An asterisk before'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: phosphoglycerate dehydrogenase
Reaction: 3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH + H+
For diagram of reaction click here.
Other name(s): PHGDH (gene name); D-3-phosphoglycerate:NAD+ oxidoreductase; α-phosphoglycerate dehydrogenase; 3-phosphoglycerate dehydrogenase; 3-phosphoglyceric acid dehydrogenase; D-3-phosphoglycerate dehydrogenase; glycerate 3-phosphate dehydrogenase; glycerate-1,3-phosphate dehydrogenase; phosphoglycerate oxidoreductase; phosphoglyceric acid dehydrogenase; SerA; 3-phosphoglycerate:NAD+ 2-oxidoreductase; SerA 3PG dehydrogenase; 3PHP reductase
Systematic name: 3-phospho-D-glycerate:NAD+ 2-oxidoreductase
Comments: This enzyme catalyses the first committed and rate-limiting step in the phosphoserine pathway of serine biosynthesis. The reaction occurs predominantly in the direction of reduction. The enzyme from the bacterium Escherichia coli also catalyses the activity of EC 1.1.1.399, 2-oxoglutarate reductase [6].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9075-29-0
References:
1. Pizer, L.I. The pathway and control of serine biosynthesis in Escherichia coli. J. Biol. Chem. 238 (1963) 3934-3944. [PMID: 14086727]
2. Walsh, D.A. and Sallach, H.J. Purification and properties of chicken liver D-3-phosphoglycerate dehydrogenase. Biochemistry 4 (1965) 1076-1085. [PMID: 4378782]
3. Slaughter, J.C. and Davies, D.D. The isolation and characterization of 3-phosphoglycerate dehydrogenase from peas. Biochem. J. 109 (1968) 743-748. [PMID: 4386930]
4. Sugimoto, E. and Pizer, L.I. The mechanism of end product inhibition of serine biosynthesis. I. Purification and kinetics of phosphoglycerate dehydrogenase. J. Biol. Chem. 243 (1968) 2081. [PMID: 4384871]
5. Schuller, D.J., Grant, G.A. and Banaszak, L.J. The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Nat. Struct. Biol. 2 (1995) 69-76. [PMID: 7719856]
6. Zhao, G. and Winkler, M.E. A novel α-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria. J. Bacteriol. 178 (1996) 232-239. [PMID: 8550422]
7. Achouri, Y., Rider, M.H., Schaftingen, E.V. and Robbi, M. Cloning, sequencing and expression of rat liver 3-phosphoglycerate dehydrogenase. Biochem. J. 323 (1997) 365-370. [PMID: 9163325]
8. Dey, S., Grant, G.A. and Sacchettini, J.C. Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits. J. Biol. Chem. 280 (2005) 14892-14899. [PMID: 15668249]
Accepted name: 5a,11a-dehydrotetracycline reductase
Reaction: tetracycline + oxidized coenzyme F420 = 5a,11a-dehydrotetracycline + reduced coenzyme F420
For diagram of reaction click here.
Other name(s): oxyR (gene name); 12-dehydrotetracycline dehydrogenase; dehydrooxytetracycline dehydrogenase; 12-dehydrotetracycline reductase
Systematic name: tetracycline:coenzyme F420 dehydrogenase
Comments: The enzyme, characterized from the bacteria Streptomyces aureofaciens and Streptomyces rimosus, catalyses the last step in the biosynthesis of the tetracycline antibiotics tetracycline and oxytetracycline.
References:
1. McCormick, J.R.D., Hirsch, U., Sjolander, N.O. and Doerschuk, A.P. Cosynthesis of tetracyclines by pairs of Streptomyces aureofaciens mutants. J. Am. Chem. Soc. 82 (1960) 5006-5007.
2. Miller, P.A., Sjolander, N.O., Nalesnyk, S., Arnold, N., Johnson, S., Doerschuk, A.P. and McCormick, J.R.D. Cosynthetic factor I, a factor involved in hydrogen-transfer in Streptomyces aureofaciens. J. Am. Chem. Soc. 82 (1960) 5002-5003.
3. McCormick, J.R.D. and Morton, G.O. Identity of cosynthetic factor I of Streptomyces aureofaciens and fragment FO from coenzyme F420 of Methanobacterium species. J. Am. Chem. Soc. 104 (1982) 4014-4015.
4. Wang, P., Bashiri, G., Gao, X., Sawaya, M.R. and Tang, Y. Uncovering the enzymes that catalyze the final steps in oxytetracycline biosynthesis. J. Am. Chem. Soc. 135 (2013) 7138-7141. [PMID: 23621493]
Accepted name: glyphosate oxidoreductase
Reaction: 2 glyphosate + O2 = 2 aminomethylphosphonate + 2 glyoxylate
Glossary: glyphosate = N-(phosphonomethyl)glycine
Other name(s): gox (gene name)
Systematic name: glyphosate oxidoreductase (aminomethylphosphonate-forming)
Comments: The enzyme, characterized from the bacterium Ochrobactrum sp. G-1, contains an FAD cofactor. The catalytic cycle starts with a reduction of the FAD cofactor by one molecule of glyphosate, yielding reduced FAD and a Schiff base of aminomethylphosphonate with glyoxylate that is hydrolysed to the single components. The reduced FAD is reoxidized by oxygen, generating water and an oxygenated flavin intermediate, which catalyses the oxygenation of a second molecule of glyphosate, forming the second pair of aminomethylphosphonate and glyoxylate.
References:
1. Barry, G. F. and Kishore. G. M. Glyphosate tolerant plants. US patent US5463175, (1995).
2. Sviridov, A.V., Shushkova, T.V., Zelenkova, N.F., Vinokurova, N.G., Morgunov, I.G., Ermakova, I.T. and Leontievsky, A.A. Distribution of glyphosate and methylphosphonate catabolism systems in soil bacteria Ochrobactrum anthropi and Achromobacter sp. Appl. Microbiol. Biotechnol. 93 (2012) 787-796. [PMID: 21789492]
Accepted name: sulfite dehydrogenase (cytochrome)
Reaction: sulfite + 2 ferricytochrome c + H2O = sulfate + 2 ferrocytochrome c + 2 H+
Other name(s): sulfite cytochrome c reductase; sulfite-cytochrome c oxidoreductase; sulfite oxidase (ambiguous); sulfite dehydrogenase (ambiguous); sorAB (gene names)
Systematic name: sulfite:ferricytochrome-c oxidoreductase
Comments: Associated with cytochrome c-551. The enzyme from the bacterium Starkeya novella contains a molybdopyranopterin cofactor and a smaller monoheme cytochrome c subunit. cf. EC 1.8.5.6, sulfite dehydrogenase (quinone).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-47-6
References:
1. Charles, A.M. and Suzuki, I. Purification and properties of sulfite:cytochrome c oxidoreductase from Thiobacillus novellus. Biochim. Biophys. Acta 128 (1966) 522-534.
2. Lyric, R.M. and Suzuki, I. Enzymes involved in the metabolism of thiosulfate by Thiobacillus thioparus. I. Survey of enzymes and properties of sulfite: cytochrome c oxidoreductase. Can. J. Biochem. 48 (1970) 334-343. [PMID: 5438321]
3. Yamanaka, T., Yoshioka, T. and Kimura, K. Purification of sulphite cytocrome c reductase of Thiobacillus novellus and reconstitution of its sulphite oxidase system with the purified constituents. Plant and Cell Physiol. 22 (1981) 631.
4. Lu, W.-P. and Kelly, D.P. Properties and role of sulphite:cytochrome c oxidoreductase purified from Thiobacillus versutus (A2). J. Gen. Microbiol. 130 (1984) 1683-1692.
5. Kappler, U., Bennett, B., Rethmeier, J., Schwarz, G., Deutzmann, R., McEwan, A.G. and Dahl, C. Sulfite:Cytochrome c oxidoreductase from Thiobacillus novellus. Purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family. J. Biol. Chem. 275 (2000) 13202-13212. [PMID: 10788424]
Accepted name: thiosulfate reductase (quinone)
Reaction: sulfite + hydrogen sulfide + a quinone = thiosulfate + a quinol
Other name(s): phsABC (gene names)
Systematic name: sulfite,hydrogen sulfide:quinone oxidoreductase
Comments: The enzyme, characterized from the bacterium Salmonella enterica, is similar to EC 1.1.5.6, formate dehydrogenase-N. It contains a molybdopterin-guanine dinucleotide, five [4Fe-4S] clusters and two heme b groups. The reaction occurs in vivo in the direction of thiosulfate disproportionation, which is highly endergonic. It is driven by the proton motive force that occurs across the cytoplasmic membrane.
References:
1. Kwan, H.S. and Barrett, E.L. Map locations and functions of Salmonella typhimurium men genes. J. Bacteriol. 159 (1984) 1090-1092. [PMID: 6384182]
2. Clark, M.A. and Barrett, E.L. The phs gene and hydrogen sulfide production by Salmonella typhimurium. J. Bacteriol. 169 (1987) 2391-2397. [PMID: 3108233]
3. Alami, N. and Hallenbeck, P.C. Cloning and characterization of a gene cluster, phsBCDEF, necessary for the production of hydrogen sulfide from thiosulfate by Salmonella typhimurium. Gene 156 (1995) 53-57. [PMID: 7737516]
4. Heinzinger, N.K., Fujimoto, S.Y., Clark, M.A., Moreno, M.S. and Barrett, E.L. Sequence analysis of the phs operon in Salmonella typhimurium and the contribution of thiosulfate reduction to anaerobic energy metabolism. J. Bacteriol. 177 (1995) 2813-2820. [PMID: 7751291]
5. Stoffels, L., Krehenbrink, M., Berks, B.C. and Unden, G. Thiosulfate reduction in Salmonella enterica is driven by the proton motive force. J. Bacteriol. 194 (2012) 475-485. [PMID: 22081391]
Accepted name: sulfite dehydrogenase (quinone)
Reaction: sulfite + a quinone + H2O = sulfate + a quinol
Other name(s): soeABC (gene names)
Systematic name: sulfite:quinone oxidoreductase
Comments: This membrane-bound bacterial enzyme catalyses the direct oxidation of sulfite to sulfate in the cytoplasm. The enzyme, characterized from the bacteria Ruegeria pomeroyi and Allochromatium vinosum, is a complex that consists of a membrane anchor (SoeC) and two cytoplasmic subunits: an iron-sulfur protein (SoeB) and a molybdoprotein that contains a [4Fe-4S] iron-sulfur cluster (SoeA). cf. EC 1.8.2.1, sulfite dehydrogenase (cytochrome).
References:
1. Dahl, C., Franz, B., Hensen, D., Kesselheim, A. and Zigann, R. Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process. Microbiology 159 (2013) 2626-2638. [PMID: 24030319]
Accepted name: dihydrophenazinedicarboxylate synthase
Reaction: (1) (1R,6R)-1,4,5,5a,6,9-hexahydrophenazine-1,6-dicarboxylate + O2 = (1R,10aS)-1,4,10,10a-tetrahydrophenazine-1,6-dicarboxylate + H2O2
(2) (1R,10aS)-1,4,10,10a-tetrahydrophenazine-1,6-dicarboxylate + O2 = (5aS)-5,5a-dihydrophenazine-1,6-dicarboxylate + H2O2
(3) (1R,10aS)-1,4,10,10a-tetrahydrophenazine-1-carboxylate + O2 = (10aS)-10,10a-dihydrophenazine-1-carboxylate + H2O2
(4) (1R)-1,4,5,10-tetrahydrophenazine-1-carboxylate + O2 = (10aS)-5,10-dihydrophenazine-1-carboxylate + H2O2
Other name(s): phzG (gene name)
Systematic name: 1,4,5a,6,9,10a-hexahydrophenazine-1,6-dicarboxylate:oxygen oxidoreductase
Comments: Requires FMN. The enzyme, isolated from the bacteria Pseudomonas fluorescens 2-79 and Burkholderia lata 383, is involved in biosynthesis of the reduced forms of phenazine, phenazine-1-carboxylate, and phenazine-1,6-dicarboxylate, where it catalyses multiple reactions.
References:
1. Xu, N., Ahuja, E.G., Janning, P., Mavrodi, D.V., Thomashow, L.S. and Blankenfeldt, W. Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 69 (2013) 1403-1413. [PMID: 23897464]
Accepted name: flavanone 3-dioxygenase
Reaction: a (2S)-flavan-4-one + 2-oxoglutarate + O2 = a (2R,3R)-dihydroflavonol + succinate + CO2
For diagram of reaction click here and mechanism click here.
Other name(s): naringenin 3-hydroxylase; flavanone 3-hydroxylase; flavanone 3β-hydroxylase; flavanone synthase I; (2S)-flavanone 3-hydroxylase; naringenin,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating); F3H; flavanone,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)
Systematic name: (2S)-flavan-4-one,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)
Comments: Requires Fe2+ and ascorbate. This plant enzyme catalyses an early step in the flavonoid biosynthesis pathway, leading to the production of flavanols and anthocyanins. Substrates include (2S)-naringenin, (2S)-eriodictyol, (2S)-dihydrotricetin and (2S)-pinocembrin. Some enzymes are bifuctional and also catalyse EC 1.14.11.23, flavonol synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 75991-43-4
References:
1. Forkmann, G., Heller, W. and Grisebach, H. Anthocyanin biosynthesis in flowers of Matthiola incana flavanone 3- and flavonoid 3'-hydroxylases. Z. Naturforsch. C: Biosci. 35 (1980) 691-695.
2. Charrier, B., Coronado, C., Kondorosi, A. and Ratet, P. Molecular characterization and expression of alfalfa (Medicago sativa L.) flavanone-3-hydroxylase and dihydroflavonol-4-reductase encoding genes. Plant Mol. Biol. 29 (1995) 773-786. [PMID: 8541503]
3. Pelletier, M.K. and Shirley, B.W. Analysis of flavanone 3-hydroxylase in Arabidopsis seedlings. Coordinate regulation with chalcone synthase and chalcone isomerase. Plant Physiol. 111 (1996) 339-345. [PMID: 8685272]
4. Wellmann, F., Matern, U. and Lukačin, R. Significance of C-terminal sequence elements for Petunia flavanone 3β-hydroxylase activity. FEBS Lett. 561 (2004) 149-154. [PMID: 15013767]
5. Jin, Z., Grotewold, E., Qu, W., Fu, G. and Zhao, D. Cloning and characterization of a flavanone 3-hydroxylase gene from Saussurea medusa. DNA Seq 16 (2005) 121-129. [PMID: 16147863]
6. Shen, G., Pang, Y., Wu, W., Deng, Z., Zhao, L., Cao, Y., Sun, X. and Tang, K. Cloning and characterization of a flavanone 3-hydroxylase gene from Ginkgo biloba. Biosci Rep 26 (2006) 19-29. [PMID: 16779664]
Accepted name: p-cumate 2,3-dioxygenase
Reaction: p-cumate + NADH + H+ + O2 = (2R,3S)-2,3-dihydroxy-2,3-dihydro-p-cumate + NAD+
For diagram of reaction click here.
Glossary: p-cumate = 4-isopropylbenzoate
(2R,3S)-2,3-dihydroxy-2,3-dihydro-p-cumate = (5S,6R)-5,6-dihydroxy-4-isopropylcyclohexa-1,3-diene-1-carboxylate
Systematic name: 4-isopropylbenzoate:oxygen 2,3-oxidoreductase
Comments: The enzyme, characterized from several Pseudomonas strains, is involved in the degradation of p-cymene and p-cumate. It comprises four components: a ferredoxin, a ferredoxin reductase, and two subunits of a catalytic component. The enzyme can also act on indole, transforming it to the water-insoluble blue dye indigo.
References:
1. DeFrank, J.J. and Ribbons, D.W. p-cymene pathway in Pseudomonas putida: initial reactions. J. Bacteriol. 129 (1977) 1356-1364. [PMID: 845117]
2. Wigmore, G.J. and Ribbons, D.W. p-Cymene pathway in Pseudomonas putida: selective enrichment of defective mutants by using halogenated substrate analogs. J. Bacteriol. 143 (1980) 816-824. [PMID: 7204334]
3. Eaton, R.W. and Chapman, P.J. Formation of indigo and related compounds from indolecarboxylic acids by aromatic acid-degrading bacteria: chromogenic reactions for cloning genes encoding dioxygenases that act on aromatic acids. J. Bacteriol. 177 (1995) 6983-6988. [PMID: 7592495]
4. Eaton, R.W. p-Cumate catabolic pathway in Pseudomonas putida Fl: cloning and characterization of DNA carrying the cmt operon. J. Bacteriol. 178 (1996) 1351-1362. [PMID: 8631713]
Accepted name: anhydrotetracycline 6-monooxygenase
Reaction: anhydrotetracycline + NADPH + H+ + O2 = 12-dehydrotetracycline + NADP+ + H2O
For diagram of reaction click here.
Glossary: anhydrotetracycline = (4S,4aS,12aS)-4-(dimethylamino)-3,10,11,12a-tetrahydroxy-6-methyl-1,12-dioxo-1,4,4a,5,12,12a-hexahydrotetracene-2-carboxamide
12-dehydrotetracycline = (4S,4aS,6S,12aS)-4-(dimethylamino)-3,6,10,12a-tetrahydroxy-6-methyl-1,11,12-trioxo-1,4,4a,5,6,11,12,12a-octahydrotetracene-2-carboxamide
Other name(s): ATC oxygenase; anhydrotetracycline oxygenase; oxyS (gene name); anhydrotetracycline monooxygenase
Systematic name: anhydrotetracycline,NADPH:oxygen oxidoreductase (6-hydroxylating)
Comments: The enzyme, characterized from the bacterium Streptomyces rimosus, participates in the biosynthesis of tetracycline antibiotics. It can also catalyse EC 1.14.13.234, 12-dehydrotetracycline 5-monooxygenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 70766-62-0
References:
1. Behal, V., Hostalek, Z. and Vanek, Z. Anhydrotetracycline oxygenase activity and biosynthesis of tetracyclines in streptomyces aureofaciens. Biotechnol. Lett. 1 (1979) 177-182.
2. Binnie, C., Warren, M. and Butler, M.J. Cloning and heterologous expression in Streptomyces lividans of Streptomyces rimosus genes involved in oxytetracycline biosynthesis. J. Bacteriol. 171 (1989) 887-895. [PMID: 2914874]
3. Vancurova, I., Volc, J., Flieger, M., Neuzil, J., Novotna, J., Vlach, J. and Behal, V. Isolation of pure anhydrotetracycline oxygenase from Streptomyces aureofaciens. Biochem. J. 253 (1988) 263-267. [PMID: 3138982]
4. Wang, P., Bashiri, G., Gao, X., Sawaya, M.R. and Tang, Y. Uncovering the enzymes that catalyze the final steps in oxytetracycline biosynthesis. J. Am. Chem. Soc. 135 (2013) 7138-7141. [PMID: 23621493]
[EC 1.14.13.41 Transferred entry: tyrosine N-monooxygenase. Now EC 1.14.14.36, tyrosine N-monooxygenase (EC 1.14.13.41 created 1992, modified 2001, modified 2005, deleted 2016)]
[EC 1.14.13.68 Transferred entry: 4-hydroxyphenylacetaldehyde oxime monooxygenase, now EC 1.14.14.37, 4-hydroxyphenylacetaldehyde oxime monooxygenase (EC 1.14.13.68 created 2000, modified 2005, deleted 2016)]
[EC 1.14.13.90 Transferred entry: zeaxanthin epoxidase. Now EC 1.14.15.21, zeaxanthin epoxidase (EC 1.14.13.90 created 2005, deleted 2016)]
Accepted name: methanesulfonate monooxygenase (NADH)
Reaction: methanesulfonate + NADH + H+ + O2 = formaldehyde + NAD+ + sulfite + H2O
Glossary: methanesulfonate = CH3-SO3–
formaldehyde = H-CHO
Other name(s): mesylate monooxygenase; mesylate,reduced-FMN:oxygen oxidoreductase; MsmABC; methanesulfonic acid monooxygenase; MSA monooxygenase; MSAMO
Systematic name: methanesulfonate,NADH:oxygen oxidoreductase
Comments: A flavoprotein. Methanesulfonate is the simplest of the sulfonates and is a substrate for the growth of certain methylotrophic microorganisms. Compared with EC 1.14.14.5, alkanesulfonate monooxygenase, this enzyme has a restricted substrate range that includes only the short-chain aliphatic sulfonates (methanesulfonate to butanesulfonate) and excludes all larger molecules, such as arylsulfonates [1]. The enzyme from the bacterium Methylosulfonomonas methylovora is a multicomponent system comprising a hydroxylase, a reductase (MsmD) and a ferredoxin (MsmC). The hydroxylase has both large (MsmA) and small (MsmB) subunits, with each large subunit containing a Rieske-type [2Fe-2S] cluster. cf. EC 1.14.14.34, methanesulfonate monooxygenase (FMNH2).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number:
References:
1. de Marco, P., Moradas-Ferreira, P., Higgins, T.P., McDonald, I., Kenna, E.M. and Murrell, J.C. Molecular analysis of a novel methanesulfonic acid monooxygenase from the methylotroph Methylosulfonomonas methylovora. J. Bacteriol. 181 (1999) 2244-2251. [PMID: 10094704]
2. Higgins, T.P., Davey, M., Trickett, J., Kelly, D.P. and Murrell, J.C. Metabolism of methanesulfonic acid involves a multicomponent monooxygenase enzyme. Microbiology 142 (1996) 251-260. [PMID: 8932698]
Accepted name: jasmonic acid 12-hydroxylase
Reaction: (–)-jasmonate + NADPH + H+ + O2 = trans-12-hydroxyjasmonate + NADP+ + H2O
Glossary: (–)-jasmonate = {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetate
trans-12-hydroxyjasmonate = {(1R,2R)-2-[(2Z)-5-hydroxypent-2-en-1-yl]-3-oxocyclopentyl}acetate
Other name(s): ABM (gene name)
Systematic name: jasmonate,NADPH:oxygen oxidoreductase (12-hydroxylating)
Comments: Although believed to occur in plants, the enzyme has so far been characterized only from the rice blast fungus, Magnaporthe oryzae. The fungus strategically deploys the enzyme to hydroxylate and inactivate endogenous jasmonate to evade the jasmonate-based innate immunity in rice plants.
References:
1. Patkar, R.N., Benke, P.I., Qu, Z., Chen, Y.Y., Yang, F., Swarup, S. and Naqvi, N.I. A fungal monooxygenase-derived jasmonate attenuates host innate immunity. Nat. Chem. Biol. 11 (2015) 733-740. [PMID: 26258762]
Accepted name: tert-butyl alcohol monooxygenase
Reaction: tert-butyl alcohol + NADPH + H+ + O2 = 2-methylpropane-1,2-diol + NADP+ + H2O
Other name(s): mdpJK (gene names); tert-butanol monooxygenase
Systematic name: tert-butyl alcohol,NADPH:oxygen oxidoreductase
Comments: The enzyme, characterized from the bacterium Aquincola tertiaricarbonis, is a Rieske nonheme mononuclear iron oxygenase. It can also act, with lower efficiency, on propan-2-ol, converting it to propane-1,2-diol. Depending on the substrate, the enzyme also catalyses EC 1.14.19.48, tert-amyl alcohol desaturase.
References:
1. Schafer, F., Breuer, U., Benndorf, D., von Bergen, M., Harms, H. and Muller, R.H. Growth of Aquincola tertiaricarbonis L108 on tert-butyl alcohol leads to the induction of a phthalate dioxygenase-related protein and its associated oxidoreductase subunit. Eng. Life Sci. 7 (2007) 512-519.
2. Schuster, J., Schafer, F., Hubler, N., Brandt, A., Rosell, M., Hartig, C., Harms, H., Muller, R.H. and Rohwerder, T. Bacterial degradation of tert-amyl alcohol proceeds via hemiterpene 2-methyl-3-buten-2-ol by employing the tertiary alcohol desaturase function of the Rieske nonheme mononuclear iron oxygenase MdpJ. J. Bacteriol. 194 (2012) 972-981. [PMID: 22194447]
Accepted name: butane monooxygenase (soluble)
Reaction: butane + NADH + H+ + O2 = butan-1-ol + NAD+ + H2O
Other name(s): sBMO; bmoBCDXYZ (gene names)
Systematic name: butane,NADH:oxygen oxidoreductase
Comments: The enzyme, characterized from the bacterium Thauera butanivorans, is similar to EC 1.14.13.25, methane monooxygenase (soluble), but has a very low activity with methane. It comprises three components - a carboxylate-bridged non-heme di-iron center-containing hydroxylase (made of three different subunits), a flavo-iron sulfur-containing NADH-oxidoreductase, and a small regulatory component protein. The enzyme can also act on other C3-C6 linear and branched aliphatic alkanes with lower activity.
References:
1. Sluis, M.K., Sayavedra-Soto, L.A. and Arp, D.J. Molecular analysis of the soluble butane monooxygenase from ‘Pseudomonas butanovora’. Microbiology 148 (2002) 3617-3629. [PMID: 12427952]
2. Dubbels, B.L., Sayavedra-Soto, L.A. and Arp, D.J. Butane monooxygenase of ‘Pseudomonas butanovora’: purification and biochemical characterization of a terminal-alkane hydroxylating diiron monooxygenase. Microbiology 153 (2007) 1808-1816. [PMID: 17526838]
3. Doughty, D.M., Kurth, E.G., Sayavedra-Soto, L.A., Arp, D.J. and Bottomley, P.J. Evidence for involvement of copper ions and redox state in regulation of butane monooxygenase in Pseudomonas butanovora. J. Bacteriol. 190 (2008) 2933-2938. [PMID: 18281403]
4. Cooley, R.B., Dubbels, B.L., Sayavedra-Soto, L.A., Bottomley, P.J. and Arp, D.J. Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly ‘Pseudomonas butanovora’. Microbiology 155 (2009) 2086-2096. [PMID: 19383682]
Accepted name: tetracycline 11a-monooxygenase
Reaction: tetracycline + NADPH + H+ + O2 = 11a-hydroxytetracycline + NADP+ + H2O
For diagram of reaction click here.
Other name(s): tetX (gene name)
Systematic name: tetracycline,NADPH:oxygen oxidoreductase (11a-hydroxylating)
Comments: A flavoprotein (FAD). This bacterial enzyme confers resistance to all clinically relevant tetracyclines when expressed under aerobic conditions. The hydroxylated products are very unstable and lead to intramolecular cyclization and non-enzymic breakdown to undefined products.
References:
1. Yang, W., Moore, I.F., Koteva, K.P., Bareich, D.C., Hughes, D.W. and Wright, G.D. TetX is a flavin-dependent monooxygenase conferring resistance to tetracycline antibiotics. J. Biol. Chem. 279 (2004) 52346-52352. [PMID: 15452119]
2. Moore, I.F., Hughes, D.W. and Wright, G.D. Tigecycline is modified by the flavin-dependent monooxygenase TetX. Biochemistry 44 (2005) 11829-11835. [PMID: 16128584]
3. Volkers, G., Palm, G.J., Weiss, M.S., Wright, G.D. and Hinrichs, W. Structural basis for a new tetracycline resistance mechanism relying on the TetX monooxygenase. FEBS Lett. 585 (2011) 1061-1066. [PMID: 21402075]
Accepted name: 6-methylpretetramide 4-monooxygenase
Reaction: 6-methylpretetramide + NADPH + H+ + O2 = 4-hydroxy-6-methylpretetramide + NADP+ + H2O
For diagram of reaction click here.
Glossary: 6-methylpretetramide = 1,3,10,11,12-pentahydroxy-6-methyltetracene-2-carboxamide
4-hydroxy-6-methylpretetramide = 1,3,4,10,11,12-hexahydroxy-6-methyltetracene-2-carboxamide
Systematic name: 6-methylpretetramide,NADPH:oxygen oxidoreductase (4-hydroxylating)
Comments: The enzyme, characterized from the bacterium Streptomyces rimosus, participates in the biosynthesis of tetracycline antibiotics. That bacterium possesses two enzymes that can catalyse the reaction - OxyE is the main isozyme, while OxyL has a lower activity. OxyL is bifunctional, and its main function is EC 1.14.13.233, 4-hydroxy-6-methylpretetramide 12a-monooxygenase. Contains FAD.
References:
1. Zhang, W., Watanabe, K., Cai, X., Jung, M.E., Tang, Y. and Zhan, J. Identifying the minimal enzymes required for anhydrotetracycline biosynthesis. J. Am. Chem. Soc. 130 (2008) 6068-6069. [PMID: 18422316]
2. Wang, P., Zhang, W., Zhan, J. and Tang, Y. Identification of OxyE as an ancillary oxygenase during tetracycline biosynthesis. Chembiochem 10 (2009) 1544-1550. [PMID: 19472250]
Accepted name: 4-hydroxy-6-methylpretetramide 12a-monooxygenase
Reaction: 4-hydroxy-6-methylpretetramide + NADPH + H+ + O2 = 4-de(dimethylamino)-4-oxoanhydrotetracycline + NADP+ + H2O
For diagram of reaction click here.
Glossary: 4-hydroxy-6-methylpretetramide = 1,3,4,10,11,12-hexahydroxy-6-methyltetracene-2-carboxamide
4-de(dimethylamino)-4-oxoanhydrotetracycline = (4aR,12aS)-3,10,11,12a-tetrahydroxy-6-methyl-1,4,12-trioxo-4a,5-dihydrotetracene-2-carboxamide
Other name(s): oxyL (gene name)
Systematic name: 4-hydroxy-6-methylpretetramide,NADPH:oxygen oxidoreductase (12a-hydroxylating)
Comments: Contains FAD. The enzyme, characterized from the bacterium Streptomyces rimosus, participates in the biosynthesis of tetracycline antibiotics. The enzyme is bifunctional, and can also catalyse EC 1.14.13.232, 6-methylpretetramide 4-monooxygenase.
References:
1. Zhang, W., Watanabe, K., Cai, X., Jung, M.E., Tang, Y. and Zhan, J. Identifying the minimal enzymes required for anhydrotetracycline biosynthesis. J. Am. Chem. Soc. 130 (2008) 6068-6069. [PMID: 18422316]
Accepted name: 5a,11a-dehydrotetracycline 5-monooxygenase
Reaction: 5a,11a-dehydrotetracycline + NADPH + H+ + O2 = 5a,11a-dehydrooxytetracycline + NADP+ + H2O
For diagram of reaction click here.
Glossary: 5a,11a-dehydrotetracycline = 12-dehydrotetracycline = (4S,4aS,6S,12aS)-4-dimethylamino-3,6,10,12a-tetrahydroxy-6-methyl-1,11,12-trioxo-1,4,4a,5,6,11,12,12a-octahydrotetracene-2-carboxamide
Other name(s): oxyS (gene name); 12-dehydrotetracycline 5-monooxygenase
Systematic name: 5a,11a-dehydrotetracycline,NADPH:oxygen oxidoreductase (5-hydroxylating)
Comments: The enzyme, characterized from the bacterium Streptomyces rimosus, is bifunctional, catalysing two successive monooxygenation reactions. It starts by catalysing the stereospecific hydroxylation of anhydrotetracycline at C-6 (EC 1.14.13.38). If the released product is captured by EC 1.3.98.4, 5a,11a-dehydrotetracycline dehydrogenase (OxyR), it is reduced to tetracycline. However, if the released product is recaptured by OxyS, it performs an additional hydroxylation at C-5, producing 5a,11a-dehydrooxytetracycline, which, following the action of OxyR, becomes oxytetracycline.
References:
1. Binnie, C., Warren, M. and Butler, M.J. Cloning and heterologous expression in Streptomyces lividans of Streptomyces rimosus genes involved in oxytetracycline biosynthesis. J. Bacteriol. 171 (1989) 887-895. [PMID: 2914874]
2. Miller, P.A., Saturnelli, A., Martin, J.H., Itscher, L.A. and Bohonos, N. A new family of tetracycline precursors. N-demethylanhydrotetracyclines. Biochem. Biophys. Res. Commun. 16 (1964) 285-291. [PMID: 4959040]
3. Vancurova, I., Volc, J., Flieger, M., Neuzil, J., Novotna, J., Vlach, J. and Behal, V. Isolation of pure anhydrotetracycline oxygenase from Streptomyces aureofaciens. Biochem. J. 253 (1988) 263-267. [PMID: 3138982]
4. Wang, P., Bashiri, G., Gao, X., Sawaya, M.R. and Tang, Y. Uncovering the enzymes that catalyze the final steps in oxytetracycline biosynthesis. J. Am. Chem. Soc. 135 (2013) 7138-7141. [PMID: 23621493]
Accepted name: ethylenediaminetetraacetate monooxygenase
Reaction: ethylenediaminetetraacetate + 2 FMNH2 + 2 O2 = ethylenediamine-N,N'-diacetate + 2 glyoxylate + 2 FMN + 2 H2O (overall reaction)
(1a) ethylenediaminetetraacetate + FMNH2 + O2 = ethylenediaminetriacetate + glyoxylate + FMN + H2O
(1b) ethylenediaminetriacetate + FMNH2 + O2 = ethylenediamine-N,N'-diacetate + glyoxylate + FMN + H2O
Glossary: ethylenediaminetetraacetate = EDTA
Systematic name: ethylenediaminetetraacetate,FMNH2:O2 oxidoreductase (glyoxylate-forming)
Comments: The enzyme is part of a two component system that also includes EC 1.5.1.42, FMN reductase (NADH), which provides reduced flavin mononucleotide for this enzyme. It acts on EDTA only when it is complexed with divalent cations such as Mg2+, Zn2+, Mn2+, Co2+, or Cu2+. While the enzyme has a substrate overlap with EC 1.14.14.10, nitrilotriacetate monooxygenase, it has a much wider substrate range, which includes nitrilotriacetate (NTA) and diethylenetriaminepentaacetate (DTPA) in addition to EDTA.
References:
1. Witschel, M., Nagel, S. and Egli, T. Identification and characterization of the two-enzyme system catalyzing oxidation of EDTA in the EDTA-degrading bacterial strain DSM 9103. J. Bacteriol. 179 (1997) 6937-6943. [PMID: 9371437]
2. Payne, J.W., Bolton, H., Jr., Campbell, J.A. and Xun, L. Purification and characterization of EDTA monooxygenase from the EDTA-degrading bacterium BNC1. J. Bacteriol. 180 (1998) 3823-3827. [PMID: 9683478]
3. Bohuslavek, J., Payne, J.W., Liu, Y., Bolton, H., Jr. and Xun, L. Cloning, sequencing, and characterization of a gene cluster involved in EDTA degradation from the bacterium BNC1. Appl. Environ. Microbiol. 67 (2001) 688-695. [PMID: 11157232]
Accepted name: methanesulfonate monooxygenase (FMNH2)
Reaction: methanesulfonate + FMNH2 + O2 = formaldehyde + FMN + sulfite + H2O
Glossary: methanesulfonate = CH3-SO3-
formaldehyde = H-CHO
Other name(s): msuD (gene name); ssuD (gene name)
Systematic name: methanesulfonate,FMNH2:oxygen oxidoreductase
Comments: The enzyme, characterized from Pseudomonas strains, allows the organisms to utilize methanesulfonate as their sulfur source. It acts in combination with a dedicated NADH-dependent FMN reductase (EC 1.5.1.42), which provides it with reduced FMN. cf. EC 1.14.13.111, methanesulfonate monooxygenase (NADH).
References:
1. Kertesz, M.A., Schmidt-Larbig, K. and Wuest, T. A novel reduced flavin mononucleotide-dependent methanesulfonate sulfonatase encoded by the sulfur-regulated msu operon of Pseudomonas aeruginosa. J. Bacteriol. 181 (1999) 1464-1473. [PMID: 10049377]
2. Endoh, T., Kasuga, K., Horinouchi, M., Yoshida, T., Habe, H., Nojiri, H. and Omori, T. Characterization and identification of genes essential for dimethyl sulfide utilization in Pseudomonas putida strain DS1. Appl. Microbiol. Biotechnol. 62 (2003) 83-91. [PMID: 12835925]
Accepted name: dimethylsulfone monooxygenase
Reaction: dimethyl sulfone + FMNH2 + O2 = methanesulfinate + formaldehyde + FMN + H2O
Other name(s): sfnG (gene name)
Systematic name: dimethyl sulfone,FMNH2:oxygen oxidoreductase
Comments: The enzyme, characterized from Pseudomonas spp., is involved in a dimethyl sulfide degradation pathway. It is dependent on NAD(P)H-dependent FMN reductase (EC 1.5.1.38, EC 1.5.1.39, or EC 1.5.1.42), which provides it with reduced FMN. The product, methanesulfinate, is oxidized spontaneously to methanesulfonate in the presence of dioxygen and FMNH2.
References:
1. Endoh, T., Habe, H., Nojiri, H., Yamane, H. and Omori, T. The σ54-dependent transcriptional activator SfnR regulates the expression of the Pseudomonas putida sfnFG operon responsible for dimethyl sulphone utilization. Mol. Microbiol. 55 (2005) 897-911. [PMID: 15661012]
2. Wicht, D.K. The reduced flavin-dependent monooxygenase SfnG converts dimethylsulfone to methanesulfinate. Arch. Biochem. Biophys. 604 (2016) 159-166. [PMID: 27392454]
Accepted name: tyrosine N-monooxygenase
Reaction: L-tyrosine + 2 O2 + 2 [reduced NADPH—hemoprotein reductase] = (E)-[4-hydroxyphenylacetaldehyde oxime] + 2 [oxidized NADPH—hemoprotein reductase] + CO2 + 3 H2O (overall reaction)
(1a) L-tyrosine + O2 + [reduced NADPH—hemoprotein reductase] = N-hydroxy-L-tyrosine + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) N-hydroxy-L-tyrosine + O2 + [reduced NADPH—hemoprotein reductase] = N,N-dihydroxy-L-tyrosine + [oxidized NADPH—hemoprotein reductase] + H2O
(1c) N,N-dihydroxy-L-tyrosine = (E)-[4-hydroxyphenylacetaldehyde oxime] + CO2 + H2O
For diagram of reaction click here.
Other name(s): tyrosine N-hydroxylase; CYP79A1
Systematic name: L-tyrosine,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (N-hydroxylating)
Comments: A cytochrome P-450 (heme-thiolate) protein. The enzyme is involved in the biosynthesis of the cyanogenic glucoside dhurrin in Sorghum, along with EC 1.14.14.37, 4-hydroxyphenylacetaldehyde oxime monooxygenase and EC 2.4.1.85, cyanohydrin β-glucosyltransferase. Some 2-(4-hydroxyphenyl)-1-nitroethane is formed as a side product.
References:
1. Halkier, B.A. and Møller, B.L. The biosynthesis of cyanogenic glucosides in higher plants. Identification of three hydroxylation steps in the biosynthesis of dhurrin in Sorghum bicolor (L.) Moench and the involvement of 1-ACI-nitro-2-(p-hydroxyphenyl)ethane as an intermediate. J. Biol. Chem. 265 (1990) 21114-21121. [PMID: 2250015]
2. Sibbesen, O., Koch, B., Halkier, B.A. and Møller, B.L. Cytochrome P-450TYR is a multifunctional heme-thiolate enzyme catalyzing the conversion of L-tyrosine to p-hydroxyphenylacetaldehyde oxime in the biosynthesis of the cyanogenic glucoside dhurrin in Sorghum bicolor (L.) Moench. J. Biol. Chem. 270 (1995) 3506-3511. [PMID: 7876084]
3. Kahn, R.A., Fahrendorf, T., Halkier, B.A. and Møller, B.L. Substrate specificity of the cytochrome P450 enzymes CYP79A1 and CYP71E1 involved in the biosynthesis of the cyanogenic glucoside dhurrin in Sorghum bicolor (L.) Moench. Arch. Biochem. Biophys. 363 (1999) 9-18. [PMID: 10049494]
4. Bak, S., Olsen, C.E., Halkier, B.A. and Moller, B.L. Transgenic tobacco and Arabidopsis plants expressing the two multifunctional sorghum cytochrome P450 enzymes, CYP79A1 and CYP71E1, are cyanogenic and accumulate metabolites derived from intermediates in Dhurrin biosynthesis. Plant Physiol. 123 (2000) 1437-1448. [PMID: 10938360]
5. Nielsen, J.S. and Møller, B.L. Cloning and expression of cytochrome P450 enzymes catalyzing the conversion of tyrosine to p-hydroxyphenylacetaldoxime in the biosynthesis of cyanogenic glucosides in Triglochin maritima. Plant Physiol. 122 (2000) 1311-1321. [PMID: 10759528]
6. Busk, P.K. and Møller, B.L. Dhurrin synthesis in sorghum is regulated at the transcriptional level and induced by nitrogen fertilization in older plants. Plant Physiol. 129 (2002) 1222-1231. [PMID: 12114576]
7. Kristensen, C., Morant, M., Olsen, C.E., Ekstrøm, C.T., Galbraith, D.W., Møller, B.L. and Bak, S. Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. Proc. Natl. Acad. Sci. USA 102 (2005) 1779-1784. [PMID: 15665094]
8. 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: 4-hydroxyphenylacetaldehyde oxime monooxygenase
Reaction: (E)-4-hydroxyphenylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + O2 = (S)-4-hydroxymandelonitrile + [oxidized NADPH—hemoprotein reductase] + 2 H2O (overall reaction)
(1a) (E)-4-hydroxyphenylacetaldehyde oxime = (Z)-4-hydroxyphenylacetaldehyde oxime
(1b) (Z)-4-hydroxyphenylacetaldehyde oxime = 4-hydroxyphenylacetonitrile + H2O
(1c) 4-hydroxyphenylacetonitrile + [reduced NADPH—hemoprotein reductase] + O2 = (S)-4-hydroxymandelonitrile + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of reaction click here.
Glossary: (S)-4-hydroxymandelonitrile = (2S)-hydroxy(4-hydroxyphenyl)acetonitrile
Other name(s): 4-hydroxybenzeneacetaldehyde oxime monooxygenase; cytochrome P450II-dependent monooxygenase; NADPH-cytochrome P450 reductase (CYP71E1); CYP71E1; 4-hydroxyphenylacetaldehyde oxime,NADPH:oxygen oxidoreductase
Systematic name: (E)-4-hydroxyphenylacetaldehyde oxime,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase
Comments: This cytochrome P-450 (heme thiolate) enzyme is involved in the biosynthesis of the cyanogenic glucoside dhurrin in sorghum. It catalyses three different activities - isomerization of the (E) isomer to the (Z) isomer, dehydration, and C-hydroxylation.
References:
1. MacFarlane, I.J., Lees, E.M. and Conn, E.E. The in vitro biosynthesis of dhurrin, the cyanogenic glycoside of Sorghum bicolor. J. Biol. Chem. 250 (1975) 4708-4713. [PMID: 237909]
2. Shimada, M. and Conn, E.E. The enzymatic conversion of p-hydroxyphenylacetaldoxime to p-hydroxymandelonitrile. Arch. Biochem. Biophys. 180 (1977) 199-207. [PMID: 193443]
3. Busk, P.K. and Møller, B.L. Dhurrin synthesis in sorghum is regulated at the transcriptional level and induced by nitrogen fertilization in older plants. Plant Physiol. 129 (2002) 1222-1231. [PMID: 12114576]
4. Kristensen, C., Morant, M., Olsen, C.E., Ekstrøm, C.T., Galbraith, D.W., Møller, B.L. and Bak, S. Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. Proc. Natl. Acad. Sci. USA 102 (2005) 1779-1784. [PMID: 15665094]
5. 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: zeaxanthin epoxidase
Reaction: zeaxanthin + 4 reduced ferredoxin [iron-sulfur] cluster + 4 H+ + 2 O2 = violaxanthin + 4 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O (overall reaction)
(1a) zeaxanthin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 = antheraxanthin + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
(1b) antheraxanthin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 = violaxanthin + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
For diagram of reaction click here.
Other name(s): Zea-epoxidase
Systematic name: zeaxanthin,reduced ferredoxin:oxygen oxidoreductase
Comments: A flavoprotein (FAD) that is active under conditions of low light. Along with EC 1.23.5.1, violaxanthin de-epoxidase, this enzyme forms part of the xanthophyll (or violaxanthin) cycle, which is involved in protecting the plant against damage by excess light. It will also epoxidize lutein in some higher-plant species.
References:
1. Buch, K., Stransky, H. and Hager, A. FAD is a further essential cofactor of the NAD(P)H and O2-dependent zeaxanthin-epoxidase. FEBS Lett. 376 (1995) 45-48. [PMID: 8521963]
2. Bugos, R.C., Hieber, A.D. and Yamamoto, H.Y. Xanthophyll cycle enzymes are members of the lipocalin family, the first identified from plants. J. Biol. Chem. 273 (1998) 15321-15324. [PMID: 9624110]
3. Thompson, A.J., Jackson, A.C., Parker, R.A., Morpeth, D.R., Burbidge, A. and Taylor, I.B. Abscisic acid biosynthesis in tomato: regulation of zeaxanthin epoxidase and 9-cis-epoxycarotenoid dioxygenase mRNAs by light/dark cycles, water stress and abscisic acid. Plant Mol. Biol. 42 (2000) 833-845. [PMID: 10890531]
4. Hieber, A.D., Bugos, R.C. and Yamamoto, H.Y. Plant lipocalins: violaxanthin de-epoxidase and zeaxanthin epoxidase. Biochim. Biophys. Acta 1482 (2000) 84-91. [PMID: 11058750]
5. Frommolt, R., Goss, R. and Wilhelm, C. The de-epoxidase and epoxidase reactions of Mantoniella squamata (Prasinophyceae) exhibit different substrate-specific reaction kinetics compared to spinach. Planta 213 (2001) 446-456. [PMID: 11506368]
6. Frommolt, R., Goss, R. and Wilhelm, C. (Erratum Report.) The de-epoxidase and epoxidase reactions of Mantoniella squamata (Prasinophyceae) exhibit different substrate-specific reaction kinetics compared to spinach. Planta 213 (2001) 492. [PMID: 11506368]
7. Matsubara, S., Morosinotto, T., Bassi, R., Christian, A.L., Fischer-Schliebs, E., Luttge, U., Orthen, B., Franco, A.C., Scarano, F.R., Forster, B., Pogson, B.J. and Osmond, C.B. Occurrence of the lutein-epoxide cycle in mistletoes of the Loranthaceae and Viscaceae. Planta 217 (2003) 868-879. [PMID: 12844265]
Accepted name: vitamin D 1,25-hydroxylase
Reaction: (1) calciol + O2 + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ = calcidiol + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
(2) calcidiol + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 = calcitriol + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
Glossary: calciol = cholecalciferol = vitamin D3 = (3S,5Z,7E)-9,10-seco-5,7,10(19)-cholestatriene-3-ol
calcidiol = 25-hydroxyvitamin D3 = (3S,5Z,7E)-9,10-seco-5,7,10(19)-cholestatriene-3,25-diol
calcitriol = 1α,25-dihydroxyvitamin D3 = (1S,3R,5Z,7E)-9,10-seco-5,7,10(19)-cholestatriene-1,3,25-triol
Other name(s): CYP105A1; Streptomyces griseolus cytochrome P450SU-1
Systematic name: calciol,ferredoxin:oxygen oxidoreductase (1,25-hydroxylating)
Comments: A P-450 (heme-thiolate) enzyme found in the bacterium Streptomyces griseolus. cf. EC 1.14.14.24, vitamin D 25-hydroxylase and EC 1.14.15.18, calcidiol 1-monooxygenase.
References:
1. Sawada, N., Sakaki, T., Yoneda, S., Kusudo, T., Shinkyo, R., Ohta, M. and Inouye, K. Conversion of vitamin D3 to 1α,25-dihydroxyvitamin D3 by Streptomyces griseolus cytochrome P450SU-1. Biochem. Biophys. Res. Commun. 320 (2004) 156-164. [PMID: 15207715]
2. Sugimoto, H., Shinkyo, R., Hayashi, K., Yoneda, S., Yamada, M., Kamakura, M., Ikushiro, S., Shiro, Y. and Sakaki, T. Crystal structure of CYP105A1 (P450SU-1) in complex with 1α,25-dihydroxyvitamin D3. Biochemistry 47 (2008) 4017-4027. [PMID: 18314962]
Accepted name: tert-amyl alcohol desaturase
Reaction: tert-amyl alcohol + NADPH + H+ + O2 = isoprenyl alcohol + NADP+ + 2 H2O
Glossary: isoprenyl alcohol = 3-methylbut-1-en-3-ol
tert-amyl alcohol = 2-methylbutan-2-ol
Other name(s): mdpJK (gene names)
Systematic name: tert-amyl alcohol,NADPH:oxygen oxidoreductase (1,2-dehydrogenating)
Comments: The enzyme, characterized from the bacterium Aquincola tertiaricarbonis, is a Rieske nonheme mononuclear iron oxygenase. It can also act, with lower efficiency, on butan-2-ol, converting it to but-1-en-3-ol. Depending on the substrate, the enzyme also catalyses EC 1.14.13.229, tert-butyl alcohol monooxygenase.
References:
1. Schafer, F., Schuster, J., Wurz, B., Hartig, C., Harms, H., Muller, R.H. and Rohwerder, T. Synthesis of short-chain diols and unsaturated alcohols from secondary alcohol substrates by the Rieske nonheme mononuclear iron oxygenase MdpJ. Appl. Environ. Microbiol. 78 (2012) 6280-6284. [PMID: 22752178]
2. Schuster, J., Schafer, F., Hubler, N., Brandt, A., Rosell, M., Hartig, C., Harms, H., Muller, R.H. and Rohwerder, T. Bacterial degradation of tert-amyl alcohol proceeds via hemiterpene 2-methyl-3-buten-2-ol by employing the tertiary alcohol desaturase function of the Rieske nonheme mononuclear iron oxygenase MdpJ. J. Bacteriol. 194 (2012) 972-981. [PMID: 22194447]
Accepted name: tetracycline 7-halogenase
Reaction: tetracycline + FADH2 + chloride + O2 + H+ = 7-chlorotetracycline + FAD + 2 H2O
For diagram of reaction click here.
Other name(s): ctcP (gene name)
Systematic name: tetracycline:FADH2 oxidoreductase (7-halogenating)
Comments: The enzyme, characterized from the bacterium Streptomyces aureofaciens, is a member of the flavin-dependent halogenase family. The enzyme forms a lysine chloramine intermediate on an internal lysine residue before transferring the chlorine to the substrate. It is stereo-selective for the 4S (natural) isomer of tetracycline. FADH2 is provided by a dedicated EC 1.5.1.36, flavin reductase (NADH).
References:
1. Dairi, T., Nakano, T., Aisaka, K., Katsumata, R. and Hasegawa, M. Cloning and nucleotide sequence of the gene responsible for chlorination of tetracycline. Biosci. Biotechnol. Biochem. 59 (1995) 1099-1106. [PMID: 7612997]
2. Zhu, T., Cheng, X., Liu, Y., Deng, Z. and You, D. Deciphering and engineering of the final step halogenase for improved chlortetracycline biosynthesis in industrial Streptomyces aureofaciens. Metab. Eng. 19 (2013) 69-78. [PMID: 23800859]
Accepted name: noroxomaritidine synthase
Reaction: (1) 4'-O-methylnorbelladine + [reduced NADPH—hemoprotein reductase] + O2 = (4aR,10bS)-noroxomaritidine + [oxidized NADPH—hemoprotein reductase] + 2 H2O
(2) 4'-O-methylnorbelladine + [reduced NADPH—hemoprotein reductase] + O2 = (4aS,10bR)-noroxomaritidine + [oxidized NADPH—hemoprotein reductase] + 2 H2O
For diagram of reaction click here.
Glossary: 4'-O-methylnorbelladine = 5-({[2-(4-hydroxyphenyl)ethyl]amino}methyl)-2-methoxyphenol
noroxomaritidine = 8-hydroxy-9-methoxy-4,4a-dihydro-3H,6H-5,10b-ethanophenanthridin-3-one
Other name(s): CYP96T1 (gene name)
Systematic name: 4'-O-methylnorbelladine,NADPH—hemoprotein reductase:oxygen oxidoreductase (noroxomaritidine-forming)
Comments: A P-450 (heme-thiolate) enzyme. The enzyme, characterized from Narcissus pseudonarcissus (daffodil), forms the two enantiomers of the Amaryllidacea alkaloid noroxomaritidine by catalysing intramolecular oxidative para-para' phenol coupling. The oxidation involves molecular oxygen without its incorporation into the product.
References:
1. Kilgore, M.B., Augustin, M.M., May, G.D., Crow, J.A. and Kutchan, T.M. CYP96T1 of Narcissus sp. aff. pseudonarcissus catalyzes formation of the para-para' C-C phenol couple in the Amaryllidaceae alkaloids. Front. Plant Sci. 7 (2016) 225. [PMID: 26941773]
Accepted name: (S)-cheilanthifoline synthase
Reaction: (S)-scoulerine + NADPH + H+ + O2 = (S)-cheilanthifoline + NADP+ + 2 H2O
For diagram of reaction click here.
Other name(s): CYP719A14 (gene name); (S)-scoulerine oxidase (methylenedioxy-bridge-forming) (ambiguous); (S)-scoulerine,NADPH:oxygen oxidoreductase (methylenedioxy-bridge-forming) (ambiguous)
Systematic name: (S)-scoulerine,NADPH:oxygen oxidoreductase [(S)-cheilanthifoline-forming]
Comments: A cytochrome P-450 (heme-thiolate) enzyme catalysing an oxidative reaction that does not incorporate oxygen into the product. Forms the methylenedioxy bridge of the protoberberine alkaloid cheilanthifoline by the oxidative ring closure of adjacent phenolic and methoxy groups of scoulerine. cf. EC 1.14.21.12, (S)-nandinine synthase, which catalyses a similar reaction at the other side of the (S)-scoulerine molecule, forming (S)-nandinine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 138791-27-2
References:
1. Bauer, W. and Zenk, M.H. Two methylenedioxy bridge-forming cytochrome P-450 dependent enzymes are involved in (S)-stylopine biosynthesis. Phytochemistry 30 (1991) 2953-2961.
2. Diaz Chavez, M.L., Rolf, M., Gesell, A. and Kutchan, T.M. Characterization of two methylenedioxy bridge-forming cytochrome P450-dependent enzymes of alkaloid formation in the Mexican prickly poppy Argemone mexicana. Arch. Biochem. Biophys. 507 (2011) 186-193. [PMID: 21094631]
[EC 1.14.99.27 Transferred entry: juglone 3-monooxygenase, now classified as EC 1.17.3.4, juglone 3-monooxygenase (EC 1.14.99.27 created 1989, deleted 2016)]
Accepted name: juglone 3-hydroxylase
Reaction: 2 juglone + O2 = 2 3,5-dihydroxy-1,4-naphthoquinone (overall reaction)
(1a) 2 juglone + 2 H2O = 2 naphthalene-1,2,4,8-tetrol
(1b) 2 naphthalene-1,2,4,8-tetrol + O2 = 2 3,5-dihydroxy-1,4-naphthoquinone + 2 H2O
Glossary: juglone = 5-hydroxy-1,4-naphthoquinone
Other name(s): juglone hydroxylase; naphthoquinone hydroxylase; naphthoquinone-hydroxylase
Systematic name: 5-hydroxy-1,4-naphthoquinone,water:oxygen oxidoreductase (3-hydroxylating)
Comments: Even though oxygen is consumed, molecular oxygen is not incorporated into the product. Catalysis starts by incorporation of an oxygen atom from a water molecule into the substrate. The naphthalene-1,2,4,8-tetrol intermediate is then oxidized by molecular oxygen, which is reduced to water. Also acts on 1,4-naphthoquinone, naphthazarin and 2-chloro-1,4-naphthoquinone.
References:
1. Rettenmaier, H. and Lingens, F. Purification and some properties of two isofunctional juglone hydroxylases from Pseudomonas putida J1. Biol. Chem. Hoppe-Seyler 366 (1985) 637-646. [PMID: 4041238]
Accepted name: bacteriochlorophyllide c C-71-hydroxylase
Reaction: S-adenosyl-L-methionine + a bacteriochlorophyllide c + H2O = a 7-(hydroxymethyl)-bacteriochlorophyllide c + 5'-deoxyadenosine + L-methionine
Other name(s): bciD (gene name)
Systematic name: bacteriochlorophyllide-c:S-adenosyl-L-methionine oxidoreductase (C-71-hydroxylating)
Comments: The enzyme, found in green sulfur bacteria (Chlorobiaceae), is a radical S-adenosyl-L-methionine (AdoMet) enzyme and contains a [4Fe-4S] cluster. It introduces a hydroxyl group at the C-71 position of a bacteriochlorophyllide c, which is subsequently oxidized to an oxo group, forming a bacteriochlorophyllide e. It is not yet known whether this enzyme also catalyses the subsequent oxidation.
References:
1. Harada, J., Mizoguchi, T., Satoh, S., Tsukatani, Y., Yokono, M., Noguchi, M., Tanaka, A. and Tamiaki, H. Specific gene bciD for C7-methyl oxidation in bacteriochlorophyll e biosynthesis of brown-colored green sulfur bacteria. PLoS One 8 (2013) e60026. [PMID: 23560066]
EC 1.19 Acting on reduced flavodoxin as donor
Accepted name: flavodoxin—NADP+ reductase
Reaction: reduced flavodoxin + NADP+ = oxidized flavodoxin + NADPH + H+
Other name(s): FPR
Systematic name: flavodoxin:NADP+ oxidoreductase
Comments: A flavoprotein (FAD). This activity occurs in some prokaryotes and algae that possess flavodoxin, and provides low-potential electrons for a variety of reactions such as nitrogen fixation, sulfur assimilation and amino acid biosynthesis. In photosynthetic organisms it is involved in the photosynthetic electron transport chain. The enzyme also catalyses EC 1.18.1.2, ferredoxin—NADP+ reductase.
References:
1. McIver, L., Leadbeater, C., Campopiano, D.J., Baxter, R.L., Daff, S.N., Chapman, S.K. and Munro, A.W. Characterisation of flavodoxin NADP+ oxidoreductase and flavodoxin; key components of electron transfer in Escherichia coli. Eur. J. Biochem. 257 (1998) 577-585. [PMID: 9839946]
2. Leadbeater, C., McIver, L., Campopiano, D.J., Webster, S.P., Baxter, R.L., Kelly, S.M., Price, N.C., Lysek, D.A., Noble, M.A., Chapman, S.K. and Munro, A.W. Probing the NADPH-binding site of Escherichia coli flavodoxin oxidoreductase. Biochem. J. 352 (2000) 257-266. [PMID: 11085917]
3. Wan, J.T. and Jarrett, J.T. Electron acceptor specificity of ferredoxin (flavodoxin):NADP+ oxidoreductase from Escherichia coli. Arch. Biochem. Biophys. 406 (2002) 116-126. [PMID: 12234497]
4. Bortolotti, A., Perez-Dorado, I., Goni, G., Medina, M., Hermoso, J.A., Carrillo, N. and Cortez, N. Coenzyme binding and hydride transfer in Rhodobacter capsulatus ferredoxin/flavodoxin NADP(H) oxidoreductase. Biochim. Biophys. Acta 1794 (2009) 199-210. [PMID: 18973834]
5. Bortolotti, A., Sanchez-Azqueta, A., Maya, C.M., Velazquez-Campoy, A., Hermoso, J.A., Medina, M. and Cortez, N. The C-terminal extension of bacterial flavodoxin-reductases: involvement in the hydride transfer mechanism from the coenzyme. Biochim. Biophys. Acta 1837 (2014) 33-43. [PMID: 24016470]
6. Skramo, S., Hersleth, H.P., Hammerstad, M., Andersson, K.K. and Rohr, A.K. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of a ferredoxin/flavodoxin-NADP(H) oxidoreductase (Bc0385) from Bacillus cereus. Acta Crystallogr. F Struct. Biol. Commun. 70 (2014) 777-780. [PMID: 24915092]
Accepted name: anaerobic magnesium-protoporphyrin IX monomethyl ester cyclase
Reaction: magnesium-protoporphyrin IX 13-monomethyl ester + 3 S-adenosyl-L-methionine + H2O = 3,8-divinyl protochlorophyllide a + 3 5'-deoxyadenosine + 3 L-methionine (overall reaction)
(1a) magnesium-protoporphyrin IX 13-monomethyl ester + S-adenosyl-L-methionine + H2O = 131-hydroxy-magnesium-protoporphyrin IX 13-monomethyl ester + 5'-deoxyadenosine + L-methionine
(1b) 131-hydroxy-magnesium-protoporphyrin IX 13-monomethyl ester + S-adenosyl-L-methionine = 131-oxo-magnesium-protoporphyrin IX 13-monomethyl ester + 5'-deoxyadenosine + L-methionine
(1c) 131-oxo-magnesium-protoporphyrin IX 13-monomethyl ester + S-adenosyl-L-methionine = 3,8-divinyl protochlorophyllide a + 5'-deoxyadenosine + L-methionine
For diagram of reaction click here.
Other name(s): bchE (gene name); MPE cyclase (ambiguous)
Systematic name: magnesium-protoporphyrin-IX 13-monomethyl ester,S-adenosyl-L-methionine:H2O oxidoreductase (hydroxylating)
Comments: This radical AdoMet enzyme participates in the biosynthesis of chlorophyllide a in anaerobic bacteria, catalysing the formation of an isocyclic ring. Contains a [4Fe-4S] cluster and a cobalamin cofactor. The same transformation is achieved in aerobic organisms by the oxygen-dependent EC 1.14.13.81, magnesium-protoporphyrin IX monomethyl ester (oxidative) cyclase. Some facultative phototrophic bacteria, such as Rubrivivax gelatinosus, possess both enzymes.
References:
1. Yang, Z.M. and Bauer, C.E. Rhodobacter capsulatus genes involved in early steps of the bacteriochlorophyll biosynthetic pathway. J. Bacteriol. 172 (1990) 5001-5010. [PMID: 2203738]
2. Gough, S.P., Petersen, B.O. and Duus, J.O. Anaerobic chlorophyll isocyclic ring formation in Rhodobacter capsulatus requires a cobalamin cofactor. Proc. Natl. Acad. Sci. USA 97 (2000) 6908-6913. [PMID: 10841582]
3. Ouchane, S., Steunou, A.S., Picaud, M. and Astier, C. Aerobic and anaerobic Mg-protoporphyrin monomethyl ester cyclases in purple bacteria: a strategy adopted to bypass the repressive oxygen control system. J. Biol. Chem. 279 (2004) 6385-6394. [PMID: 14617630]
4. Booker, S.J. Anaerobic functionalization of unactivated C-H bonds. Curr. Opin. Chem. Biol. 13 (2009) 58-73. [PMID: 19297239]
Accepted name: demethylphylloquinol methyltransferase
Reaction: S-adenosyl-L-methionine + demethylphylloquinol = S-adenosyl-L-homocysteine + phylloquinol
For diagram of reaction click here.
Glossary: demethylphylloquinol = 2-phytyl-1,4-naphthoquinol
phylloquinol = 2-methyl-3-phytyl-1,4-naphthoquinol = vitamin K1
Other name(s): menG (gene name); 2-phytyl-1,4-naphthoquinol methyltransferase
Systematic name: S-adenosyl-L-methionine:2-phytyl-1,4-naphthoquinol C-methyltransferase
Comments: The enzyme, found in plants and cyanobacteria, catalyses the final step in the biosynthesis of phylloquinone (vitamin K1), an electron carrier associated with photosystem I. The enzyme is specific for the quinol form of the substrate, and does not act on the quinone form [3].
References:
1. Sakuragi, Y., Zybailov, B., Shen, G., Jones, A.D., Chitnis, P.R., van der Est, A., Bittl, R., Zech, S., Stehlik, D., Golbeck, J.H. and Bryant, D.A. Insertional inactivation of the menG gene, encoding 2-phytyl-1,4-naphthoquinone methyltransferase of Synechocystis sp. PCC 6803, results in the incorporation of 2-phytyl-1,4-naphthoquinone into the A1 site and alteration of the equilibrium constant between A1 and F(X) in photosystem I. Biochemistry 41 (2002) 394-405. [PMID: 11772039]
2. Lohmann, A., Schottler, M.A., Brehelin, C., Kessler, F., Bock, R., Cahoon, E.B. and Dormann, P. Deficiency in phylloquinone (vitamin K1) methylation affects prenyl quinone distribution, photosystem I abundance, and anthocyanin accumulation in the Arabidopsis AtmenG mutant. J. Biol. Chem. 281 (2006) 40461-40472. [PMID: 17082184]
3. Fatihi, A., Latimer, S., Schmollinger, S., Block, A., Dussault, P.H., Vermaas, W.F., Merchant, S.S. and Basset, G.J. A dedicated type II NADPH dehydrogenase performs the penultimate step in the biosynthesis of vitamin K1 in Synechocystis and Arabidopsis. Plant Cell 27 (2015) 1730-1741. [PMID: 26023160]
Accepted name: 5'-demethylyatein 5'-O-methyltransferase
Reaction: S-adenosyl-L-methionine + (–)-5'-demethylyatein = S-adenosyl-L-homocysteine + (-)-yatein
For diagram of reaction click here.
Glossary: (–)-5'-demethylyatein = (3R,4R)-4-(2,3-benzodioxol-5-ylmethyl)-3-(3-hydroxy-4,5-dimethoxybenzyl)dihydrofuran-2(3H)-one
(–)-yatein = (3R,4R)-4-(1,3-benzodioxol-5-ylmethyl)-3-(3,4,5-trimethoxybenzyl)dihydrofuran-2(3H)-one
Other name(s): OMT1 (gene name)
Systematic name: S-adenosyl-L-methionine:(–)-5'-demethylyatein 5'-O-methyltransferase
Comments: The enzyme, characterized from the plant Sinopodophyllum hexandrum, is involved in the biosynthetic pathway of podophyllotoxin, a non-alkaloid toxin lignan whose derivatives are important anticancer drugs.
References:
1. Lau, W. and Sattely, E.S. Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone. Science 349 (2015) 1224-1228. [PMID: 26359402]
Accepted name: bacteriochlorophyllide d C-121-methyltransferase
Reaction: S-adenosyl-L-methionine + 8-ethyl-12-methyl-3-vinylbacteriochlorophyllide d = S-adenosyl-L-homocysteine + 8,12-diethyl-3-vinylbacteriochlorophyllide d
For diagram of reaction click here.
Other name(s): bchR (gene name)
Systematic name: S-adenosyl-L-methionine:8-ethyl-12-methyl-3-vinylbacteriochlorophyllide-d C-121-methyltransferase
Comments: This enzyme, found in green sulfur bacteria (Chlorobiaceae) and green flimentous bacteria (Chloroflexaceae), is a radical S-adenosyl-L-methionine (AdoMet) enzyme and contains a [4Fe-4S] cluster. It adds a methyl group at the C-121 position of bacteriochlorophylls of the c, d and e types. This methylation plays a role in fine-tuning the structural arrangement of the bacteriochlorophyll aggregates in chlorosomes and therefore directly influences the chlorosomes absorption properties.
References:
1. Gomez Maqueo Chew, A., Frigaard, N.U. and Bryant, D.A. Bacteriochlorophyllide c C-82 and C-121 methyltransferases are essential for adaptation to low light in Chlorobaculum tepidum. J. Bacteriol. 189 (2007) 6176-6184. [PMID: 17586634]
Accepted name: bacteriochlorophyllide d C-82-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + 8,12-diethyl-3-vinylbacteriochlorophyllide d = S-adenosyl-L-homocysteine + 12-ethyl-8-propyl-3-vinylbacteriochlorophyllide d
(2) S-adenosyl-L-methionine + 12-ethyl-8-propyl-3-vinylbacteriochlorophyllide d = S-adenosyl-L-homocysteine + 12-ethyl-8-isobutyl-3-vinylbacteriochlorophyllide d
For diagram of reaction click here.
Other name(s): bchQ (gene name)
Systematic name: S-adenosyl-L-methionine:8,12-diethyl-3-vinylbacteriochlorophyllide-d C-82-methyltransferase
Comments: This enzyme, found in green sulfur bacteria (Chlorobiaceae) and green flimentous bacteria (Chloroflexaceae), is a radical S-adenosyl-L-methionine (AdoMet) enzyme and contains a [4Fe-4S] cluster. It adds one or two methyl groups at the C-82 position of bacteriochlorophylls of the c, d and e types. These methylations play a role in fine-tuning the structural arrangement of the bacteriochlorophyll aggregates in chlorosomes and therefore directly influence chlorosomal absorption properties.
References:
1. Gomez Maqueo Chew, A., Frigaard, N.U. and Bryant, D.A. Bacteriochlorophyllide c C-82 and C-121 methyltransferases are essential for adaptation to low light in Chlorobaculum tepidum. J. Bacteriol. 189 (2007) 6176-6184. [PMID: 17586634]
Accepted name: bacteriochlorophyllide d C-20 methyltransferase
Reaction: S-adenosyl-L-methionine + a bacteriochlorophyllide d = S-adenosyl-homo-L-homocysteine + a bacteriochlorophyllide c
For diagram of reaction click here.
Other name(s): bchU (gene name)
Systematic name: S-adenosyl-L-methionine:bacteriochlorophyllide-d C-20 methyltransferase
Comments: The enzyme, found in green sulfur bacteria (Chlorobiaceae) and green flimentous bacteria (Chloroflexaceae), catalyses the methylation of the C-20 methine bridge position in bacteriochlorophyllide d, forming bacteriochlorophyllide c.
References:
1. Maresca, J.A., Gomez Maqueo Chew, A., Ponsati, M.R., Frigaard, N.U., Ormerod, J.G. and Bryant, D.A. The bchU gene of Chlorobium tepidum encodes the c-20 methyltransferase in bacteriochlorophyll c biosynthesis. J. Bacteriol. 186 (2004) 2558-2566. [PMID: 15090495]
Accepted name: methanethiol S-methyltransferase
Reaction: S-adenosyl-L-methionine + methanethiol = S-adenosyl-L-homocysteine + dimethyl sulfide
Other name(s): mddA (gene name)
Systematic name: S-adenosyl-L-methionine:methanethiol S-methyltransferase
Comments: The enzyme, found in many bacterial taxa, is involved in a pathway that converts L-methionine to dimethyl sulfide.
References:
1. Carrion, O., Curson, A.R., Kumaresan, D., Fu, Y., Lang, A.S., Mercade, E. and Todd, J.D. A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments. Nat Commun 6 (2015) 6579. [PMID: 25807229]
Accepted name: 4-amino-anhydrotetracycline N4-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + 4-amino-4-de(dimethylamino)anhydrotetracycline = S-adenosyl-L-homocysteine + 4-methylamino-4-de(dimethylamino)anhydrotetracycline
(2) S-adenosyl-L-methionine + 4-methylamino-4-de(dimethylamino)anhydrotetracycline = S-adenosyl-L-homocysteine + anhydrotetracycline
For diagram of reaction click here.
Glossary: 4-amino-4-de(dimethylamino)anhydrotetracycline = (4S,4aS,12aS)-4-amino-3,10,11,12a-tetrahydroxy-6-methyl-1,12-dioxo-4a,5-dihydro-4H-tetracene-2-carboxamide
4-methylamino-4-de(dimethylamino)anhydrotetracycline = (4S,4aS,12aS)-3,10,11,12a-tetrahydroxy-6-methyl-4-(methylamino)-1,12-dioxo-4a,5-dihydro-4H-tetracene-2-carboxamide
anhydrotetracycline = (4S,4aS,12aS)-4-(dimethylamino)-3,10,11,12a-tetrahydroxy-6-methyl-1,12-dioxo-1,4,4a,5,12,12a-hexahydrotetracene-2-carboxamide
Other name(s): oxyT (gene name); ctcO (gene name)
Systematic name: S-adenosyl-L-methionine:(4S,4aS,12aS)-4-amino-3,10,11,12a-tetrahydroxy-6-methyl-1,12-dioxo-4a,5-dihydro-4H-tetracene-2-carboxamide Nα-methyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces rimosus, participates in the biosynthesis of tetracycline antibiotics.
References:
1. Zhang, W., Watanabe, K., Cai, X., Jung, M.E., Tang, Y. and Zhan, J. Identifying the minimal enzymes required for anhydrotetracycline biosynthesis. J. Am. Chem. Soc. 130 (2008) 6068-6069. [PMID: 18422316]
Accepted name: norbelladine O-methyltransferase
Reaction: S-adenosyl-L-methionine + norbelladine = S-adenosyl-L-homocysteine + 4'-O-methylnorbelladine
For diagram of reaction click here.
Glossary: norbelladine = 4-({[2-(4-hydroxyphenyl)ethyl]amino}methyl)benzene-1,2-diol
4'-O-methylnorbelladine = 5-({[2-(4-hydroxyphenyl)ethyl]amino}methyl)-2-methoxyphenol
Other name(s): N4OMT1 (gene name)
Systematic name: S-adenosyl-L-methionine:norbelladine O-methyltransferase
Comments: The enzyme, characterized from the plants Nerine bowdenii and Narcissus pseudonarcissus (daffodil), participates in the biosynthesis of alkaloids produced by plants that belong to the Amaryllidaceae family.
References:
1. Mann, J.D., Fales, H.M. and Mudd, S.H. Alkaloids and plant metabolism. VI. O-methylation in vitro of norbelladine, a precursor of Amaryllidaceae alkaloids. J. Biol. Chem. 238 (1963) 3820-3823. [PMID: 14109227]
2. Kilgore, M.B., Augustin, M.M., Starks, C.M., O'Neil-Johnson, M., May, G.D., Crow, J.A. and Kutchan, T.M. Cloning and characterization of a norbelladine 4'-O-methyltransferase involved in the biosynthesis of the Alzheimer’s drug galanthamine in Narcissus sp. aff. pseudonarcissus. PLoS One 9 (2014) e103223. [PMID: 25061748]
[EC 2.3.1.88 Transferred entry: peptide α-N-acetyltransferase. Now covered by EC 2.3.1.254, N-terminal methionine Nα-acetyltransferase NatB, EC 2.3.1.255, N-terminal amino-acid Nα-acetyltransferase NatA, EC 2.3.1.256, N-terminal methionine Nα-acetyltransferase NatC, EC 2.3.1.257, N-terminal L-serine Nα-acetyltransferase NatD, EC 2.3.1.258, N-terminal methionine Nα-acetyltransferase NatE and EC 2.3.1.259, N-terminal methionine Nα-acetyltransferase NatF (EC 2.3.1.88 created 1986, modified 1989, deleted 2016)]
Accepted name: 2-methylbutanoate polyketide synthase
Reaction: 2 malonyl-CoA + [2-methylbutanoate polyketide synthase] + 2 NADPH + 3 H+ + S-adenosyl-L-methionine = (S)-2-methylbutanoyl-[2-methylbutanoate polyketide synthase] + 2 CoA + 2 CO2 + 2 NADP+ + S-adenosyl-L-homocysteine + H2O
For diagram of reaction click here.
Other name(s): LovF
Systematic name: acyl-CoA:malonyl-CoA C-acyltransferase (2-methylbutanoate-forming)
Comments: This polyketide synthase enzyme forms the (S)-2-methylbutanoate side chain during lovastatin biosynthesis by the filamentous fungus Aspergillus terreus. The overall reaction comprises a single condensation reaction followed by α-methylation, β-ketoreduction, dehydration, and α,β-enoyl reduction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Kennedy, J., Auclair, K., Kendrew, S.G., Park, C., Vederas, J.C. and Hutchinson, C.R. Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science 284 (1999) 1368-1372. [PMID: 10334994]
2. Meehan, M.J., Xie, X., Zhao, X., Xu, W., Tang, Y. and Dorrestein, P.C. FT-ICR-MS characterization of intermediates in the biosynthesis of the α-methylbutyrate side chain of lovastatin by the 277 kDa polyketide synthase LovF. Biochemistry 50 (2011) 287-299. [PMID: 21069965]
Accepted name: phloroglucinol synthase
Reaction: 3 malonyl-CoA = phloroglucinol + 3 CO2 + 3 CoA
For diagram of reaction click here.
Glossary: phloroglucinol = 1,3,5-trihydroxybenzene
Other name(s): phlD (gene name)
Systematic name: malonyl-CoA:malonyl-CoA malonyltransferase (decarboxylating, phloroglucinol-forming)
Comments: The enzyme, characterized from the bacterium Pseudomonas protegens Pf-5, is a type III polyketide synthase. The mechanism involves the cyclization of an activated 3,5-dioxoheptanedioate intermediate. The enzyme exhibits broad substrate specificity, and can accept C4-C12 aliphatic acyl-CoAs and phenylacetyl-CoA as the starter molecules, forming 6-(polyoxoalkylated)-α-pyrones by sequential condensation with malonyl-CoA.
References:
1. Achkar, J., Xian, M., Zhao, H. and Frost, J.W. Biosynthesis of phloroglucinol. J. Am. Chem. Soc. 127 (2005) 5332-5333.
2. Zha, W., Rubin-Pitel, S.B. and Zhao, H. Characterization of the substrate specificity of PhlD, a type III polyketide synthase from Pseudomonas fluorescens. J. Biol. Chem. 281 (2006) 32036-32047. [PMID: 16931521]
Accepted name: N-terminal methionine Nα-acetyltransferase NatB
Reaction: (1) acetyl-CoA + an N-terminal L-methionyl-L-asparaginyl-[protein] = an N-terminal Nα-acetyl-L-methionyl-L-asparginyl-[protein] + CoA
(2) acetyl-CoA + an N-terminal L-methionyl-L-glutaminyl-[protein] = an N-terminal Nα-acetyl-L-methionyl-L-glutaminyl-[protein] + CoA
(3) acetyl-CoA + an N-terminal L-methionyl-L-aspartyl-[protein] = an N-terminal Nα-acetyl-L-methionyl-L-aspartyl-[protein] + CoA
(4) acetyl-CoA + an N-terminal L-methionyl-L-glutamyl-[protein] = an N-terminal Nα-acetyl-L-methionyl-L-glutamyl-[protein] + CoA
Other name(s): NAA20 (gene name); NAA25 (gene name)
Systematic name: acetyl-CoA:N-terminal Met-Asn/Gln/Asp/Glu-[protein] Met-Nα-acetyltransferase
Comments: N-terminal acetylases (NATs) catalyse the covalent attachment of an acetyl moiety from acetyl-CoA to the free α-amino group at the N-terminus of a protein. This irreversible modification neutralizes the positive charge at the N-terminus and makes the N-terminal residue larger and more hydrophobic, and may also play a role in membrane targeting and gene silencing. The NatB complex is found in all eukaryotic organisms, and specifically targets N-terminal L-methionine residues attached to Asn, Asp, Gln, or Glu residues at the second position.
References:
1. Starheim, K.K., Arnesen, T., Gromyko, D., Ryningen, A., Varhaug, J.E. and Lillehaug, J.R. Identification of the human Nα-acetyltransferase complex B (hNatB): a complex important for cell-cycle progression. Biochem. J. 415 (2008) 325-331. [PMID: 18570629]
2. Ferrandez-Ayela, A., Micol-Ponce, R., Sanchez-Garcia, A.B., Alonso-Peral, M.M., Micol, J.L. and Ponce, M.R. Mutation of an Arabidopsis NatB N-α-terminal acetylation complex component causes pleiotropic developmental defects. PLoS One 8 (2013) e80697. [PMID: 24244708]
3. Lee, K.E., Ahn, J.Y., Kim, J.M. and Hwang, C.S. Synthetic lethal screen of NAA20, a catalytic subunit gene of NatB N-terminal acetylase in Saccharomyces cerevisiae. J Microbiol 52 (2014) 842-848. [PMID: 25163837]
Accepted name: N-terminal amino-acid Nα-acetyltransferase NatA
Reaction: (1) acetyl-CoA + an N-terminal-glycyl-[protein] = an N-terminal-Nα-acetyl-glycyl-[protein] + CoA
(2) acetyl-CoA + an N-terminal-L-alanyl-[protein] = an N-terminal-Nα-acetyl-L-alanyl-[protein] + CoA
(3) acetyl-CoA + an N-terminal-L-seryl-[protein] = an N-terminal-Nα-acetyl-L-seryl-[protein] + CoA
(4) acetyl-CoA + an N-terminal-L-valyl-[protein] = an N-terminal-Nα-acetyl-L-valyl-[protein] + CoA
(5) acetyl-CoA + an N-terminal-L-cysteinyl-[protein] = an N-terminal-Nα-acetyl-L-cysteinyl-[protein] + CoA
(6) acetyl-CoA + an N-terminal-L-threonyl-[protein] = an N-terminal-Nα-acetyl-L-threonyl-[protein] + CoA
Other name(s): NAA10 (gene name); NAA15 (gene name); ARD1 (gene name)
Systematic name: acetyl-CoA:N-terminal-Gly/Ala/Ser/Val/Cys/Thr-[protein] Nα-acetyltransferase
Comments: N-terminal-acetylases (NATs) catalyse the covalent attachment of an acetyl moiety from acetyl-CoA to the free α-amino group at the N-terminus of a protein. This irreversible modification neutralizes the positive charge at the N-terminus and makes the N-terminal residue larger and more hydrophobic. The NatA complex is found in all eukaryotic organisms, and specifically targets N-terminal Ala, Gly, Cys, Ser, Thr, and Val residues, that became available after removal of the initiator methionine.
References:
1. Mullen, J.R., Kayne, P.S., Moerschell, R.P., Tsunasawa, S., Gribskov, M., Colavito-Shepanski, M., Grunstein, M., Sherman, F. and Sternglanz, R. Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast. EMBO J. 8 (1989) 2067-2075. [PMID: 2551674]
2. Park, E.C. and Szostak, J.W. ARD1 and NAT1 proteins form a complex that has N-terminal acetyltransferase activity. EMBO J. 11 (1992) 2087-2093. [PMID: 1600941]
3. Sugiura, N., Adams, S.M. and Corriveau, R.A. An evolutionarily conserved N-terminal acetyltransferase complex associated with neuronal development. J. Biol. Chem. 278 (2003) 40113-40120. [PMID: 12888564]
4. Gautschi, M., Just, S., Mun, A., Ross, S., Rucknagel, P., Dubaquie, Y., Ehrenhofer-Murray, A. and Rospert, S. The yeast Nα-acetyltransferase NatA is quantitatively anchored to the ribosome and interacts with nascent polypeptides. Mol. Cell Biol. 23 (2003) 7403-7414. [PMID: 14517307]
5. Xu, F., Huang, Y., Li, L., Gannon, P., Linster, E., Huber, M., Kapos, P., Bienvenut, W., Polevoda, B., Meinnel, T., Hell, R., Giglione, C., Zhang, Y., Wirtz, M., Chen, S. and Li, X. Two N-terminal acetyltransferases antagonistically regulate the stability of a nod-like receptor in Arabidopsis. Plant Cell 27 (2015) 1547-1562. [PMID: 25966763]
6. Dorfel, M.J. and Lyon, G.J. The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 567 (2015) 103-131. [PMID: 25987439]
Accepted name: N-terminal methionine Nα-acetyltransferase NatC
Reaction: (1) acetyl-CoA + an N-terminal-L-methionyl-L-leucyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-leucyl-[protein] + CoA
(2) acetyl-CoA + an N-terminal-L-methionyl-L-isoleucyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-isoleucyl-[protein] + CoA
(3) acetyl-CoA + an N-terminal-L-methionyl-L-phenylalanyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-phenylalanyl-[protein] + CoA
(4) acetyl-CoA + an N-terminal-L-methionyl-L-tryptophyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-tryptophyl-[protein] + CoA
(5) acetyl-CoA + an N-terminal-L-methionyl-L-tyrosinyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-tyrosinyl-[protein] + CoA
Other name(s): NAA30 (gene name); NAA35 (gene name); NAA38 (gene name); MAK3 (gene name); MAK10 (gene name); MAK31 (gene name)
Systematic name: acetyl-CoA:N-terminal-Met-Leu/Ile/Phe/Trp/Tyr-[protein] Met Nα-acetyltransferase
Comments: N-terminal-acetylases (NATs) catalyse the covalent attachment of an acetyl moiety from acetyl-CoA to the free α-amino group at the N-terminus of a protein. This irreversible modification neutralizes the positive charge at the N-terminus and makes the N-terminal residue larger and more hydrophobic, and may also play a role in membrane targeting and gene silencing. The NatC complex is found in all eukaryotic organisms, and specifically targets N-terminal L-methionine residues attached to bulky hydrophobic residues at the second position, including Leu, Ile, Phe, Trp, and Tyr residues.
References:
1. Polevoda, B. and Sherman, F. NatC Nα-terminal acetyltransferase of yeast contains three subunits, Mak3p, Mak10p, and Mak31p. J. Biol. Chem. 276 (2001) 20154-20159. [PMID: 11274203]
2. Polevoda, B. and Sherman, F. Composition and function of the eukaryotic N-terminal acetyltransferase subunits. Biochem. Biophys. Res. Commun. 308 (2003) 1-11. [PMID: 12890471]
3. Pesaresi, P., Gardner, N.A., Masiero, S., Dietzmann, A., Eichacker, L., Wickner, R., Salamini, F. and Leister, D. Cytoplasmic N-terminal protein acetylation is required for efficient photosynthesis in Arabidopsis. Plant Cell 15 (2003) 1817-1832. [PMID: 12897255]
4. Wenzlau, J.M., Garl, P.J., Simpson, P., Stenmark, K.R., West, J., Artinger, K.B., Nemenoff, R.A. and Weiser-Evans, M.C. Embryonic growth-associated protein is one subunit of a novel N-terminal acetyltransferase complex essential for embryonic vascular development. Circ. Res. 98 (2006) 846-855. [PMID: 16484612]
5. Starheim, K.K., Gromyko, D., Evjenth, R., Ryningen, A., Varhaug, J.E., Lillehaug, J.R. and Arnesen, T. Knockdown of human Nα-terminal acetyltransferase complex C leads to p53-dependent apoptosis and aberrant human Arl8b localization. Mol. Cell Biol. 29 (2009) 3569-3581. [PMID: 19398576]
Accepted name: N-terminal L-serine Nα-acetyltransferase NatD
Reaction: (1) acetyl-CoA + an N-terminal-L-seryl-[histone H4] = an N-terminal-Nα-acetyl-L-seryl-[histone H4] + CoA
(2) acetyl-CoA + an N-terminal-L-seryl-[histone H2A] = an N-terminal-Nα-acetyl-L-seryl-[histone H2A] + CoA
Other name(s): NAA40 (gene name)
Systematic name: acetyl-CoA:N-terminal-L-seryl-[histone 4/2A] L-serine Nα-acetyltransferase
Comments: N-terminal-acetylases (NATs) catalyse the covalent attachment of an acetyl moiety from acetyl-CoA to the free α-amino group at the N-terminus of a protein. This irreversible modification neutralizes the positive charge at the N-terminus and makes the N-terminal residue larger and more hydrophobic. NatD is found in all eukaryotic organisms, and acetylates solely the serine residue at the N-terminus of histones H2A or H4. Efficient recognition and acetylation by NatD requires at least the first 30 to 50 highly conserved amino acid residues of the histone N terminus.
References:
1. Song, O.K., Wang, X., Waterborg, J.H. and Sternglanz, R. An Nα-acetyltransferase responsible for acetylation of the N-terminal residues of histones H4 and H2A. J. Biol. Chem. 278 (2003) 38109-38112. [PMID: 12915400]
2. Polevoda, B., Hoskins, J. and Sherman, F. Properties of Nat4, an Nα-acetyltransferase of Saccharomyces cerevisiae that modifies N termini of histones H2A and H4. Mol. Cell Biol. 29 (2009) 2913-2924. [PMID: 19332560]
3. Magin, R.S., Liszczak, G.P. and Marmorstein, R. The molecular basis for histone H4- and H2A-specific amino-terminal acetylation by NatD. Structure 23 (2015) 332-341. [PMID: 25619998]
Accepted name: N-terminal methionine Nα-acetyltransferase NatE
Reaction: (1) acetyl-CoA + an N-terminal-L-methionyl-L-alanyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-alanyl-[protein] + CoA
(2) acetyl-CoA + an N-terminal-L-methionyl-L-seryl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-seryl-[protein] + CoA
(3) acetyl-CoA + an N-terminal-L-methionyl-L-valyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-valyl-[protein] + CoA
(4) acetyl-CoA + an N-terminal-L-methionyl-L-threonyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-threonyl-[protein] + CoA
(5) acetyl-CoA + an N-terminal-L-methionyl-L-lysyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-lysyl-[protein] + CoA
(6) acetyl-CoA + an N-terminal-L-methionyl-L-leucyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-leucyl-[protein] + CoA
(7) acetyl-CoA + an N-terminal-L-methionyl-L-phenylalanyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-phenylalany-[protein] + CoA
(8) acetyl-CoA + an N-terminal-L-methionyl-L-tyrosyl-[protein] = an N-terminal-Nα-acetyl-L-methionyl-L-tyrosyl-[protein] + CoA
Other name(s): NAA50 (gene name); NAT5; SAN
Systematic name: acetyl-CoA:N-terminal-Met-Ala/Ser/Val/Thr/Lys/Leu/Phe/Tyr-[protein] Met-Nα-acetyltransferase
Comments: N-terminal-acetylases (NATs) catalyse the covalent attachment of an acetyl moiety from acetyl-CoA to the free α-amino group at the N-terminus of a protein. This irreversible modification neutralizes the positive charge at the N-terminus, makes the N-terminal residue larger and more hydrophobic, and prevents its removal by hydrolysis. It may also play a role in membrane targeting and gene silencing. NatE is found in all eukaryotic organisms and plays an important role in chromosome resolution and segregation. It specifically targets N-terminal L-methionine residues attached to Lys, Val, Ala, Tyr, Phe, Leu, Ser, and Thr. There is some substrate overlap with EC 2.3.1.256, N-terminal methionine Nα-acetyltransferase NatC. In addition, the acetylation of Met followed by small residues such as Ser, Thr, Ala, or Val suggests a kinetic competition between NatE and EC 3.4.11.18, methionyl aminopeptidase.The enzyme also has the activity of EC 2.3.1.48, histone acetyltransferase, and autoacetylates several of its own lysine residues.
References:
1. Hou, F., Chu, C.W., Kong, X., Yokomori, K. and Zou, H. The acetyltransferase activity of San stabilizes the mitotic cohesin at the centromeres in a shugoshin-independent manner. J. Cell Biol. 177 (2007) 587-597. [PMID: 17502424]
2. Pimenta-Marques, A., Tostoes, R., Marty, T., Barbosa, V., Lehmann, R. and Martinho, R.G. Differential requirements of a mitotic acetyltransferase in somatic and germ line cells. Dev. Biol. 323 (2008) 197-206. [PMID: 18801358]
3. Evjenth, R., Hole, K., Karlsen, O.A., Ziegler, M., Arnesen, T. and Lillehaug, J.R. Human Naa50p (Nat5/San) displays both protein Nα- and Nε-acetyltransferase activity. J. Biol. Chem. 284 (2009) 31122-31129. [PMID: 19744929]
4. Van Damme, P., Hole, K., Gevaert, K. and Arnesen, T. N-terminal acetylome analysis reveals the specificity of Naa50 (Nat5) and suggests a kinetic competition between N-terminal acetyltransferases and methionine aminopeptidases. Proteomics 15 (2015) 2436-2446. [PMID: 25886145]
Accepted name: N-terminal methionine Nα-acetyltransferase NatF
Reaction: acetyl-CoA + an N-terminal-L-methionyl-[transmembrane protein] = an N-terminal-Nα-acetyl-L-methionyl-[transmembrane protein] + CoA
Other name(s): NAA60 (gene name)
Systematic name: acetyl-CoA:N-terminal-Met-Lys/Ser/Val/Leu/Gln/Ile/Tyr/Thr-[transmembrane protein] Met-Nα-acetyltransferase
Comments: N-terminal-acetylases (NATs) catalyse the covalent attachment of an acetyl moiety from acetyl-CoA to the free α-amino group at the N-terminus of a protein. This irreversible modification neutralizes the positive charge at the N-terminus, makes the N-terminal residue larger and more hydrophobic, and prevents its removal by hydrolysis. NatF is found only in higher eukaryotes, and is absent from yeast. Unlike other Nat systems the enzyme is located in the Golgi apparatus. It faces the cytosolic side of intracellular membranes, and specifically acetylates transmembrane proteins whose N termini face the cytosol. NatF targets N-terminal L-methionine residues attached to Lys, Ser, Val, Leu, Gln, Ile, Tyr and Thr residues.
References:
1. Van Damme, P., Hole, K., Pimenta-Marques, A., Helsens, K., Vandekerckhove, J., Martinho, R.G., Gevaert, K. and Arnesen, T. NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation. PLoS Genet 7 (2011) e1002169. [PMID: 21750686]
2. Aksnes, H., Van Damme, P., Goris, M., Starheim, K.K., Marie, M., Støve, S.I., Hoel, C., Kalvik, T.V., Hole, K., Glomnes, N., Furnes, C., Ljostveit, S., Ziegler, M., Niere, M., Gevaert, K. and Arnesen, T. An organellar Nα-acetyltransferase, Naa60, acetylates cytosolic N termini of transmembrane proteins and maintains Golgi integrity. Cell Rep 10 (2015) 1362-1374. [PMID: 25732826]
Accepted name: tetracycline polyketide synthase
Reaction: malonamoyl-[OxyC acyl-carrier protein] + 8 malonyl-CoA = 18-carbamoyl-3,5,7,9,11,13,15,17-octaoxooctadecanoyl-[OxyC acyl-carrier protein] + 8 CO2 + 8 CoA
For diagram of reaction click here.
Systematic name: malonyl-CoA:malonamoyl-[OxyC acyl-carrier protein] malonyltransferase
Comments: The synthesis, in the bacterium Streptomyces rimosus, of the tetracycline antibiotics core skeleton requires a minimal polyketide synthase (PKS) consisting of a ketosynthase (KS), a chain length factor (CLF), and an acyl-carrier protein (ACP). Initiation involves an amide-containing starter unit that becomes the C-2 amide that is present in the tetracycline compounds. Following the initiation, the PKS catalyses the iterative condensation of 8 malonyl-CoA molecules to yield the polyketide backbone of tetracycline. Throughout the proccess, the nascent chain is attached to the OxyC acyl-carrier protein.
References:
1. Thomas, R. and Williams, D.J. Oxytetracycline biosynthesis: origin of the carboxamide substituent. J. Chem. Soc., Chem. Commun. (1983) 677-679.
2. Zhang, W., Ames, B.D., Tsai, S.C. and Tang, Y. Engineered biosynthesis of a novel amidated polyketide, using the malonamyl-specific initiation module from the oxytetracycline polyketide synthase. Appl. Environ. Microbiol. 72 (2006) 2573-2580. [PMID: 16597959]
3. Yu, L., Cao, N., Wang, L., Xiao, C., Guo, M., Chu, J., Zhuang, Y. and Zhang, S. Oxytetracycline biosynthesis improvement in Streptomyces rimosus following duplication of minimal PKS genes. Enzyme Microb. Technol. 50 (2012) 318-324. [PMID: 22500899]
Accepted name: lysine/arginine leucyltransferase
Reaction: (1) L-leucyl-tRNALeu + N-terminal L-lysyl-[protein] = tRNALeu + N-terminal L-leucyl-L-lysyl-[protein]
(2) L-leucyl-tRNALeu + N-terminal L-arginyl-[protein] = tRNALeu + N-terminal L-leucyl-L-arginyl-[protein]
Other name(s): leucyl, phenylalanine-tRNA-protein transferase; leucyl-phenylalanine-transfer ribonucleate-protein aminoacyltransferase; leucyl-phenylalanine-transfer ribonucleate-protein transferase; L-leucyl-tRNA:protein leucyltransferase; leucyltransferase (misleading); L/FK,R-transferase; aat (gene name); L-leucyl-tRNALeu:protein leucyltransferase
Systematic name: L-leucyl-tRNALeu:[protein] N-terminal L-lysine/L-arginine leucyltransferase
Comments: Requires a univalent cation. The enzyme participates in the N-end rule protein degradation pathway in certain bacteria, by attaching the primary destabilizing residue L-leucine to the N-termini of proteins that have an N-terminal L-arginine or L-lysine residue. Once modified, the proteins are recognized by EC 3.4.21.92, the ClpAP/ClpS endopeptidase system. The enzyme also transfers L-phenylalanine in vitro, but this has not been observed in vivo [5]. cf. EC 2.3.2.29, aspartate/glutamate leucyltransferase, and EC 2.3.2.8, arginyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37257-22-0
References:
1. Leibowitz, M.J. and Soffer, R.L. A soluble enzyme from Escherichia coli which catalyzes the transfer of leucine and phenylalanine from tRNA to acceptor proteins. Biochem. Biophys. Res. Commun. 36 (1969) 47-53. [PMID: 4894363]
2. Leibowitz, M.J. and Soffer, R.L. Enzymatic modification of proteins. 3. Purification and properties of a leucyl, phenylalanyl transfer ribonucleic acid protein transferase from Escherichia coli. J. Biol. Chem. 245 (1970) 2066-2073. [PMID: 4909560]
3. Soffer, R.L. Peptide acceptors in the leucine, phenylalanine transfer reaction. J. Biol. Chem. 248 (1973) 8424-8428. [PMID: 4587124]
4. Tobias, J.W., Shrader, T.E., Rocap, G. and Varshavsky, A. The N-end rule in bacteria. Science 254 (1991) 1374-1377. [PMID: 1962196]
5. Shrader, T.E., Tobias, J.W. and Varshavsky, A. The N-end rule in Escherichia coli: cloning and analysis of the leucyl, phenylalanyl-tRNA-protein transferase gene aat. J. Bacteriol. 175 (1993) 4364-4374. [PMID: 8331068]
6. Abramochkin, G. and Shrader, T.E. The leucyl/phenylalanyl-tRNA-protein transferase. Overexpression and characterization of substrate recognition, domain structure, and secondary structure. J. Biol. Chem. 270 (1995) 20621-20628. [PMID: 7657641]
Accepted name: aspartate/glutamate leucyltransferase
Reaction: (1) L-leucyl-tRNALeu + N-terminal L-glutamyl-[protein] = tRNALeu + N-terminal L-leucyl-L-glutamyl-[protein]
(2) L-leucyl-tRNALeu + N-terminal L-aspartyl-[protein] = tRNALeu + N-terminal L-leucyl-L-aspartyl-[protein]
Other name(s): leucylD,E-transferase; bpt (gene name)
Systematic name: L-leucyl-tRNALeu:[protein] N-terminal L-glutamate/L-aspartate leucyltransferase
Comments: The enzyme participates in the N-end rule protein degradation pathway in certain bacteria, by attaching the primary destabilizing residue L-leucine to the N-termini of proteins that have an N-terminal L-aspartate or L-glutamate residue. Once modified, the proteins are recognized by EC 3.4.21.92, the ClpAP/ClpS endopeptidase system. cf. EC 2.3.2.6, lysine/arginine leucyltransferase, and EC 2.3.2.8, arginyltransferase.
References:
1. Graciet, E., Hu, R.G., Piatkov, K., Rhee, J.H., Schwarz, E.M. and Varshavsky, A. Aminoacyl-transferases and the N-end rule pathway of prokaryotic/eukaryotic specificity in a human pathogen. Proc. Natl. Acad. Sci. USA 103 (2006) 3078-3083. [PMID: 16492767]
Accepted name: methylthioalkylmalate synthase
Reaction: an ω-(methylthio)-2-oxoalkanoate + acetyl-CoA + H2O = a 2-[ω-(methylthio)alkyl]malate + CoA
For diagram of reaction click here.
Other name(s): MAM1 (gene name); MAM3 (gene name)
Systematic name: acetyl-CoA:ω-(methylthio)-2-oxoalkanoate C-acetyltransferase
Comments: The enzyme, characterized from the plant Arabidopsis thaliana, is involved in the L-methionine side-chain elongation pathway, forming substrates for the biosynthesis of aliphatic glucosinolates. Two forms are known - MAM1 catalyses only only the first two rounds of methionine chain elongation, while MAM3 catalyses all six cycles, up to formation of L-hexahomomethionine.
References:
1. Textor, S., Bartram, S., Kroymann, J., Falk, K.L., Hick, A., Pickett, J.A. and Gershenzon, J. Biosynthesis of methionine-derived glucosinolates in Arabidopsis thaliana: recombinant expression and characterization of methylthioalkylmalate synthase, the condensing enzyme of the chain-elongation cycle. Planta 218 (2004) 1026-1035. [PMID: 14740211]
2. Textor, S., de Kraker, J.W., Hause, B., Gershenzon, J. and Tokuhisa, J.G. MAM3 catalyzes the formation of all aliphatic glucosinolate chain lengths in Arabidopsis. Plant Physiol. 144 (2007) 60-71. [PMID: 17369439]
[EC 2.4.1.45 Deleted entry: 2-hydroxyacylsphingosine 1-β-galactosyltransferase, now included with EC 2.4.1.47, N-acylsphingosine galactosyltransferase (EC 2.4.1.45 created 1972, deleted 2016)]
Accepted name: N-acetylgalactosaminide β-1,3-galactosyltransferase
Reaction: UDP-α-D-galactose + N-acetyl-α-D-galactosaminyl-R = UDP + β-D-galactosyl-(1→3)-N-acetyl-α-D-galactosaminyl-R
Other name(s): glycoprotein-N-acetylgalactosamine 3-β-galactosyltransferase; uridine diphosphogalactose-mucin β-(1→3)-galactosyltransferase; UDP-galactose:glycoprotein-N-acetyl-D-galactosamine 3-β-D-galactosyltransferase; UDP-Gal:α-D-GalNAc-1,3-α-D-GalNAc-diphosphoundecaprenol β-1,3-galactosyltransferase; wbnJ (gene name); wbiP (gene name); C1GALT1 (gene name); UDP-α-D-galactose:glycoprotein-N-acetyl-D-galactosamine 3-β-D-galactosyltransferase
Systematic name: UDP-α-D-galactose:N-acetyl-α-D-galactosaminyl-R β-1,3-galactosyltransferase (configuration-inverting)
Comments: The eukaryotic enzyme can act on non-reducing O-serine-linked N-acetylgalactosamine residues in mucin glycoproteins, forming the T-antigen. The bacterial enzyme, found in some pathogenic strains, is involved in biosynthesis of the O-antigen repeating unit.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 97089-61-7
References:
1. Hesford, F.J., Berger, E.G. and van den Eijnden, D.H. Identification of the product formed by human erythrocyte galactosyltransferase. Biochim. Biophys. Acta 659 (1981) 302-311. [PMID: 6789880]
2. Mendicino, J., Sivakami, S., Davila, M. and Chandrasekaran, E.V. Purification and properties of UDP-gal:N-acetylgalactosaminide mucin:β1,3-galactosyltransferase from swine trachea mucosa. J. Biol. Chem. 257 (1982) 3987-3994. [PMID: 6801057]
3. 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]
4. Ju, T., Brewer, K., D'Souza, A., Cummings, R.D. and Canfield, W.M. Cloning and expression of human core 1 β1,3-galactosyltransferase. J. Biol. Chem. 277 (2002) 178-186. [PMID: 11677243]
5. Yi, W., Perali, R.S., Eguchi, H., Motari, E., Woodward, R. and Wang, P.G. Characterization of a bacterial β-1,3-galactosyltransferase with application in the synthesis of tumor-associated T-antigen mimics. Biochemistry 47 (2008) 1241-1248. [PMID: 18179256]
6. Woodward, R., Yi, W., Li, L., Zhao, G., Eguchi, H., Sridhar, P.R., Guo, H., Song, J.K., Motari, E., Cai, L., Kelleher, P., Liu, X., Han, W., Zhang, W., Ding, Y., Li, M. and Wang, P.G. In vitro bacterial polysaccharide biosynthesis: defining the functions of Wzy and Wzz. Nat. Chem. Biol. 6 (2010) 418-423. [PMID: 20418877]
Accepted name: N-acetyllactosaminide β-1,3-N-acetylglucosaminyltransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-R = UDP + N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-R
Other name(s): uridine diphosphoacetylglucosamine-acetyllactosaminide β1→3-acetylglucosaminyltransferase; poly-N-acetyllactosamine extension enzyme; Galβ1→4GlcNAc-R β1→3 N-acetylglucosaminyltransferase; UDP-GlcNAc:GalR β-D-3-N-acetylglucosaminyltransferase; N-acetyllactosamine β(1-3)N-acetylglucosaminyltransferase; UDP-GlcNAc:Galβ1→4GlcNAcβ-Rβ1→3-N-acetylglucosaminyltransferase; GnTE; UDP-N-acetyl-D-glucosamine:β-D-galactosyl-1,4-N-acetyl-D-glucosamine β-1,3-acetyl-D-glucosaminyltransferase; β-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide β-1,3-acetylglucosaminyltransferase; UDP-N-acetyl-D-glucosamine:β-D-galactosyl-(1→4)-N-acetyl-D-glucosamine 3-β-N-acetyl-D-glucosaminyltransferase
Systematic name: UDP-N-acetyl-α-D-glucosamine:β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-R 3-β N-acetylglucosaminyltransferase (configuration-inverting)
Comments: Acts on β-galactosyl-1,4-N-acetylglucosaminyl termini on glycoproteins, glycolipids, and oligosaccharides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 85638-39-7
References:
1. Van den Eijnden, D.H., Winterwerp, H., Smeeman, P. and Schiphorst, W.E.C.M. Novikoff ascites tumor cells contain N-acetyllactosaminide β1→3 and β1→6 N-acetylglucosaminyltransferase activity. J. Biol. Chem. 258 (1983) 3435-3437. [PMID: 6219989]
2. Basu, M. and Basu, S. Biosynthesis in vitro of Ii core glycosphingolipids from neolactotetraosylceramide by β1-3- and β1-6-N-acetylglucosaminyltransferases from mouse T-lymphoma. J. Biol. Chem. 259 (1984) 12557-12562. [PMID: 6238026]
3. Takeya, A., Hosomi, O. and Kogure, T. The presence of N-acetyllactosamine and lactose: β(1-3)N-acetylglucosaminyltransferase activity in human urine. Jpn. J. Med. Sci. Biol. 38 (1985) 1-8. [PMID: 3160874]
[EC 2.4.1.163 Transferred entry: β-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide β-1,3-acetylglucosaminyltransferase, now included in EC 2.4.1.149, N-acetyllactosaminide β-1,3-N-acetylglucosaminyltransferase (EC 2.4.1.163 created 1989, deleted 2016)]
Accepted name: glucuronosyl-galactosyl-proteoglycan 4-α-N-acetylglucosaminyltransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + [protein]-3-O-(β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine = UDP + [protein]-3-O-(α-D-GlcNAc-(1→4)-β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine
For diagram of reaction click here.
Glossary: [protein]-3-O-(β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine = [protein]-3-O-(β-D-glucuronosyl-(1→3)-β-D-galactosyl-(1→3)-β-D-galactosyl-(1→4)-β-D-xylosyl)-L-serine
Other name(s): α-N-acetylglucosaminyltransferase I; α1,4-N-acetylglucosaminyltransferase; glucuronosylgalactosyl-proteoglycan 4-α-N-acetylglucosaminyltransferase; UDP-N-acetyl-D-glucosamine:β-D-glucuronosyl-(1→3)-β-D-galactosyl-(1→3)-β-D-galactosyl-(1→4)-β-D-xylosyl-proteoglycan 4IV-α-N-acetyl-D-glucosaminyltransferase; glucuronyl-galactosyl-proteoglycan 4-α-N-acetylglucosaminyltransferase
Systematic name: UDP-N-acetyl-α-D-glucosamine:[protein]-3-O-(β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine 4IV-α-N-acetyl-D-glucosaminyltransferase (configuration-retaining)
Comments: Enzyme involved in the initiation of heparin and heparan sulfate synthesis, transferring GlcNAc to the (GlcA-Gal-Gal-Xyl-)Ser core. Apparently products of both the human EXTL2 and EXTL3 genes can catalyse this reaction. In Caenorhabditis elegans, the product of the rib-2 gene displays this activity as well as that of EC 2.4.1.224, glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-α-N-acetylglucosaminyltransferase. For explanation of the use of a superscript in the systematic name, see 2-Carb-37.2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 179241-74-8
References:
1. Kitagawa, H., Shimakawa, H. and Sugahara, K. The tumor suppressor EXT-like gene EXTL2 encodes an α1,4-N-acetylhexosaminyltransferase that transfers N-acetylgalactosamine and N-acetylglucosamine to the common glycosaminoglycan-protein linkage region. The key enzyme for the chain initiation of heparan sulfate. J. Biol. Chem. 274 (1999) 13933-13937. [PMID: 10318803]
2. Kitagawa, H., Egusa, N., Tamura, J.I., Kusche-Gullberg, M., Lindahl, U. and Sugahara, K. rib-2, a Caenorhabditis elegans homolog of the human tumor suppressor EXT genes encodes a novel α1,4-N-acetylglucosaminyltransferase involved in the biosynthetic initiation and elongation of heparan sulfate. J. Biol. Chem. 276 (2001) 4834-4838. [PMID: 11121397]
Accepted name: D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphosphoundecaprenol 2-β-glucuronosyltransferase
Reaction: UDP-α-D-glucuronate + α-D-Man-(1→3)-β-D-Glc-(1→4)-α-D-Glc-1-diphospho-ditrans,octacis-undecaprenol = UDP + β-D-GlcA-(1→2)-α-D-Man-(1→3)-β-D-Glc-(1→4)-α-D-Glc-1-diphospho-ditrans,octacis-undecaprenol
For diagram of reaction click here
Other name(s): GumK; UDP-glucuronate:D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol β-1,2-glucuronyltransferase; D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphosphoundecaprenol 2-β-glucuronyltransferase
Systematic name: UDP-α-D-glucuronate:α-D-Man-(1→3)-β-D-Glc-(1→4)-α-D-Glc-1-diphospho-ditrans,octacis-undecaprenol β-1,2-glucuronosyltransferase (configuration-inverting)
Comments: The enzyme is involved in the biosynthesis of the exopolysaccharides xanthan (in the bacterium Xanthomonas campestris) and acetan (in the bacterium Gluconacetobacter xylinus).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Katzen, F., Ferreiro, D.U., Oddo, C.G., Ielmini, M.V., Becker, A., Puhler, A. and Ielpi, L. Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence. J. Bacteriol. 180 (1998) 1607-1617. [PMID: 9537354]
2. Ielpi, L., Couso, R.O. and Dankert, M.A. Sequential assembly and polymerization of the polyprenol-linked pentasaccharide repeating unit of the xanthan polysaccharide in Xanthomonas campestris. J. Bacteriol. 175 (1993) 2490-2500. [PMID: 7683019]
3. Kim, S.Y., Kim, J.G., Lee, B.M. and Cho, J.Y. Mutational analysis of the gum gene cluster required for xanthan biosynthesis in Xanthomonas oryzae pv oryzae. Biotechnol. Lett. 31 (2009) 265-270. [PMID: 18854951]
4. Barreras, M., Bianchet, M.A. and Ielpi, L. Crystallization and preliminary crystallographic characterization of GumK, a membrane-associated glucuronosyltransferase from Xanthomonas campestris required for xanthan polysaccharide synthesis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (2006) 880-883. [PMID: 16946469]
5. Barreras, M., Salinas, S.R., Abdian, P.L., Kampel, M.A. and Ielpi, L. Structure and mechanism of GumK, a membrane-associated glucuronosyltransferase. J. Biol. Chem. 283 (2008) 25027-25035. [PMID: 18596046]
6. Vojnov, A.A., Bassi, D.E., Daniels, M.J. and Dankert, M.A. Biosynthesis of a substituted cellulose from a mutant strain of Xanthomonas campestris. Carbohydr. Res. 337 (2002) 315-326. [PMID: 11841812]
7. Barreras, M., Abdian, P.L. and Ielpi, L. Functional characterization of GumK, a membrane-associated β-glucuronosyltransferase from Xanthomonas campestris required for xanthan polysaccharide synthesis. Glycobiology 14 (2004) 233-241. [PMID: 14736729]
[EC 2.4.1.307 Deleted entry: UDP-Gal:α-D-GalNAc-1,3-α-D-GalNAc-diphosphoundecaprenol β-1,3-galactosyltransferase. Now included in EC 2.4.1.122, glycoprotein-N-acetylgalactosamine β-1,3-galactosyltransferase (EC 2.4.1.307 created 2013, deleted 2016)]
Accepted name: α-maltose-1-phosphate synthase
Reaction: ADP-α-D-glucose + α-D-glucose-1-phosphate = ADP + α-maltose-1-phosphate
Glossary: maltose = α-D-glucopyranosyl-(1→4)-D-glucose
Other name(s): glgM (gene name)
Systematic name: ADP-α-D-glucose:α-D-glucose-1-phosphate 4-α-D-glucosyltransferase (configuration-retaining)
Comments: The enzyme, found in Mycobacteria, can also use UDP-α-D-glucose with much lower catalytic efficiency.
References:
1. Koliwer-Brandl, H., Syson, K., van de Weerd, R., Chandra, G., Appelmelk, B., Alber, M., Ioerger, T.R., Jacobs, W.R., Jr., Geurtsen, J., Bornemann, S. and Kalscheuer, R. Metabolic network for the biosynthesis of intra- and extracellular α-glucans required for virulence of Mycobacterium tuberculosis. PLoS Pathog. 12 (2016) e1005768. [PMID: 27513637]
Accepted name: protein xylosyltransferase
Reaction: UDP-α-D-xylose + [protein]-L-serine = UDP + [protein]-3-O-(β-D-xylosyl)-L-serine
For diagram of reaction click here
Other name(s): UDP-D-xylose:core protein β-D-xylosyltransferase; UDP-D-xylose:core protein xylosyltransferase; UDP-D-xylose:proteoglycan core protein β-D-xylosyltransferase; UDP-xylose-core protein β-D-xylosyltransferase; uridine diphosphoxylose-core protein β-xylosyltransferase; uridine diphosphoxylose-protein xylosyltransferase; UDP-D-xylose:protein β-D-xylosyltransferase
Systematic name: UDP-α-D-xylose:protein β-D-xylosyltransferase (configuration-inverting)
Comments: Involved in the biosynthesis of the linkage region of glycosaminoglycan chains as part of proteoglycan biosynthesis (chondroitin, dermatan and heparan sulfates).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 55576-38-0
References:
1. Stoolmiller, A.C., Horwitz, A.L. and Dorfman, A. Biosynthesis of the chondroitin sulfate proteoglycan. Purification and properties of xylosyltransferase. J. Biol. Chem. 247 (1972) 3525-3532. [PMID: 5030630]
2. Götting, C., Kuhn, J., Zahn, R., Brinkmann, T. and Kleesiek, K. Molecular cloning and expression of human UDP-D-xylose:proteoglycan core protein β-D-xylosyltransferase and its first isoform XT-II. J. Mol. Biol. 304 (2000) 517-528. [PMID: 11099377]
[EC 2.4.99.11 Deleted entry: lactosylceramide α-2,6-N-sialyltransferase, now included with EC 2.4.99.1, β-galactoside α-2,6-sialyltransferase (EC 2.4.99.11 created 1992, deleted 2016)]
Accepted name: isonocardicin synthase
Reaction: S-adenosyl-L-methionine + nocardicin G = S-methyl-5'-thioadenosine + isonocardicin C
For diagram of reaction click here Other name(s): nocardicin aminocarboxypropyltransferase; S-adenosyl-L-methionine:nocardicin-E 3-amino-3-carboxypropyltransferase
Systematic name: S-adenosyl-L-methionine:nocardicin-G 3-amino-3-carboxypropyltransferase
Comments: The enzyme, characterized from the bacterium Nocardia uniformis, is involved in the biosynthesis of the β-lactam antibiotic nocardicin A. The enzyme can act on nocardicin E, F, and G, producing isonocardicin A, B, and C, respectively. However, the in vivo substrate is believed to be nocardicin G [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 118246-74-5
References:
1. Wilson, B.A., Bantia, S., Salituro, G.M., Reeve, A.M. and Townsend, C.A. Cell-free biosynthesis of nocardicin A from nocardicin E and S-adenosylmethionine. J. Am. Chem. Soc. 110 (1988) 8238-8239.
2. Reeve, A.M., Breazeale, S.D. and Townsend, C.A. Purification, characterization, and cloning of an S-adenosylmethionine-dependent 3-amino-3-carboxypropyltransferase in nocardicin biosynthesis. J. Biol. Chem. 273 (1998) 30695-30703. [PMID: 9804844]
3. Kelly, W.L. and Townsend, C.A. Mutational analysis of nocK and nocL in the nocardicin a producer Nocardia uniformis. J. Bacteriol. 187 (2005) 739-746. [PMID: 15629944]
Accepted name: validamine 7-phosphate valienyltransferase
Reaction: GDP-valienol + validamine 7-phosphate = validoxylamine A 7'-phosphate + GDP
For diagram of reaction click here
Glossary: valienol = (1S,2S,3S,4R)-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol
validamine = (1R,2S,3S,4S,6R)-4-amino-6-(hydroxymethyl)cyclohexane-1,2,3-triol
Other name(s): vldE (gene name); valL (gene name)
Systematic name: GDP-valienol:validamine 7-phosphate valienyltransferase
Comments: The enzyme, characterized from several Streptomyces strains, is involved in the biosynthesis of the antifungal agent validamycin A.
References:
1. Asamizu, S., Yang, J., Almabruk, K.H. and Mahmud, T. Pseudoglycosyltransferase catalyzes nonglycosidic C-N coupling in validamycin a biosynthesis. J. Am. Chem. Soc. 133 (2011) 12124-12135. [PMID: 21766819]
2. Zheng, L., Zhou, X., Zhang, H., Ji, X., Li, L., Huang, L., Bai, L. and Zhang, H. Structural and functional analysis of validoxylamine A 7'-phosphate synthase ValL involved in validamycin A biosynthesis. PLoS One 7 (2012) e32033. [PMID: 22384130]
3. Cavalier, M.C., Yim, Y.S., Asamizu, S., Neau, D., Almabruk, K.H., Mahmud, T. and Lee, Y.H. Mechanistic insights into validoxylamine A 7'-phosphate synthesis by VldE using the structure of the entire product complex. PLoS One 7 (2012) e44934. [PMID: 23028689]
[EC 2.7.4.30 Transferred entry: lipid A phosphoethanolamine transferase, now EC 2.7.8.43, lipid A phosphoethanolamine transferase (EC 2.7.4.30 created 2015, deleted 2016)]
Accepted name: ADP ribose phosphorylase
Reaction: ADP + D-ribose 5-phosphate = phosphate + ADP-D-ribose
Glossary: ADP-D-ribose = adenosine 5'-(5-deoxy-D-ribofuranos-5-yl diphosphate)
Other name(s): ; ribose-5-phosphate adenylyltransferase (ambiguous); adenosine diphosphoribose phosphorylase (ambiguous)
Systematic name: ADP:D-ribose-5-phosphate adenylyltransferase
Comments: The enzyme, characterized from the single-celled alga Euglena gracilis, catalyses an irreversible reaction in the direction of ADP formation. cf. EC 2.7.7.96, ADP-D-ribose pyrophosphorylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9054-55-1
References:
1. Evans, W.R. and San Pietro, A. Phosphorolysis of adenosine diphosphoribose. Arch. Biochem. Biophys. 113 (1966) 236-244. [PMID: 4287446]
2. Stern, A.I. and Avron, M. An adenosine 5'-diphosphate ribose:orthophosphate adenylyltransferase from Euglena gracilis. Biochim. Biophys. Acta 118 (1966) 577-591. [PMID: 5970863]
Accepted name: mycocerosic acid adenylyltransferase
Reaction: ATP + a mycocerosate = diphosphate + a mycocerosoyl-adenylate
Other name(s): fadD28 (gene name)
Systematic name: ATP:mycocerosate adenylyltransferase
Comments: The enzyme, found in certain mycobacteria, catalyses the activation of the methylated long-chain fatty acids, mycocerosic acids, by adenylation. The activated acids are transferred to the two hydroxyl groups of phthiocerols and phenolphthiocerols by PapA5, leading to formation of dimycocerosates (DIM) and dimycocerosyl triglycosyl phenolphthiocerol (PGL), respectively.
References:
1. Fitzmaurice, A.M. and Kolattukudy, P.E. Open reading frame 3, which is adjacent to the mycocerosic acid synthase gene, is expressed as an acyl coenzyme A synthase in Mycobacterium bovis BCG. J. Bacteriol. 179 (1997) 2608-2615. [PMID: 9098059]
2. Arora, P., Goyal, A., Natarajan, V.T., Rajakumara, E., Verma, P., Gupta, R., Yousuf, M., Trivedi, O.A., Mohanty, D., Tyagi, A., Sankaranarayanan, R. and Gokhale, R.S. Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis. Nat. Chem. Biol. 5 (2009) 166-173. [PMID: 19182784]
3. Menendez-Bravo, S., Comba, S., Sabatini, M., Arabolaza, A. and Gramajo, H. Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli. Metab. Eng. 24 (2014) 97-106. [PMID: 24831705]
4. 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: ADP-D-ribose pyrophosphorylase
Reaction: ATP + D-ribose 5-phosphate = diphosphate + ADP-D-ribose
Other name(s): NUDIX5; NUDT5 (gene name); diphosphate—ADP-D-ribose adenylyltransferase; diphosphate adenylyltransferase (ambiguous)
Systematic name: ATP:D-ribose 5-phosphate adenylyltransferase
Comments: The human enzyme produces ATP in nuclei in situations of high energy demand, such as chromatin remodeling. The reaction is dependent on the presence of diphosphate. In its absence the enzyme catalyses the reaction of EC 3.6.1.13, ADP-ribose diphosphatase. cf. EC 2.7.7.35, ADP ribose phosphorylase.
References:
1. Wright, R.H., Lioutas, A., Le Dily, F., Soronellas, D., Pohl, A., Bonet, J., Nacht, A.S., Samino, S., Font-Mateu, J., Vicent, G.P., Wierer, M., Trabado, M.A., Schelhorn, C., Carolis, C., Macias, M.J., Yanes, O., Oliva, B. and Beato, M. ADP-ribose-derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling. Science 352 (2016) 1221-1225. [PMID: 27257257]
Accepted name: 3-hydroxy-4-methylanthranilate adenylyltransferase
Reaction: ATP + 3-hydroxy-4-methylanthranilate = diphosphate + 3-hydroxy-4-methylanthranilyl-adenylate
Other name(s): acmA (gene name); sibE (gene name); actinomycin synthase I; 4-MHA-activating enzyme; ACMS I; actinomycin synthetase I; 4-MHA pentapeptide lactone synthase AcmA
Systematic name: ATP:3-hydroxy-4-methylanthranilate adenylyltransferase
Comments: The enzyme, characterized from the bacteria Streptomyces anulatus and Streptosporangium sibiricum, activates 3-hydroxy-4-methylanthranilate, a precursor of actinomycin antibiotics and the antitumor antibiotic sibiromycin, to an adenylate form, so it can be loaded onto a dedicated aryl-carrier protein.
References:
1. Pfennig, F., Schauwecker, F. and Keller, U. Molecular characterization of the genes of actinomycin synthetase I and of a 4-methyl-3-hydroxyanthranilic acid carrier protein involved in the assembly of the acylpeptide chain of actinomycin in Streptomyces. J. Biol. Chem. 274 (1999) 12508-12516. [PMID: 10212227]
2. Giessen, T.W., Kraas, F.I. and Marahiel, M.A. A four-enzyme pathway for 3,5-dihydroxy-4-methylanthranilic acid formation and incorporation into the antitumor antibiotic sibiromycin. Biochemistry 50 (2011) 5680-5692. [PMID: 21612226]
Accepted name: lipid A phosphoethanolamine transferase
Reaction: (1) diacylphosphatidylethanolamine + lipid A = diacylglycerol + lipid A 1-(2-aminoethyl diphosphate)
(2) diacylphosphatidylethanolamine + lipid A = diacylglycerol + lipid A 4'-(2-aminoethyl diphosphate)
(3) diacylphosphatidylethanolamine + lipid A 1-(2-aminoethyl diphosphate) = diacylglycerol + lipid A 1,4'-bis(2-aminoethyl diphosphate)
Glossary: lipid A (Campylobacter jejuni) = 2,3-dideoxy-2,3-bis[(3R)-3-(hexadecanoyloxy)tetradecanamido]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid A (Escherichia coli) =
2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid A (Helicobacter pylori) = 2-deoxy-2-[(3R)-3-(octadecanoyloxy)octadecanamido]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyhexadecanoyl]-2-[(3R)-3-hydroxyoctadecanamido]-α-D-glucopyranosyl phosphate
lipid A (Neisseria meningitidis) =
2-deoxy-3-O-[(3R)-3-hydroxydodecanoyl]-2-[(3R)-3-(dodecanoyloxy)tetradecanamido]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxydodecanoyl]-2-[(3R)-3-(dodecanoyloxy)tetradecanamido]-α-D-glucopyranosyl phosphate
lipid A 1-[(2-aminoethyl) diphosphate] = P1-(2-aminoethyl)
P2-(2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl) diphosphate
lipid A 1,4'-bis(2-aminoethyl diphosphate) = P1-(2-aminoethyl)
P2-(2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-(2-aminoethyldiphospho)-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl) diphosphate
Other name(s): lipid A PEA transferase; LptA
Systematic name: diacylphosphatidylethanolamine:lipid-A ethanolaminephosphotransferase
Comments: The enzyme adds one or two ethanolamine phosphate groups to lipid A giving a diphosphate, sometimes in combination with EC 2.4.2.43 (lipid IVA 4-amino-4-deoxy-L-arabinosyltransferase) giving products with 4-amino-4-deoxy-β-L-arabinose groups at the phosphates of lipid A instead of diphosphoethanolamine groups. It will also act on lipid IVA and Kdo2-lipid A.
References:
1. Tran, A.X., Karbarz, M.J., Wang, X., Raetz, C.R., McGrath, S.C., Cotter, R.J. and Trent, M.S. Periplasmic cleavage and modification of the 1-phosphate group of Helicobacter pylori lipid A. J. Biol. Chem. 279 (2004) 55780-55791. [PMID: 15489235]
2. Herrera, C.M., Hankins, J.V. and Trent, M.S. Activation of PmrA inhibits LpxT-dependent phosphorylation of lipid A promoting resistance to antimicrobial peptides. Mol. Microbiol. 76 (2010) 1444-1460. [PMID: 20384697]
3. Cullen, T.W. and Trent, M.S. A link between the assembly of flagella and lipooligosaccharide of the Gram-negative bacterium Campylobacter jejuni. Proc. Natl. Acad. Sci. USA 107 (2010) 5160-5165. [PMID: 20194750]
4. Anandan, A., Piek, S., Kahler, C.M. and Vrielink, A. Cloning, expression, purification and crystallization of an endotoxin-biosynthesis enzyme from Neisseria meningitidis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 (2012) 1494-1497. [PMID: 23192031]
5. Wanty, C., Anandan, A., Piek, S., Walshe, J., Ganguly, J., Carlson, R.W., Stubbs, K.A., Kahler, C.M. and Vrielink, A. The structure of the neisserial lipooligosaccharide phosphoethanolamine transferase A (LptA) required for resistance to polymyxin. J. Mol. Biol. 425 (2013) 3389-3402. [PMID: 23810904]
Accepted name: teichoic acid glycerol-phosphate primase
Reaction: CDP-glycerol + N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = CDP + 4-O-[(2R)-1-glycerophospho]-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): Tag primase; CDP-glycerol:glycerophosphate glycerophosphotransferase; tagB (gene name); tarB (gene name)
Systematic name: CDP-glycerol: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 bacterial cell walls. This enzyme adds the first glycerol unit to the disaccharide linker of the teichoic acid.
References:
1. Bhavsar, A.P., Truant, R. and Brown, E.D. The TagB protein in Bacillus subtilis 168 is an intracellular peripheral membrane protein that can incorporate glycerol phosphate onto a membrane-bound acceptor in vitro. J. Biol. Chem. 280 (2005) 36691-36700. [PMID: 16150696]
2. Ginsberg, C., Zhang, Y.H., Yuan, Y. and Walker, S. In vitro reconstitution of two essential steps in wall teichoic acid biosynthesis. ACS Chem. Biol. 1 (2006) 25-28. [PMID: 17163636]
3. 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]
[EC 3.1.3.98 Transferred entry: geranyl diphosphate phosphohydrolase, transferred to EC 3.6.1.68, geranyl diphosphate phosphohydrolase (EC 3.1.3.98 created 2015, deleted 2016)]
Accepted name: gellan tetrasaccharide unsaturated glucuronosyl hydrolase
Reaction: β-D-4-deoxy-Δ4-GlcAp-(1→4)-β-D-Glcp-(1→4)-α-L-Rhap-(1→3)-D-Glcp + H2O = 5-dehydro-4-deoxy-D-glucuronate + β-D-Glcp-(1→4)-α-L-Rhap-(1→3)-D-Glcp
Glossary: 5-dehydro-4-deoxy-D-glucuronate = (4S,5R)-4,5-dihydroxy-2,6-dioxohexanoate
β-D-4-deoxy-Δ4-GlcAp-(1→3)-D-GalNAc = 3-(4-deoxy-β-D-gluc-4-enuronosyl)-N-acetyl-D-galactosamine = 3-(4-deoxy-α-L-threo-hex-4-enopyranosyluronic acid)-2-acetamido-2-deoxy-D-galactose
Other name(s): UGL (ambiguous); unsaturated glucuronyl hydrolase (ambiguous); gellan tetrasaccharide unsaturated glucuronyl hydrolase
Systematic name: β-D-4-deoxy-Δ4-GlcAp-(1→4)-β-D-Glcp-(1→4)-α-L-Rhap-(1→3)-D-Glcp β-D-4-deoxy-Δ4-GlcAp hydrolase
Comments: The enzyme releases 4-deoxy-4(5)-unsaturated D-glucuronic acid from oligosaccharides produced by polysaccharide lyases, e.g. the tetrasaccharide β-D-4-deoxy-Δ4-GlcAp-(1→4)-β-D-Glcp-(1→4)-α-L-Rhap-(1→3)-D-Glcp produced by EC 4.2.2.25, gellan lyase. The enzyme can also hydrolyse unsaturated chondroitin and hyaluronate disaccharides (β-D-4-deoxy-Δ4-GlcAp-(1→3)-D-GalNAc, β-D-4-deoxy-Δ4-GlcAp-(1→3)-D-GalNAc6S, β-D-4-deoxy-Δ4-GlcAp2S-(1→3)-D-GalNAc, β-D-4-deoxy-Δ4-GlcAp-(1→3)-D-GlcNAc), preferring the unsulfated disaccharides to the sulfated disaccharides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Itoh, T., Akao, S., Hashimoto, W., Mikami, B. and Murata, K. Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 Å resolution. J. Biol. Chem. 279 (2004) 31804-31812. [PMID: 15148314]
2. Hashimoto, W., Kobayashi, E., Nankai, H., Sato, N., Miya, T., Kawai, S. and Murata, K. Unsaturated glucuronyl hydrolase of Bacillus sp. GL1: novel enzyme prerequisite for metabolism of unsaturated oligosaccharides produced by polysaccharide lyases. Arch. Biochem. Biophys. 368 (1999) 367-374. [PMID: 10441389]
3. Itoh, T., Hashimoto, W., Mikami, B. and Murata, K. Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1. Biochem. Biophys. Res. Commun. 344 (2006) 253-262. [PMID: 16630576]
Accepted name: lysoplasmalogenase
Reaction: (1) 1-(1-alkenyl)-sn-glycero-3-phosphocholine + H2O = an aldehyde + sn-glycero-3-phosphocholine
(2) 1-(1-alkenyl)-sn-glycero-3-phosphoethanolamine + H2O = an aldehyde + sn-glycero-3-phosphoethanolamine
Other name(s): alkenylglycerophosphocholine hydrolase; alkenylglycerophosphoethanolamine hydrolase; 1-(1-alkenyl)-sn-glycero-3-phosphocholine aldehydohydrolase
Systematic name: lysoplasmalogen aldehydohydrolase
Comments: Lysoplasmalogenase is specific for the sn-2-deacylated (lyso) form of plasmalogen and catalyses hydrolytic cleavage of the vinyl ether bond, releasing a fatty aldehyde and sn-glycero-3-phosphocholine or sn-glycero-3-phosphoethanolamine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37288-65-6
References:
1. Warner, H.R. and Lands, W.E.M. The metabolism of plasmalogen: enzymatic hydrolysis of the vinyl ether. J. Biol. Chem. 236 (1961) 2404-2409. [PMID: 13783189]
2. Ellingson, J.S. and Lands, W.E.M. Phospholipid reactivation of plasmalogen metabolism. Lipids 3 (1968) 111-120. [PMID: 17805898]
3. Gunawan, J. and Debuch, H. Liberation of free aldehyde from 1-(1-alkenyl)-sn-glycero-3-phosphoethanolamine (lysoplasmalogen) by rat liver microsomes. Hoppe-Seyler's Z. Physiol. Chem. 362 (1981) 445-452. [PMID: 7239443]
4. Arthur, G., Page, L., Mock, T. and Choy, P.C. The catabolism of plasmenylcholine in the guinea pig heart. Biochem. J. 236 (1986) 475-480. [PMID: 3753461]
5. Wu, L.C., Pfeiffer, D.R., Calhoon, E.A., Madiai, F., Marcucci, G., Liu, S. and Jurkowitz, M.S. Purification, identification, and cloning of lysoplasmalogenase, the enzyme that catalyzes hydrolysis of the vinyl ether bond of lysoplasmalogen. J. Biol. Chem. 286 (2011) 24916-24930. [PMID: 21515882]
Accepted name: desampylase
Reaction: an N6-[small archaeal modifier protein]-[protein]-L-lysine + H2O = a [protein]-L-lysine + a small archaeal modifier protein
Glossary: SAMP = small archaeal modifier protein
Other name(s): SAMP-protein conjugate cleaving protease; HvJAMM1
Systematic name: N6-[small archaeal modifier protein]-[protein]-L-lysine hydrolase
Comments: The enzyme, characterized from the archaeon Haloferax volcanii, specifically cleaves the ubiquitin-like small modifier proteins SAMP1 and SAMP2 from protein conjugates, hydrolysing the isopeptide bond between a lysine residue of the target protein and the C-terminal glycine of the modifier protein. The enzyme contains Zn2+. cf. EC 3.4.19.12, ubiquitinyl hydrolase 1. In peptidase family M67.
References:
1. Hepowit, N.L., Uthandi, S., Miranda, H.V., Toniutti, M., Prunetti, L., Olivarez, O., De Vera, I.M., Fanucci, G.E., Chen, S. and Maupin-Furlow, J.A. Archaeal JAB1/MPN/MOV34 metalloenzyme (HvJAMM1) cleaves ubiquitin-like small archaeal modifier proteins (SAMPs) from protein-conjugates. Mol. Microbiol. 86 (2012) 971-987. [PMID: 22970855]
[EC 3.4.24.88 Transferred entry: desampylase. Transferred to EC 3.4.19.15 desampylase (EC 3.4.24.88 created 2015, deleted 2016)]
Accepted name: protein N-terminal asparagine amidohydrolase
Reaction: N-terminal L-asparaginyl-[protein] + H2O = N-terminal L-aspartyl-[protein] + NH3
Other name(s): NTAN1 (gene name)
Systematic name: protein N-terminal asparagine amidohydrolase
Comments: This enzyme participates in the eukaryotic ubiquitin-dependent Arg/N-end rule pathway of protein degradation, promoting the turnover of intracellular proteins that initiate with Met-Asn. Following the acetylation and removal of the initiator methionine, the exposed N-terminal asparagine is deaminated, resulting in its conversion to L-aspartate. The latter serves as a substrate for EC 2.3.2.8, arginyltransferase, making the protein susceptible to arginylation, polyubiquitination and degradation as specified by the N-end rule.
References:
1. Stewart, A.E., Arfin, S.M. and Bradshaw, R.A. Protein NH2-terminal asparagine deamidase. Isolation and characterization of a new enzyme. J. Biol. Chem. 269 (1994) 23509-23517. [PMID: 8089117]
2. Grigoryev, S., Stewart, A.E., Kwon, Y.T., Arfin, S.M., Bradshaw, R.A., Jenkins, N.A., Copeland, N.G. and Varshavsky, A. A mouse amidase specific for N-terminal asparagine. The gene, the enzyme, and their function in the N-end rule pathway. J. Biol. Chem. 271 (1996) 28521-28532. [PMID: 8910481]
3. Cantor, J.R., Stone, E.M. and Georgiou, G. Expression and biochemical characterization of the human enzyme N-terminal asparagine amidohydrolase. Biochemistry 50 (2011) 3025-3033. [PMID: 21375249]
Accepted name: protein N-terminal glutamine amidohydrolase
Reaction: N-terminal L-glutaminyl-[protein] + H2O = N-terminal L-glutamyl-[protein] + NH3
Other name(s): NTAQ1 (gene name)
Systematic name: protein N-terminal glutamine amidohydrolase
Comments: This enzyme participates in the eukaryotic ubiquitin-dependent Arg/N-end rule pathway of protein degradation, promoting the turnover of intracellular proteins that initiate with Met-Gln. Following the acetylation and removal of the initiator methionine, the exposed N-terminal glutamine is deaminated, resulting in its conversion to L-glutamate. The latter serves as a substrate for EC 2.3.2.8, arginyltransferase, making the protein susceptible to arginylation, polyubiquitination and degradation as specified by the N-end rule.
References:
1. Wang, H., Piatkov, K.I., Brower, C.S. and Varshavsky, A. Glutamine-specific N-terminal amidase, a component of the N-end rule pathway. Mol. Cell 34 (2009) 686-695. [PMID: 19560421]
Accepted name: γ-glutamylanilide hydrolase
Reaction: N5-phenyl-L-glutamine + H2O = L-glutamate + aniline
Glossary: γ-glutamylanilide = N5-phenyl-L-glutamine
Other name(s): atdA2 (gene name)
Systematic name: N5-phenyl-L-glutamine amidohydrolase
Comments: The enzyme, characterized from the bacterium Acinetobacter sp. YAA, catalyses the opposite reaction from that cayalysed by EC 6.3.1.18, γ-glutamylanilide synthase, which is part of an aniline degradation pathway. Its purpose is likely to maintain a low concentration of N5-phenyl-L-glutamine, which is potentially toxic.
References:
1. Takeo, M., Ohara, A., Sakae, S., Okamoto, Y., Kitamura, C., Kato, D. and Negoro, S. Function of a glutamine synthetase-like protein in bacterial aniline oxidation via γ-glutamylanilide. J. Bacteriol. 195 (2013) 4406-4414. [PMID: 23893114]
Accepted name: protein deglycase
Reaction: (1) an Nω-(1-hydroxy-2-oxopropyl)-[protein]-L-arginine + H2O = a [protein]-L-arginine + (R)-lactate
(2) an N6-(1-hydroxy-2-oxopropyl)-[protein]-L-lysine + H2O = a [protein]-L-lysine + (R)-lactate
(3) an S-(1-hydroxy-2-oxopropyl)-[protein]-L-cysteine + H2O = a [protein]-L-cysteine + (R)-lactate
Glossary: 2-oxopropanal = methylglyoxal
Other name(s): PARK7 (gene name); DJ-1 protein; yhbO (gene name); yajL (gene name); glyoxylase III (incorrect)
Systematic name: a [protein]-L-amino acid-1-hydroxypropan-2-one hydrolase [(R)-lactate-forming]
Comments: The enzyme, previously thought to be a glyoxalase, acts on glycated L-arginine, L-lysine, and L-cysteine residues within proteins that have been attacked and modified by glyoxal or 2-oxopropanal. The attack forms hemithioacetal in the case of cysteines and aminocarbinols in the case of arginines and lysines. The enzyme repairs the amino acids, releasing glycolate or (R)-lactate, depending on whether the attacking agent was glyoxal or 2-oxopropanal, respectively.
References:
1. Misra, K., Banerjee, A.B., Ray, S. and Ray, M. Glyoxalase III from Escherichia coli: a single novel enzyme for the conversion of methylglyoxal into D-lactate without reduced glutathione. Biochem. J. 305 (1995) 999-1003. [PMID: 7848303]
2. Subedi, K.P., Choi, D., Kim, I., Min, B. and Park, C. Hsp31 of Escherichia coli K-12 is glyoxalase III. Mol. Microbiol. 81 (2011) 926-936. [PMID: 21696459]
3. Richarme, G., Mihoub, M., Dairou, J., Bui, L.C., Leger, T. and Lamouri, A. Parkinsonism-associated protein DJ-1/Park7 is a major protein deglycase that repairs methylglyoxal- and glyoxal-glycated cysteine, arginine, and lysine residues. J. Biol. Chem. 290 (2015) 1885-1897. [PMID: 25416785]
4. Mihoub, M., Abdallah, J., Gontero, B., Dairou, J. and Richarme, G. The DJ-1 superfamily member Hsp31 repairs proteins from glycation by methylglyoxal and glyoxal. Biochem. Biophys. Res. Commun. 463 (2015) 1305-1310. [PMID: 26102038]
5. Abdallah, J., Mihoub, M., Gautier, V. and Richarme, G. The DJ-1 superfamily members YhbO and YajL from Escherichia coli repair proteins from glycation by methylglyoxal and glyoxal. Biochem. Biophys. Res. Commun. 470 (2016) 282-286. [PMID: 26774339]
Accepted name: geranyl diphosphate phosphohydrolase
Reaction: geranyl diphosphate + H2O = geranyl phosphate + phosphate
For diagram of reaction click here.
Other name(s): NUDX1 (gene name)
Systematic name: geranyl-diphosphate phosphohydrolase
Comments: The enzyme, characterized from roses, is involved in a cytosolic pathway for the biosynthesis of free monoterpene alcohols that contribute to fragrance. In vitro the enzyme also acts on (2E,6E)-farnesyl diphosphate.
References:
1. Magnard, J.L., Roccia, A., Caissard, J.C., Vergne, P., Sun, P., Hecquet, R., Dubois, A., Hibrand-Saint Oyant, L., Jullien, F., Nicole, F., Raymond, O., Huguet, S., Baltenweck, R., Meyer, S., Claudel, P., Jeauffre, J., Rohmer, M., Foucher, F., Hugueney, P., Bendahmane, M. and Baudino, S. Plant volatiles. Biosynthesis of monoterpene scent compounds in roses. Science 349 (2015) 81-83. [PMID: 26138978]
Accepted name: carbonic anhydrase
Reaction: H2CO3 = CO2 + H2O
Other name(s): carbonate dehydratase; anhydrase; carbonate anhydrase; carbonic acid anhydrase; carboxyanhydrase; carbonic anhydrase A; carbonate hydro-lyase; carbonate hydro-lyase (carbon-dioxide-forming)
Systematic name: carbonic acid hydro-lyase (carbon-dioxide-forming)
Comments: The enzyme catalyses the reversible hydration of gaseous CO2 to carbonic acid, which dissociates to give hydrogencarbonate above neutral pH. It is widespread and found in archaea, bacteria, and eukaryotes. Three distinct classes exist, and appear to have evolved independently. Contains zinc.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9001-03-0
References:
1. Keilin, D. and Mann, T. Carbonic anhydrase. Nature 144 (1939) 442-443.
2. Kannan, K.K., Ramanadham, M. and Jones, T.A. Structure, refinement, and function of carbonic anhydrase isozymes: refinement of human carbonic anhydrase I. Ann. N.Y. Acad. Sci. 429 (1984) 49-60. [PMID: 6430186]
3. Murakami, H. and Sly, W.S. Purification and characterization of human salivary carbonic anhydrase. J. Biol. Chem. 262 (1987) 1382-1388. [PMID: 2433278]
4. Iverson, T.M., Alber, B.E., Kisker, C., Ferry, J.G. and Rees, D.C. A closer look at the active site of γ-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. Biochemistry 39 (2000) 9222-9231. [PMID: 10924115]
5. Smith, K.S. and Ferry, J.G. Prokaryotic carbonic anhydrases. FEMS Microbiol. Rev. 24 (2000) 335-366. [PMID: 10978542]
6. Cronk, J.D., Endrizzi, J.A., Cronk, M.R., O'neill, J.W. and Zhang, K.Y. Crystal structure of E. coli β-carbonic anhydrase, an enzyme with an unusual pH-dependent activity. Protein Sci. 10 (2001) 911-922. [PMID: 11316870]
7. Merlin, C., Masters, M., McAteer, S. and Coulson, A. Why is carbonic anhydrase essential to Escherichia coli. J. Bacteriol. 185 (2003) 6415-6424. [PMID: 14563877]
Accepted name: 3-vinyl bacteriochlorophyllide d 31-hydratase
Reaction: a 3-(1-hydroxyethyl) bacteriochlorophyllide d = a 3-vinyl bacteriochlorophyllide d + H2O
For diagram of reaction click here.
Other name(s): bchV (gene name)
Systematic name: 3-vinylbacteriochlorophyllide-d 31-hydro-lyase
Comments: This enzyme, found in green sulfur bacteria (Chlorobiaceae) and green flimentous bacteria (Chloroflexaceae), is involved in the biosynthesis of bacteriochlorophylls c, d and e. It acts in the direction of hydration, and the hydroxyl group that is formed is essential for the ability of the resulting bacteriochlorophylls to self-aggregate in the chlorosomes, unique light-harvesting antenna structures found in these organisms. The product is formed preferentially in the (R)-configuration.
References:
1. Frigaard, N.U., Chew, A.G., Li, H., Maresca, J.A. and Bryant, D.A. Chlorobium tepidum: insights into the structure, physiology, and metabolism of a green sulfur bacterium derived from the complete genome sequence. Photosynth. Res. 78 (2003) 93-117. [PMID: 16245042]
2. Harada, J., Teramura, M., Mizoguchi, T., Tsukatani, Y., Yamamoto, K. and Tamiaki, H. Stereochemical conversion of C3-vinyl group to 1-hydroxyethyl group in bacteriochlorophyll c by the hydratases BchF and BchV: adaptation of green sulfur bacteria to limited-light environments. Mol. Microbiol. 98 (2015) 1184-1198. [PMID: 26331578]
Accepted name: 2-(ω-methylthio)alkylmalate dehydratase
Reaction: (1) a 2-[(ω-methylthio)alkyl]malate = a 2-[(ω-methylthio)alkyl]maleate + H2O
(2) a 3-[(ω-methylthio)alkyl]malate = a 2-[(ω-methylthio)alkyl]maleate + H2O
For diagram of reaction click here.
Other name(s): IPMI (gene name)
Systematic name: 2-[(ω-methylthio)alkyl]malate hydro-lyase (2-[(ω-methylthio)alkyl]maleate-forming)
Comments: The enzyme, characterized from the plant Arabidopsis thaliana, is involved in the L-methionine side-chain elongation pathway, forming substrates for the biosynthesis of aliphatic glucosinolates. By catalysing a dehydration of a 2-[(ω-methylthio)alkyl]maleate, followed by a hydration at a different position, the enzyme achieves the isomerization of its substrates. The enzyme is a heterodimer comprising a large and a small subunits. The large subunit can also bind to an alternative small subunit, forming EC 4.2.1.33, 3-isopropylmalate dehydratase, which participates in L-leucine biosynthesis.
References:
1. Knill, T., Reichelt, M., Paetz, C., Gershenzon, J. and Binder, S. Arabidopsis thaliana encodes a bacterial-type heterodimeric isopropylmalate isomerase involved in both Leu biosynthesis and the Met chain elongation pathway of glucosinolate formation. Plant Mol. Biol. 71 (2009) 227-239. [PMID: 19597944]
Accepted name: α-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase
Reaction: α-D-ribose 1-methylphosphonate 5-phosphate + S-adenosyl-L-methionine + reduced electron acceptor = α-D-ribose 1,2-cyclic phosphate 5-phosphate + methane + L-methionine + 5'-deoxyadenosine + oxidized electron acceptor
For diagram of reaction click here.
Other name(s): phnJ (gene name)
Systematic name: α-D-ribose-1-methylphosphonate-5-phosphate C-P-lyase (methane forming)
Comments: This radical SAM (AdoMet) enzyme is part of the C-P lyase complex, which is responsible for processing phophonates into usable phosphate. Contains an [4Fe-4S] cluster. The enzyme from the bacterium Escherichia coli can act on additional α-D-ribose phosphonate substrates with different substituents attached to the phosphonate phosphorus (e.g. α-D-ribose-1-[N-(phosphonomethyl)glycine]-5-phosphate and α-D-ribose-1-(2-N-acetamidomethylphosphonate)-5-phosphate).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Kamat, S.S., Williams, H.J. and Raushel, F.M. Intermediates in the transformation of phosphonates to phosphate by bacteria. Nature 480 (2011) 570-573. [PMID: 22089136]
2. Jochimsen, B., Lolle, S., McSorley, F.R., Nabi, M., Stougaard, J., Zechel, D.L. and Hove-Jensen, B. Five phosphonate operon gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway. Proc. Natl. Acad. Sci. USA 108 (2011) 11393-11398. [PMID: 21705661]
3. Zhang, Q. and van der Donk, W.A. Answers to the carbon-phosphorus lyase conundrum. Chembiochem 13 (2012) 627-629. [PMID: 22334536]
Accepted name: DNA ligase (NAD+)
Reaction: NAD+ + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + β-nicotinamide D-nucleotide (overall reaction)
(1a) NAD+ + [DNA ligase]-L-lysine = [DNA ligase]-N6-(5'-adenylyl)-L-lysine + β-nicotinamide D-nucleotide
(1b) [DNA ligase]-N6-(5'-adenylyl)-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(1c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
Other name(s): polydeoxyribonucleotide synthase (NAD+); polynucleotide ligase (NAD+); DNA repair enzyme (ambiguous); DNA joinase (ambiguous); polynucleotide synthetase (nicotinamide adenine dinucleotide); deoxyribonucleic-joining enzyme (ambiguous); deoxyribonucleic ligase (ambiguous); deoxyribonucleic repair enzyme (ambiguous); deoxyribonucleic joinase (ambiguous); DNA ligase (ambiguous); deoxyribonucleate ligase (ambiguous); polynucleotide ligase (ambiguous); deoxyribonucleic acid ligase (ambiguous); polynucleotide synthetase (ambiguous); deoxyribonucleic acid joinase (ambiguous); DNA-joining enzyme (ambiguous); polynucleotide ligase (nicotinamide adenine dinucleotide); poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming)
Systematic name: poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (NAD+)
Comments: The enzyme, typically found in bacteria, catalyses the ligation of DNA strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in duplex DNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by NAD+, forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine)-[DNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3'-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the adenylate. RNA can also act as substrate, to some extent. cf. EC 6.5.1.1, DNA ligase (ATP), EC 6.5.1.6, DNA ligase (ATP or NAD+), and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37259-52-2
References:
1. Zimmerman, S.B., Little, J.W., Oshinsky, C.K. and Gellert, M. Enzymatic joining of DNA strands: a novel reaction of diphosphopyridine nucleotide. Proc. Natl. Acad. Sci. USA 57 (1967) 1841-1848. [PMID: 4291949]
2. Little, J.W., Zimmerman, S.B., Oshinsky, C.K. and Gellert, M. Enzymatic joining of DNA strands, II. An enzyme-adenylate intermediate in the dpn-dependent DNA ligase reaction. Proc. Natl. Acad. Sci. USA 58 (1967) 2004-2011. [PMID: 4295585]
3. Modorich, P. and Lehman, I.R. Deoxyribonucleic acid ligase. A steady state kinetic analysis of the reaction catalyzed by the enzyme from Escherichia coli. J. Biol. Chem. 248 (1973) 7502-7511. [PMID: 4355585]
4. Modrich, P., Anraku, Y. and Lehman, I.R. Deoxyribonucleic acid ligase. Isolation and physical characterization of the homogeneous enzyme from Escherichia coli. J. Biol. Chem. 248 (1973) 7495-7501. [PMID: 4355584]
5. Uphoff, S., Reyes-Lamothe, R., Garza de Leon, F., Sherratt, D.J. and Kapanidis, A.N. Single-molecule DNA repair in live bacteria. Proc. Natl. Acad. Sci. USA 110 (2013) 8063-8068. [PMID: 23630273]
Accepted name: RNA 3'-terminal-phosphate cyclase (ATP)
Reaction: ATP + [RNA]-3'-(3'-phospho-ribonucleoside) = AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside (overall reaction)
(1a) ATP + [RNA 3'-phosphate cyclase]-L-histidine = [RNA 3'-phosphate cyclase]-Nτ-(5'-adenylyl)-L-histidine + diphosphate
(1b) [RNA 3'-phosphate cyclase]-Nτ-(5'-adenylyl)-L-histidine + [RNA]-3'-(3'-phospho-ribonucleoside) = [RNA 3'-phosphate cyclase]-L-histidine + [RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)
(1c) [RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine) = [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside + AMP
Other name(s): rtcA (gene name); RNA cyclase (ambiguous); RNA-3'-phosphate cyclase (ambiguous)
Systematic name: RNA-3'-phosphate:RNA ligase (cyclizing, AMP-forming)
Comments: The enzyme converts the 3'-terminal phosphate of various RNA substrates into the 2',3'-cyclic phosphodiester in an ATP-dependent reaction. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a histidine residue [5,6]. The adenylate group is then transferred to the 3'-phosphate terminus of the substrate, forming the capped structure [RNA]-3'-(5'-diphosphoadenosine). Finally, the enzyme catalyses an attack of the vicinal O2' on the 3'-phosphorus, which results in formation of cyclic phosphate and release of the adenylate. The enzyme also has a polynucleotide 5' adenylylation activity [7]. cf. EC 6.5.1.5, RNA 3'-terminal-phosphate cyclase (GTP).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 85638-41-1
References:
1. Filipowicz, W., Konarska, M., Gross, H.J. and Shatkin, A.J. RNA 3'-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract. Nucleic Acids Res. 11 (1983) 1405-1418. [PMID: 6828385]
2. Reinberg, D., Arenas, J. and Hurwitz, J. The enzymatic conversion of 3'-phosphate terminated RNA chains to 2',3'-cyclic phosphate derivatives. J. Biol. Chem. 260 (1985) 6088-6097. [PMID: 2581947]
3. Genschik, P., Billy, E., Swianiewicz, M. and Filipowicz, W. The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea. EMBO J. 16 (1997) 2955-2967. [PMID: 9184239]
4. Genschik, P., Drabikowski, K. and Filipowicz, W. Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its σ54-regulated operon. J. Biol. Chem. 273 (1998) 25516-25526. [PMID: 9738023]
5. Billy, E., Hess, D., Hofsteenge, J. and Filipowicz, W. Characterization of the adenylation site in the RNA 3'-terminal phosphate cyclase from Escherichia coli. J. Biol. Chem. 274 (1999) 34955-34960. [PMID: 10574971]
6. Tanaka, N. and Shuman, S. Structure-activity relationships in human RNA 3'-phosphate cyclase. RNA 15 (2009) 1865-1874. [PMID: 19690099]
7. Chakravarty, A.K. and Shuman, S. RNA 3'-phosphate cyclase (RtcA) catalyzes ligase-like adenylylation of DNA and RNA 5'-monophosphate ends. J. Biol. Chem. 286 (2011) 4117-4122. [PMID: 21098490]
8. Das, U. and Shuman, S. 2'-Phosphate cyclase activity of RtcA: a potential rationale for the operon organization of RtcA with an RNA repair ligase RtcB in Escherichia coli and other bacterial taxa. RNA 19 (2013) 1355-1362. [PMID: 23945037]
Accepted name: RNA 3'-terminal-phosphate cyclase (GTP)
Reaction: GTP + [RNA]-3'-(3'-phospho-ribonucleoside) = GMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside (overall reaction)
(1a) GTP + [RNA 3'-phosphate cyclase]-L-histidine = 5'-guanosyl [RNA 3'-phosphate cyclase]-Nτ-phosphono-L-histidine + diphosphate
(1b) 5'-guanosyl [RNA 3'-phosphate cyclase]-Nτ-phosphono-L-histidine + [RNA]-3'-(3'-phospho-ribonucleoside) = [RNA 3'-phosphate cyclase]-L-histidine + [RNA]-3'-ribonucleoside-3'-(5'-diphosphoguanosine)
(1c) [RNA]-3'-ribonucleoside-3'-(5'-diphosphoguanosine) = [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside + GMP
Other name(s): Pf-Rtc; RNA-3'-phosphate cyclase (GTP)
Systematic name: RNA-3'-phosphate:RNA ligase (cyclizing, GMP-forming)
Comments: The enzyme, which is specific for GTP, was characterized from the archaeon Pyrococcus furiosus. The enzyme converts the 3'-terminal phosphate of various RNA substrates into the 2',3'-cyclic phosphodiester in a GTP-dependent reaction. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by GTP, forming a phosphoramide bond between guanylate and a histidine residue. The guanylate group is then transferred to the 3'-phosphate terminus of the substrate, forming the capped structure [RNA]-3'-(5'-diphosphoguanosine). Finally, the enzyme catalyses an attack of the vicinal O2' on the 3'-phosphorus, which results in formation of cyclic phosphate and release of the guanylate. cf. EC 6.5.1.4, RNA-3'-phosphate cyclase (ATP).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Sato, A., Soga, T., Igarashi, K., Takesue, K., Tomita, M. and Kanai, A. GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus. Genes Cells 16 (2011) 1190-1199. [PMID: 22074260]
Accepted name: DNA ligase (ATP or NAD+)
Reaction: (1) ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate (overall reaction)
(1a) ATP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nε-phosphono-L-lysine + diphosphate
(1b) 5'-adenosyl [DNA ligase]-Nε-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(1c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
(2) NAD+ + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + β-nicotinamide D-nucleotide (overall reaction)
(2a) NAD+ + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nε-phosphono-L-lysine + β-nicotinamide D-nucleotide
(2b) 5'-adenosyl [DNA ligase]-Nε-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(2c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
Systematic name: poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP or NAD+)
Comments: The enzymes from the archaea Thermococcus fumicolans and Thermococcus onnurineus show high activity with either ATP or NAD+, and significantly lower activity with TTP, GTP, and CTP. The enzyme catalyses the ligation of DNA strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in duplex DNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP or NAD+, forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine)-[DNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3'-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the adenylate. Different from EC 6.5.1.1, DNA ligase (ATP), EC 6.5.1.2, DNA ligase (NAD+) and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Rolland, J.L., Gueguen, Y., Persillon, C., Masson, J.M. and Dietrich, J. Characterization of a thermophilic DNA ligase from the archaeon Thermococcus fumicolans. FEMS Microbiol. Lett. 236 (2004) 267-273. [PMID: 15251207]
2. Kim, Y.J., Lee, H.S., Bae, S.S., Jeon, J.H., Yang, S.H., Lim, J.K., Kang, S.G., Kwon, S.T. and Lee, J.H. Cloning, expression, and characterization of a DNA ligase from a hyperthermophilic archaeon Thermococcus sp. Biotechnol. Lett. 28 (2006) 401-407. [PMID: 16614906]
Accepted name: DNA ligase (ATP, ADP or GTP)
Reaction: (1) ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate (overall reaction)
(1a) ATP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nε-phosphono-L-lysine + diphosphate
(1b) 5'-adenosyl [DNA ligase]-Nε-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(1c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
(2) ADP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + Pi (overall reaction)
(2a) ADP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-Nε-phosphono-L-lysine + Pi
(2b) 5'-adenosyl [DNA ligase]-Nε-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(2c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
(3) GTP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP + diphosphate (overall reaction)
(3a) GTP + [DNA ligase]-L-lysine = 5'-guanosyl [DNA ligase]-Nε-phosphono-L-lysine + diphosphate
(3b) 5'-guanosyl [DNA ligase]-Nε-phosphono-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoguanosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(3c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoguanosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP
Systematic name: poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP, ADP or GTP)
Comments: The enzymes from the archaea Hyperthermus butylicus and Sulfophobococcus zilligii are active with ATP, ADP or GTP. They show no activity with NAD+. The enzyme catalyses the ligation of DNA strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in duplex DNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, ADP, or GTP, forming a phosphoramide bond between adenylate/guanylate and a lysine residue. The nucleotide is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine/guanosine)-[DNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3'-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the nucleotide. Different from EC 6.5.1.1, DNA ligase (ATP), and EC 6.5.1.6, DNA ligase (ATP or NAD+), which cannot utilize GTP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Sun, Y., Seo, M.S., Kim, J.H., Kim, Y.J., Kim, G.A., Lee, J.I., Lee, J.H. and Kwon, S.T. Novel DNA ligase with broad nucleotide cofactor specificity from the hyperthermophilic crenarchaeon Sulfophobococcus zilligii: influence of ancestral DNA ligase on cofactor utilization. Environ Microbiol 10 (2008) 3212-3224. [PMID: 18647334]
2. Kim, J.H., Lee, K.K., Sun, Y., Seo, G.J., Cho, S.S., Kwon, S.H. and Kwon, S.T. Broad nucleotide cofactor specificity of DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus and its evolutionary significance. Extremophiles 17 (2013) 515-522. [PMID: 23546841]