 3'-5' nucleic acid ligase with the ability to join RNA with 3'-phosphate or 2',3'-cyclic-phosphate ends to RNA with 5'-hydroxy ends. It can also join DNA with 3'-phosphate ends to DNA with 5'-hydroxy ends, provided the DNA termini are unpaired [6]. The enzyme is found in members of all three kingdoms of life, and is essential in metazoa for the splicing of intron-containing tRNAs. The reaction follows a three-step mechanism with initial activation of the enzyme by GTP hydrolysis, forming a phosphoramide bond between the guanylate and a histidine residue. The guanylate group is transferred to the 3'-phosphate terminus of the substrate, forming the capped structure [DNA/RNA]-3'-(5'-diphosphoguanosine). When a suitable 5'-OH end is available, the enzyme catalyses an attack of the 5'-OH on the capped end to form a 3'-5' phosphodiester splice junction, releasing the guanylate. When acting on an RNA 2',3'-cyclic-phosphate, the enzyme cayalyses an additional reaction, hydrolysing the cyclic phosphate to a 3'-phosphate [9]. The metazoan enzyme requires activating cofactors in order to achieve multiple turnover catalysis [8].
References:
1. Tanaka, N., Meineke, B. and Shuman, S. RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo. J. Biol. Chem. 286 (2011) 30253-30257. [PMID: 21757685]
2. Tanaka, N. and Shuman, S. RtcB is the RNA ligase component of an Escherichia coli RNA repair operon. J. Biol. Chem. 286 (2011) 7727-7731. [PMID: 21224389]
3. Tanaka, N., Chakravarty, A.K., Maughan, B. and Shuman, S. Novel mechanism of RNA repair by RtcB via sequential 2',3'-cyclic phosphodiesterase and 3'-phosphate/5'-hydroxyl ligation reactions. J. Biol. Chem. 286 (2011) 43134-43143. [PMID: 22045815]
4. Desai, K.K. and Raines, R.T. tRNA ligase catalyzes the GTP-dependent ligation of RNA with 3'-phosphate and 5'-hydroxyl termini. Biochemistry 51 (2012) 1333-1335. [PMID: 22320833]
5. Chakravarty, A.K., Subbotin, R., Chait, B.T. and Shuman, S. RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-(histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates. Proc. Natl. Acad. Sci. USA 109 (2012) 6072-6077. [PMID: 22474365]
6. Chakravarty, A.K. and Shuman, S. The sequential 2',3'-cyclic phosphodiesterase and 3'-phosphate/5'-OH ligation steps of the RtcB RNA splicing pathway are GTP-dependent. Nucleic Acids Res. 40 (2012) 8558-8567. [PMID: 22730297]
7. Das, U., Chakravarty, A.K., Remus, B.S. and Shuman, S. Rewriting the rules for end joining via enzymatic splicing of DNA 3'-PO4 and 5'-OH ends. Proc. Natl. Acad. Sci. USA 110 (2013) 20437-20442. [PMID: 24218597]
8. Desai, K.K., Beltrame, A.L. and Raines, R.T. Coevolution of RtcB and Archease created a multiple-turnover RNA ligase. RNA 21 (2015) 1866-1872. [PMID: 26385509]
9. Maughan, W.P. and Shuman, S. Distinct contributions of enzymic functional groups to the 2',3'-cyclic phosphodiesterase, 3'-phosphate guanylylation, and 3'-ppG/5'-OH ligation steps of the Escherichia coli RtcB nucleic acid splicing pathway. J. Bacteriol. 198 (2016) 1294-1304. [PMID: 26858100]