An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: L-idonate 5-dehydrogenase
Reaction: L-idonate + NAD(P)+ = 5-dehydro-D-gluconate + NAD(P)H + H+
Other name(s): L-idonate 5-dehydrogenase
Systematic name: L-idonate:NAD(P)+ oxidoreductase
Comments: The enzyme from the bacterium Escherichia coli is specific for 5-dehydro-D-gluconate. cf. EC 1.1.1.366, L-idonate 5-dehydrogenase (NAD+).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 211737-68-7
References:
1. Bausch, C., Peekhaus, N., Utz, C., Blais, T., Murray, E., Lowary, T. and Conway, T. Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli. J. Bacteriol. 180 (1998) 3704-3710. [PMID: 9658018]
EC 1.1.1.364
Accepted name: dTDP-4-dehydro-6-deoxy-α-D-gulose 4-ketoreductase
Reaction: dTDP-6-deoxy-α-D-allose + NAD(P)+ = dTDP-4-dehydro-6-deoxy-α-D-gulose + NAD(P)H + H+
For diagram of reaction, click here
Glossary: dTDP-4-dehydro-6-deoxy-α-D-gulose = dTDP-4-dehydro-6-deoxy-α-D-allose
Other name(s): dTDP-4-dehydro-6-deoxygulose reductase; tylD (gene name); gerKI (gene name); chmD (gene name); mydI (gene name)
Systematic name: dTDP-6-deoxy-α-D-allose:NAD(P)+ oxidoreductase
Comments: The enzyme forms an activated deoxy-α-D-allose, which is converted to mycinose after attachment to the aglycones of several macrolide antibiotics, including tylosin, chalcomycin, dihydrochalcomycin, and mycinamicin II.
References:
1. Bate, N. and Cundliffe, E. The mycinose-biosynthetic genes of Streptomyces fradiae, producer of tylosin. J Ind Microbiol Biotechnol 23 (1999) 118-122. [PMID: 10510490]
2. Anzai, Y., Saito, N., Tanaka, M., Kinoshita, K., Koyama, Y. and Kato, F. Organization of the biosynthetic gene cluster for the polyketide macrolide mycinamicin in Micromonospora griseorubida. FEMS Microbiol. Lett. 218 (2003) 135-141. [PMID: 12583909]
3. Thuy, T.T., Liou, K., Oh, T.J., Kim, D.H., Nam, D.H., Yoo, J.C. and Sohng, J.K. Biosynthesis of dTDP-6-deoxy-β-D-allose, biochemical characterization of dTDP-4-keto-6-deoxyglucose reductase (GerKI) from Streptomyces sp. KCTC 0041BP. Glycobiology 17 (2007) 119-126. [PMID: 17053005]
4. Kubiak, R.L., Phillips, R.K., Zmudka, M.W., Ahn, M.R., Maka, E.M., Pyeatt, G.L., Roggensack, S.J. and Holden, H.M. Structural and functional studies on a 3′-epimerase involved in the biosynthesis of dTDP-6-deoxy-D-allose. Biochemistry 51 (2012) 9375-9383. [PMID: 23116432]
EC 1.1.1.365
Accepted name: D-galacturonate reductase
Reaction: L-galactonate + NADP+ = D-galacturonate + NADPH + H+
Other name(s): GalUR; gar1 (gene name)
Systematic name: L-galactonate:NADP+ oxidoreductase
Comments: The enzyme from plants is involved in ascorbic acid (vitamin C) biosynthesis [1,2]. The enzyme from the fungus Trichoderma reesei (Hypocrea jecorina) is involved in a eukaryotic degradation pathway of D-galacturonate. It is also active with D-glucuronate and glyceraldehyde [3]. Neither enzyme shows any activity with NADH.
References:
1. Isherwood, F.A. and Mapson, L.W. Biological synthesis of ascorbic acid: the conversion of derivatives of D-galacturonic acid into L-ascorbic acid by plant extracts. Biochem. J. 64 (1956) 13-22. [PMID: 13363799]
2. Agius, F., Gonzalez-Lamothe, R., Caballero, J.L., Munoz-Blanco, J., Botella, M.A. and Valpuesta, V. Engineering increased vitamin C levels in plants by overexpression of a D-galacturonic acid reductase. Nat. Biotechnol. 21 (2003) 177-181. [PMID: 12524550]
3. Kuorelahti, S., Kalkkinen, N., Penttila, M., Londesborough, J. and Richard, P. Identification in the mold Hypocrea jecorina of the first fungal D-galacturonic acid reductase. Biochemistry 44 (2005) 11234-11240. [PMID: 16101307]
4. Martens-Uzunova, E.S. and Schaap, P.J. An evolutionary conserved D-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet. Biol. 45 (2008) 1449-1457. [PMID: 18768163]
EC 1.1.1.366
Accepted name: L-idonate 5-dehydrogenase (NAD+)
Reaction: L-idonate + NAD+ = 5-dehydro-D-gluconate + NADH + H+
Systematic name: L-idonate:NAD+ oxidoreductase
Comments: Involved in the catabolism of ascorbate (vitamin C) to tartrate. No activity is observed with NADP+ (cf. EC 1.1.1.264, L-idonate 5-dehydrogenase [NAD(P)+]).
References:
1. DeBolt, S., Cook, D.R. and Ford, C.M. L-tartaric acid synthesis from vitamin C in higher plants. Proc. Natl. Acad. Sci. USA 103 (2006) 5608-5613. [PMID: 16567629]
EC 1.1.98.4
Accepted name: F420H2:quinone oxidoreductase
Reaction: a quinol + oxidized coenzyme F420 = a quinone + reduced coenzyme F420
Other name(s): FqoF protein
Systematic name: quinol:coenzyme-F420 oxidoreductase
Comments: An enzyme complex that contains FAD and iron-sulfur clusters. The enzyme has been described in the archaea Methanosarcina mazei and Archaeoglobus fulgidus.
References:
1. Bruggemann, H., Falinski, F. and Deppenmeier, U. Structure of the F420H2:quinone oxidoreductase of Archaeoglobus fulgidus identification and overproduction of the F420H2-oxidizing subunit. Eur. J. Biochem. 267 (2000) 5810-5814. [PMID: 10971593]
2. Kunow, J., Linder, D., Stetter, K.O. and Thauer, R.K. F420H2: quinone oxidoreductase from Archaeoglobus fulgidus. Characterization of a membrane-bound multisubunit complex containing FAD and iron-sulfur clusters. Eur. J. Biochem. 223 (1994) 503-511. [PMID: 8055920]
3. Abken, H.-J. and Deppenmeier, U. Purification and properties of an F420H2 dehydrogenase from Methanosarcina mazei Gö1. FEMS Microbiol. Lett. 154 (1997) 231-237.
EC 1.1.98.5
Accepted name: secondary-alcohol dehydrogenase (coenzyme-F420)
Reaction: R-CHOH-R′ + oxidized coenzyme F420 = R-CO-R′ + reduced coenzyme F420
Glossary: oxidized coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): F420-dependent alcohol dehydrogenase; secondary alcohol:F420 oxidoreductase; F420-dependent secondary alcohol dehydrogenase
Systematic name: secondary-alcohol:coenzyme F420 oxidoreductase
Comments: The enzyme isolated from the methanogenic archaea Methanogenium liminatans catalyses the reversible oxidation of various secondary and cyclic alcohols to the corresponding ketones.
References:
1. Bleicher, K. and Winter, J. Purification and properties of F420- and NADP(+)-dependent alcohol dehydrogenases of Methanogenium liminatans and Methanobacterium palustre, specific for secondary alcohols. Eur. J. Biochem. 200 (1991) 43-51. [PMID: 1879431]
2. Aufhammer, S.W., Warkentin, E., Berk, H., Shima, S., Thauer, R.K. and Ermler, U. Coenzyme binding in F420-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family. Structure 12 (2004) 361-370. [PMID: 15016352]
*EC 1.1.99.2
Accepted name: L-2-hydroxyglutarate dehydrogenase
Reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor
Other name(s): α-ketoglutarate reductase; α-hydroxyglutarate dehydrogenase; L-α-hydroxyglutarate dehydrogenase; hydroxyglutaric dehydrogenase; α-hydroxyglutarate oxidoreductase; L-α-hydroxyglutarate:NAD+ 2-oxidoreductase; α-hydroxyglutarate dehydrogenase (NAD+ specific); (S)-2-hydroxyglutarate:(acceptor) 2-oxidoreductase
Systematic name: (S)-2-hydroxyglutarate:acceptor 2-oxidoreductase
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
CAS registry number: 9028-80-2
References:
1. Weil-Malherbe, H. The oxidation of l(-)α-hydroxyglutaric acid in animal tissues. Biochem. J. 31 (1937) 2080-2094. [PMID: 16746551]
*EC 1.1.99.6
Accepted name: D-lactate dehydrogenase (acceptor)
Reaction: (R)-lactate + acceptor = pyruvate + reduced acceptor
Other name(s): D-2-hydroxy acid dehydrogenase; D-2-hydroxy-acid dehydrogenase; (R)-2-hydroxy-acid:acceptor 2-oxidoreductase
Systematic name: (R)-lactate:acceptor 2-oxidoreductase
Comments: The zinc flavoprotein (FAD) from the archaeon Archaeoglobus fulgidus cannot utilize NAD+, cytochrome c, methylene blue or dimethylnaphthoquinone as acceptors. In vitro it is active with artificial electron acceptors such as 2,6-dichlorophenolindophenol, but the physiological acceptor is not yet known.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
CAS registry number: 9028-83-5
References:
1. Reed, D.W. and Hartzell, P.L. The Archaeoglobus fulgidus D-lactate dehydrogenase is a Zn2+ flavoprotein. J. Bacteriol. 181 (1999) 7580-7587. [PMID: 10601217]
EC 1.1.99.39
Accepted name: D-2-hydroxyglutarate dehydrogenase
Reaction: (R)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor
Other name(s): AtD-2HGDH
Systematic name: (R)-2-hydroxyglutarate:acceptor 2-oxidoreductase
Comments: The enzyme, which has been characterized from the plant Arabidopsis thaliana, is highly specific for (R)-2-hydroxyglutarate. It has low activity with (R)-lactate, (R)-2-hydroxybutyrate and meso-tartrate, and no activity with the (S) isomers.
References:
1. Engqvist, M., Drincovich, M.F., Flugge, U.I. and Maurino, V.G. Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and β-oxidation pathways. J. Biol. Chem. 284 (2009) 25026-25037. [PMID: 19586914]
EC 1.3.1.105
Accepted name: 2-methylene-furan-3-one reductase
Reaction: 4-hydroxy-2,5-dimethylfuran-3(2H)-one + NAD(P)+ = 4-hydroxy-5-methyl-2-methylenefuran-3(2H)-one + NAD(P)H + H+
Other name(s): FaEO; SIEO; enone oxidoreductase
Systematic name: 4-hydroxy-2,5-dimethylfuran-3(2H)-one:NAD(P)+ oxidoreductase
Comments: In the fruit-ripening process of strawberry (Fragaria x ananassa) the reaction is catalysed in the reverse direction from that shown. 4-hydroxy-2,5-dimethylfuran-3(2H)-one is one of the major aroma compounds in the fruits. The enzyme has also been detected in tomato (Solanum lycopersicum) fruits [2]. NADPH is the preferred cofactor.
References:
1. Raab, T., Lopez-Raez, J.A., Klein, D., Caballero, J.L., Moyano, E., Schwab, W. and Munoz-Blanco, J. FaQR, required for the biosynthesis of the strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone, encodes an enone oxidoreductase. Plant Cell 18 (2006) 1023-1037. [PMID: 16517758]
2. Klein, D., Fink, B., Arold, B., Eisenreich, W. and Schwab, W. Functional characterization of enone oxidoreductases from strawberry and tomato fruit. J. Agric. Food Chem. 55 (2007) 6705-6711. [PMID: 17636940]
3. Schiefner, A., Sinz, Q., Neumaier, I., Schwab, W. and Skerra, A. Structural basis for the enzymatic formation of the key strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone. J. Biol. Chem. 288 (2013) 16815-16826. [PMID: 23589283]
*EC 1.3.5.4
Accepted name: fumarate reductase (quinol)
Reaction: succinate + a quinone = fumarate + a quinol
Other name(s): FRD; menaquinol-fumarate oxidoreductase; succinate dehydrogenase (menaquinone); succinate:menaquinone oxidoreductase; fumarate reductase (menaquinone); complex II (ambiguous)
Systematic name: succinate:quinone oxidoreductase
Comments: The reaction is catalysed in the opposite direction. The enzyme, which is found in anaerobic and facultative organisms such as bacteria, parasitic helminthes, and lower marine organisms, utilizes low potential quinols, such as menaquinol and rhodoquinol, to reduce fumarate as the final step of an anaerobic respiratory chain. The enzyme is known as complex II of the electron transfer chain, similarly to EC 1.3.5.1, succinate dehydrogenase (quinone), to which it is closely related.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc
References:
1. Van Hellemond, J.J. and Tielens, A.G. Expression and functional properties of fumarate reductase. Biochem. J. 304 (1994) 321-331. [PMID: 7998964]
2. Iverson, T.M., Luna-Chavez, C., Cecchini, G. and Rees, D.C. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284 (1999) 1961-1966. [PMID: 10373108]
3. Cecchini, G., Schroder, I., Gunsalus, R.P. and Maklashina, E. Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim. Biophys. Acta 1553 (2002) 140-157. [PMID: 11803023]
4. Iverson, T.M., Luna-Chavez, C., Croal, L.R., Cecchini, G. and Rees, D.C. Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. J. Biol. Chem. 277 (2002) 16124-16130. [PMID: 11850430]
5. van Hellemond, J.J., van der Klei, A., van Weelden, S.W. and Tielens, A.G. Biochemical and evolutionary aspects of anaerobically functioning mitochondria. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358 (2003) 205. [PMID: 12594928]
EC 1.3.8.10
Accepted name: cyclohex-1-ene-1-carbonyl-CoA dehydrogenase
Reaction: cyclohex-1-ene-1-carbonyl-CoA + electron-transfer flavoprotein = (E)-2-cyclohex-1,5-diene-1-carbonyl-CoA + reduced electron-transfer flavoprotein
Systematic name: cyclohex-1-ene-1-carbonyl-CoA:electron transfer flavoprotein oxidoreductase
Comments: Contains FAD. The enzyme, characterized from the strict anaerobic bacterium Syntrophus aciditrophicus, is involved in production of cyclohexane-1-carboxylate, a byproduct produced by that organism during fermentation of benzoate and crotonate to acetate.
References:
1. Kung, J.W., Seifert, J., von Bergen, M. and Boll, M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J. Bacteriol. 195 (2013) 3193-3200. [PMID: 23667239]
EC 1.3.8.11
Accepted name: cyclohexane-1-carbonyl-CoA dehydrogenase
Reaction: cyclohexane-1-carbonyl-CoA + electron-transfer flavoprotein = cyclohex-1-ene-1-carbonyl-CoA + reduced electron-transfer flavoprotein
Systematic name: cyclohexane-1-carbonyl-CoA:electron transfer flavoprotein oxidoreductase
Comments: Contains FAD. The enzyme, characterized from the strict anaerobic bacterium Syntrophus aciditrophicus, is involved in production of cyclohexane-1-carboxylate, a byproduct produced by that organism during fermentation of benzoate and crotonate to acetate.
References:
1. Kung, J.W., Seifert, J., von Bergen, M. and Boll, M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J. Bacteriol. 195 (2013) 3193-3200. [PMID: 23667239]
EC 1.5.3.22
Accepted name: coenzyme F420H2 oxidase
Reaction: 2 reduced coenzyme F420 + O2 = 2 oxidized coenzyme F420 + 2 H2O
Glossary: oxidized coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): FprA
Systematic name: reduced coenzyme F420:oxygen oxidoreductase
Comments: The enzyme contains FMN and a binuclear iron center. The enzyme from the archaeon Methanothermobacter marburgensis is Si-face specific with respect to C-5 of coenzyme F420 [2].
References:
1. Seedorf, H., Dreisbach, A., Hedderich, R., Shima, S. and Thauer, R.K. F420H2 oxidase (FprA) from Methanobrevibacter arboriphilus, a coenzyme F420-dependent enzyme involved in O2 detoxification. Arch. Microbiol. 182 (2004) 126-137. [PMID: 15340796]
2. Seedorf, H., Kahnt, J., Pierik, A.J. and Thauer, R.K. Si-face stereospecificity at C5 of coenzyme F420 for F420H2 oxidase from methanogenic Archaea as determined by mass spectrometry. FEBS J. 272 (2005) 5337-5342. [PMID: 16218963]
3. Seedorf, H., Hagemeier, C.H., Shima, S., Thauer, R.K., Warkentin, E. and Ermler, U. Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O. FEBS J. 274 (2007) 1588-1599. [PMID: 17480207]
EC 1.5.7.2
Accepted name: coenzyme F420 oxidoreductase (ferredoxin)
Reaction: reduced coenzyme F420 + 2 oxidized ferredoxin = oxidized coenzyme F420 + 2 reduced ferredoxin + 2 H+
For diagram of reaction, click here
Glossary: oxidized coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): Fd:F420 oxidoreductase; FpoF protein; ferredoxin:F420 oxidoreductase
Systematic name: coenzyme F420:ferredoxin oxidoreductase
Comments: The enzyme from the archaeon Methanosarcina mazei contains iron-sulfur centres and FAD.
References:
1. Welte, C. and Deppenmeier, U. Re-evaluation of the function of the F420 dehydrogenase in electron transport of Methanosarcina mazei. FEBS J. 278 (2011) 1277-1287. [PMID: 21306561]
*EC 1.10.2.2
Accepted name: quinol—cytochrome-c reductase
Reaction: quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H+
Other name(s): ubiquinol—cytochrome-c reductase; coenzyme Q-cytochrome c reductase; dihydrocoenzyme Q-cytochrome c reductase; reduced ubiquinone-cytochrome c reductase; complex III (mitochondrial electron transport); ubiquinone-cytochrome c reductase; ubiquinol-cytochrome c oxidoreductase; reduced coenzyme Q-cytochrome c reductase; ubiquinone-cytochrome c oxidoreductase; reduced ubiquinone-cytochrome c oxidoreductase; mitochondrial electron transport complex III; ubiquinol-cytochrome c-2 oxidoreductase; ubiquinone-cytochrome b-c1 oxidoreductase; ubiquinol-cytochrome c2 reductase; ubiquinol-cytochrome c1 oxidoreductase; CoQH2-cytochrome c oxidoreductase; ubihydroquinol:cytochrome c oxidoreductase; coenzyme QH2-cytochrome c reductase; QH2:cytochrome c oxidoreductase; ubiquinol:ferricytochrome-c oxidoreductase
Systematic name: quinol:ferricytochrome-c oxidoreductase
Comments: The enzyme, often referred to as the cytochrome bc1 complex or complex III, is the third complex in the electron transport chain. It is present in the mitochondria of all aerobic eukaryotes and in the inner membranes of most bacteria. The mammalian enzyme contains cytochromes b-562, b-566 and c1, and a 2-iron ferredoxin. Depending on the organism and physiological conditions, the enzyme extrudes either two or four protons from the cytoplasmic to the non-cytoplasmic compartment (cf. EC 1.6.99.3, NADH dehydrogenase).
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
PDB,
CAS registry number: 9027-03-6
References:
1. Marres, C.A.M. and Slater, E.C. Polypeptide composition of purified QH2:cytochrome c oxidoreductase from beef-heart mitochondria. Biochim. Biophys. Acta 462 (1977) 531-548. [PMID: 597492]
2. Rieske, J.S. Composition, structure, and function of complex III of the respiratory chain. Biochim. Biophys. Acta 456 (1976) 195-247. [PMID: 788795]
3. Wikström, M., Krab, K. and Saraste, M. Proton-translocating cytochrome complexes. Annu. Rev. Biochem. 50 (1981) 623-655. [PMID: 6267990]
4. Sone, N., Tsuchiya, N., Inoue, M. and Noguchi, S. Bacillus stearothermophilus qcr operon encoding rieske FeS protein, cytochrome b6, and a novel-type cytochrome c1 of quinol-cytochrome c reductase. J. Biol. Chem. 271 (1996) 12457-12462. [PMID: 8647852]
5. Yu, J. and Le Brun, N.E. Studies of the cytochrome subunits of menaquinone:cytochrome c reductase (bc complex) of Bacillus subtilis. Evidence for the covalent attachment of heme to the cytochrome b subunit. J. Biol. Chem. 273 (1998) 8860-8866. [PMID: 9535866]
6. Elbehti, A., Nitschke, W., Tron, P., Michel, C. and Lemesle-Meunier, D. Redox components of cytochrome bc-type enzymes in acidophilic prokaryotes. I. Characterization of the cytochrome bc1-type complex of the acidophilic ferrous ion-oxidizing bacterium Thiobacillus ferrooxidans. J. Biol. Chem. 274 (1999) 16760-16765. [PMID: 10358017]
EC 1.13.11.77
Accepted name: oleate 10S-lipoxygenase
Reaction: (1) oleate + O2 = (8E,10S)-10-hydroperoxyoctadeca-8-enoate
Other name(s): 10S-DOX; (10S)-dioxygenase; 10S-dioxygenase
Systematic name: oleate:oxygen (10S)-oxidoreductase
Comments: Binds Fe2+. The enzyme isolated from the bacterium Pseudomonas sp. 42A2 has similar activity with all the three Δ9 fatty acids. cf. EC 1.13.11.62, linoleate 10R-lipoxygenase.
References:
1. Busquets, M., Deroncele, V., Vidal-Mas, J., Rodriguez, E., Guerrero, A. and Manresa, A. Isolation and characterization of a lipoxygenase from Pseudomonas 42A2 responsible for the biotransformation of oleic acid into (S)-(E)-10-hydroxy-8-octadecenoic acid. Antonie Van Leeuwenhoek 85 (2004) 129-139. [PMID: 15028873]
*EC 1.14.11.37
Accepted name: kanamycin B dioxygenase
Reaction: kanamycin B + 2-oxoglutarate + O2 = 2′-dehydrokanamycin A + succinate + NH3 + CO2
For diagram of reaction, click here
Other name(s): kanJ (gene name)
Systematic name: kanamycin-B,2-oxoglutarate:oxygen oxidoreductase (deaminating, 2′-hydroxylating)
Comments: Requires Fe2+ and ascorbate. Found in the bacterium Streptomyces kanamyceticus where it is involved in the conversion of the aminoglycoside antibiotic kanamycin B to kanamycin A.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc
References:
1. Sucipto, H., Kudo, F. and Eguchi, T. The last step of kanamycin biosynthesis: unique deamination reaction catalyzed by the α-ketoglutarate-dependent nonheme iron dioxygenase KanJ and the NADPH-dependent reductase KanK. Angew. Chem. Int. Ed. Engl. 51 (2012) 3428-3431. [PMID: 22374809]
[EC 1.14.13.60 Transferred entry: 27-hydroxycholesterol 7α-monooxygenase. Now included with EC 1.14.13.100, 25-hydroxycholesterol 7α-hydroxylase (EC 1.14.13.60 created 1999, deleted 2013)]
*EC 1.14.13.100
Accepted name: 25/26-hydroxycholesterol 7α-hydroxylase
Reaction: (1) cholest-5-ene-3β,25-diol + NADPH + H+ + O2 = cholest-5-ene-3β,7α,25-triol + NADP+ + H2O
For diagram of reaction, click here
Other name(s): 25-hydroxycholesterol 7α-monooxygenase; CYP7B1; CYP7B1 oxysterol 7α-hydroxylase; 27-hydroxycholesterol 7-monooxygenase; 27-hydroxycholesterol 7α-hydroxylase; cholest-5-ene-3β,25-diol,NADPH:oxygen oxidoreductase (7α-hydroxylating); 25-hydroxycholesterol 7α-hydroxylase
Systematic name: cholest-5-ene-3β,25/26-diol,NADPH:oxygen oxidoreductase (7α-hydroxylating)
Comments: A heme-thiolate protein (P-450). Unlike EC 1.14.13.99, 24-hydroxycholesterol 7α-monooxygenase, which is specific for its oxysterol substrate, this enzyme can also metabolize the oxysterols 24,25-epoxycholesterol, 22-hydroxycholesterol and 24-hydroxycholesterol, but to a lesser extent [2].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
CAS registry number: 149316-80-3
References:
1. Kumiko, O.M., Budai, K. and Javitt, N.B. Cholesterol and 27-hydroxycholesterol 7α-hydroxylation: evidence for two different enzymes. J. Lipid Res. 34 (1993) 581-588.
2. Toll, A., Wikvall, K., Sudjana-Sugiaman, E., Kondo, K.H. and Björkhem, I. 7α hydroxylation of 25-hydroxycholesterol in liver microsomes.
Evidence that the enzyme involved is different from cholesterol 7α-hydroxylase. Eur. J. Biochem. 224 (1994) 309-316. [PMID: 7925343]
3. Li-Hawkins, J., Lund, E.G., Bronson, A.D. and Russell, D.W. Expression cloning of an oxysterol 7α-hydroxylase selective for 24-hydroxycholesterol. J. Biol. Chem. 275 (2000) 16543-16549. [PMID: 10748047]
4. Ren, S., Marques, D., Redford, K., Hylemon, P.B., Gil, G., Vlahcevic, Z.R. and Pandak, W.M. Regulation of oxysterol 7alpha-hydroxylase (CYP7B1) in the rat. Metabolism 52 (2003) 636-642. [PMID: 12759897]
5. Russell, D.W. The enzymes, regulation, and genetics of bile acid synthesis. Annu. Rev. Biochem. 72 (2003) 137-174. [PMID: 12543708]
EC 1.14.13.183
Accepted name: dammarenediol 12-hydroxylase
Reaction: dammarenediol-II + NADPH + H+ + O2 = protopanaxadiol + NADP+ + H2O
For diagram of reaction, click here
Glossary: dammarenediol-II = dammar-24-ene-3β,20-diol
Other name(s): protopanaxadiol synthase; CYP716A47
Systematic name: dammarenediol-II,NADPH:O2 oxidoreductase (12β-hydroxylating)
Comments: A heme-thiolate protein (P-450). Involved in the biosynthetic pathway of ginsenosides. Isolated from ginseng (Panax ginseng).
References:
1. Han, J.Y., Kim, H.J., Kwon, Y.S. and Choi, Y.E. The Cyt P450 enzyme CYP716A47 catalyzes the formation of protopanaxadiol from dammarenediol-II during ginsenoside biosynthesis in Panax ginseng. Plant Cell Physiol 52 (2011) 2062-2073. [PMID: 22039120]
EC 1.14.13.184
Accepted name: protopanaxadiol 6-hydroxylase
Reaction: protopanaxadiol + NADPH + H+ + O2 = protopanaxatriol + NADP+ + H2O
For diagram of reaction, click here
Glossary: protopanaxadiol = dammar-24-ene-3β,12β,20-triol
Other name(s): protopanaxatriol synthase; P6H; CYP716A53v2
Systematic name: protopanaxadiol,NADPH:O2 oxidoreductase (6α-hydroxylating)
Comments: A heme-thiolate protein (P-450). Involved in the biosynthetic pathway of ginsenosides. Isolated from the rhizomes of ginseng (Panax ginseng).
References:
1. Yue, C.J., Zhou, X. and Zhong, J.J. Protopanaxadiol 6-hydroxylase and its role in regulating the ginsenoside heterogeneity in Panax notoginseng cells. Biotechnol. Bioeng. 100 (2008) 933-940. [PMID: 18351680]
2. Han, J.Y., Hwang, H.S., Choi, S.W., Kim, H.J. and Choi, Y.E. Cytochrome P450 CYP716A53v2 catalyzes the formation of protopanaxatriol from protopanaxadiol during ginsenoside biosynthesis in Panax ginseng. Plant Cell Physiol 53 (2012) 1535-1545. [PMID: 22875608]
*EC 2.1.1.196
Accepted name: cobalt-precorrin-6B (C15)-methyltransferase [decarboxylating]
Reaction: cobalt-precorrin-6B + S-adenosyl-L-methionine = cobalt-precorrin-7 + S-adenosyl-L-homocysteine + CO2
For diagram of reaction, click here
Other name(s): cbiT (gene name); S-adenosyl-L-methionine:precorrin-7 C15-methyltransferase (C-12-decarboxylating); cobalt-precorrin-7 (C15)-methyltransferase [decarboxylating]
Systematic name: S-adenosyl-L-methionine:precorrin-6B C15-methyltransferase (C-12-decarboxylating)
Comments: This enzyme catalyses both methylation at C-15 and decarboxylation of the C-12 acetate side chain of cobalt-precorrin-6B, a step in the anaerobic (early cobalt insertion) adenosylcobalamin biosynthesis pathway.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc
References:
1. Keller, J.P., Smith, P.M., Benach, J., Christendat, D., deTitta, G.T. and Hunt, J.F. The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase. Structure 10 (2002) 1475-1487. [PMID: 12429089]
2. Santander, P.J., Kajiwara, Y., Williams, H.J. and Scott, A.I. Structural characterization of novel cobalt corrinoids synthesized by enzymes of the vitamin B12 anaerobic pathway. Bioorg. Med. Chem. 14 (2006) 724-731. [PMID: 16198574]
3. Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12). Proc. Natl. Acad. Sci. USA 110 (2013) 14906-14911. [PMID: 23922391]
*EC 2.1.1.222
Accepted name: 2-polyprenyl-6-hydroxyphenol methylase
Reaction: S-adenosyl-L-methionine + 3-(all-trans-polyprenyl)benzene-1,2-diol = S-adenosyl-L-homocysteine + 2-methoxy-6-(all-trans-polyprenyl)phenol
For diagram of reaction, click here
Other name(s): ubiG (gene name, ambiguous); ubiG methyltransferase (ambiguous); 2-octaprenyl-6-hydroxyphenol methylase
Systematic name: S-adenosyl-L-methionine:3-(all-trans-polyprenyl)benzene-1,2-diol 2-O-methyltransferase
Comments: UbiG catalyses both methylation steps in ubiquinone biosynthesis in Escherichia coli. The second methylation is classified as EC 2.1.1.64 (3-demethylubiquinol 3-O-methyltransferase) [2]. In eukaryotes Coq3 catalyses the two methylation steps in ubiquinone biosynthesis. However, while the second methylation is common to both enzymes, the first methylation by Coq3 occurs at a different position within the pathway, and thus involves a different substrate and is classified as EC 2.1.1.114 (polyprenyldihydroxybenzoate methyltransferase). The substrate of the eukaryotic enzyme (3,4-dihydroxy-5-all-trans-polyprenylbenzoate) differs by an additional carboxylate moiety.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc
References:
1. Poon, W.W., Barkovich, R.J., Hsu, A.Y., Frankel, A., Lee, P.T., Shepherd, J.N., Myles, D.C. and Clarke, C.F. Yeast and rat Coq3 and Escherichia coli UbiG polypeptides catalyze both O-methyltransferase steps in coenzyme Q biosynthesis. J. Biol. Chem. 274 (1999) 21665-21672. [PMID: 10419476]
2. Hsu, A.Y., Poon, W.W., Shepherd, J.A., Myles, D.C. and Clarke, C.F. Complementation of coq3 mutant yeast by mitochondrial targeting of the Escherichia coli UbiG polypeptide: evidence that UbiG catalyzes both O-methylation steps in ubiquinone biosynthesis. Biochemistry 35 (1996) 9797-9806. [PMID: 8703953]
EC 2.1.1.289
Accepted name: cobalt-precorrin-7 (C5)-methyltransferase
Reaction: cobalt-precorrin-7 + S-adenosyl-L-methionine = cobalt-precorrin-8 + S-adenosyl-L-homocysteine
For diagram of reaction, click here
Other name(s): CbiE
Systematic name: S-adenosyl-L-methionine:precorrin-7 C5-methyltransferase
Comments: This enzyme catalyses the methylation at C-5 of cobalt-precorrin-7, a step in the anaerobic (early cobalt insertion) adenosylcobalamin biosynthesis pathway.
References:
1. Santander, P.J., Kajiwara, Y., Williams, H.J. and Scott, A.I. Structural characterization of novel cobalt corrinoids synthesized by enzymes of the vitamin B12 anaerobic pathway. Bioorg. Med. Chem. 14 (2006) 724-731. [PMID: 16198574]
2. Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12). Proc. Natl. Acad. Sci. USA 110 (2013) 14906-14911. [PMID: 23922391]
EC 2.1.1.290
Accepted name: tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase
Reaction: S-adenosyl-L-methionine + 7-[(3S)-3-amino-3-carboxypropyl]wyosine37 in tRNAPhe = S-adenosyl-L-homocysteine + 7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37 in tRNAPhe
For diagram of reaction, click here
Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW4 (ambiguous); tRNA-yW synthesizing enzyme-4 (ambiguous)
Systematic name: S-adenosyl-L-methionine:tRNAPhe {7-[(3S)-3-amino-3-carboxypropyl]wyosine37-O}-methyltransferase
Comments: The enzyme is found only in eukaryotes, where it is involved in the biosynthesis of wybutosine, a hypermodified tricyclic base found at position 37 of certain tRNAs. The modification is important for translational reading-frame maintenance. In some species that produce hydroxywybutosine the enzyme uses 7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine37 in tRNAPhe as substrate. The enzyme also has the activity of EC 2.3.1.231, tRNAPhe 7-[(3S)-4-methoxy-(3-amino-3-carboxypropyl)wyosine37-O]-carbonyltransferase [2].
References:
1. Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142-2154. [PMID: 16642040]
2. Suzuki, Y., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. 37 (2009) 2910-2925. [PMID: 19287006]
3. Kato, M., Araiso, Y., Noma, A., Nagao, A., Suzuki, T., Ishitani, R. and Nureki, O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res. 39 (2011) 1576-1585. [PMID: 20972222]
EC 2.1.1.291
Accepted name: (R,S)-reticuline 7-O-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + (S)-reticuline = S-adenosyl-L-homocysteine + (S)-laudanine
For diagram of reaction, click here
Glossary: (S)-reticuline = (1S)-1-[(3-hydroxy-4-methoxyphenyl)methyl]-6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-ol
Systematic name: S-adenosyl-L-methionine:(R,S)-reticuline 7-O-methyltransferase
Comments: The enzyme from the plant Papaver somniferum (opium poppy) methylates (S)- and (R)-reticuline with equal efficiency and is involved in the biosynthesis of tetrahydrobenzylisoquinoline alkaloids.
References:
1. Ounaroon, A., Decker, G., Schmidt, J., Lottspeich, F. and Kutchan, T.M. (R,S)-Reticuline 7-O-methyltransferase and (R,S)-norcoclaurine 6-O-methyltransferase of Papaver somniferum - cDNA cloning and characterization of methyl transfer enzymes of alkaloid biosynthesis in opium poppy. Plant J. 36 (2003) 808-819. [PMID: 14675446]
2. Weid, M., Ziegler, J. and Kutchan, T.M. The roles of latex and the vascular bundle in morphine biosynthesis in the opium poppy, Papaver somniferum. Proc. Natl. Acad. Sci. USA 101 (2004) 13957-13962. [PMID: 15353584]
EC 2.1.1.292
Accepted name: carminomycin 4-O-methyltransferase
Reaction: S-adenosyl-L-methionine + carminomycin = S-adenosyl-L-homocysteine + daunorubicin
For diagram of reaction, click here
Glossary: daunorubicin = (+)-daunomycin = (8S,10S)-8-acetyl-10-[(2S,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy-6,8,11-trihydroxy-1-methoxy-9,10-dihydro-7H-tetracene-5,12-dione
Other name(s): DnrK; DauK
Systematic name: S-adenosyl-L-methionine:carminomycin 4-O-methyltransferase
Comments: The enzymes from the Gram-positive bacteria Streptomyces sp. C5 and Streptomyces peucetius are involved in the biosynthesis of the anthracycline daunorubicin. In vitro the enzyme from Streptomyces sp. C5 also catalyses the 4-O-methylation of 13-dihydrocarminomycin, rhodomycin D and 10-carboxy-13-deoxycarminomycin [3].
References:
1. Connors, N.C. and Strohl, W.R. Partial purification and properties of carminomycin 4-O-methyltransferase from Streptomyces sp. strain C5. J. Gen. Microbiol. 139 Pt 6 (1993) 1353-1362. [PMID: 8360627]
2. Jansson, A., Koskiniemi, H., Mantsala, P., Niemi, J. and Schneider, G. Crystal structure of a ternary complex of DnrK, a methyltransferase in daunorubicin biosynthesis, with bound products. J. Biol. Chem. 279 (2004) 41149-41156. [PMID: 15273252]
3. Dickens, M.L., Priestley, N.D. and Strohl, W.R. In vivo and in vitro bioconversion of ε-rhodomycinone glycoside to doxorubicin: functions of DauP, DauK, and DoxA. J. Bacteriol. 179 (1997) 2641-2650. [PMID: 9098063]
EC 2.1.1.293
Accepted name: 6-hydroxytryprostatin B O-methyltransferase
Reaction: S-adenosyl-L-methionine + 6-hydroxytryprostatin B = S-adenosyl-L-homocysteine + tryprostatin A
For diagram of reaction, click here
Glossary: 6-hydroxytryprostatin B = (3S,8aS)-3-{[6-hydroxy-2-(3-methylbut-2-en-1-yl)-1H-indol-3-yl]methyl}hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
Other name(s): ftmD (gene name)
Systematic name: S-adenosyl-L-methionine:6-hydroxytryprostatin B O-methyltransferase
Comments: Involved in the biosynthetic pathways of several indole alkaloids such as tryprostatins, fumitremorgins and verruculogen.
References:
1. Kato, N., Suzuki, H., Okumura, H., Takahashi, S. and Osada, H. A point mutation in ftmD blocks the fumitremorgin biosynthetic pathway in Aspergillus fumigatus strain Af293. Biosci. Biotechnol. Biochem. 77 (2013) 1061-1067. [PMID: 23649274]
*EC 2.3.1.86
Accepted name: fatty-acyl-CoA synthase
Reaction: acetyl-CoA + n malonyl-CoA + 2n NADPH + 4n H+ = long-chain-acyl-CoA + n CoA + n CO2 + 2n NADP+
Other name(s): yeast fatty acid synthase; FAS1 (gene name); FAS2 (gene name)
Systematic name: acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl- reducing)
Comments: The enzyme from yeasts (Ascomycota and Basidiomycota) is a multi-functional protein complex composed of two subunits. One subunit catalyses the reactions EC 1.1.1.100, 3-oxoacyl-[acyl-carrier-protein] reductase and EC 2.3.1.41, 3-oxoacyl-[acyl-carrier-protein] synthase, while the other subunit catalyses the reactions of EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, EC 2.3.1.39, [acyl-carrier-protein] S-malonyltransferase, EC 4.2.1.59, 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase, EC 1.3.1.10, enoyl-[acyl-carrier-protein] reductase (NADPH, Si-specific) and EC 1.1.1.279, (R)-3-hydroxyacid ester dehydrogenase. The enzyme differs from the animal enzyme (EC 2.3.1.85) in that the enoyl reductase domain requires FMN as a cofactor, and the ultimate product is an acyl-CoA (usually palmitoyl-CoA) instead of a free fatty acid.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
PDB,
CAS registry number: 94219-29-1
References:
1. Schweitzer, E., Kniep, B., Castorph, H. and Holzner, U. Pantetheine-free mutants of the yeast fatty-acid-synthetase complex. Eur. J. Biochem. 39 (1973) 353-362. [PMID: 4590449]
2. Wakil, S.J., Stoops, J.K. and Joshi, V.C. Fatty acid synthesis and its regulation. Annu. Rev. Biochem. 52 (1983) 537-579. [PMID: 6137188]
3. Tehlivets, O., Scheuringer, K. and Kohlwein, S.D. Fatty acid synthesis and elongation in yeast. Biochim. Biophys. Acta 1771 (2007) 255-270. [PMID: 16950653]
EC 2.3.1.230
Accepted name: 2-heptyl-4(1H)-quinolone synthase
Reaction: (1) 3-oxodecanoate + anthraniloyl-CoA = CoA + 2-heptyl-4(1H)-quinolone + CO2 + H2O
Glossary: 4-hydroxy-2(1H)-quinolone = 2,4-dihydroxyquinoline
Systematic name: malonyl-CoA:anthraniloyl-CoA C-acetyltransferase (decarboxylating)
Comments: The enzyme from the Gram-negative bacterium Pseudomonas aeruginosa is involved in the biosynthesis of 2-heptyl-4-hydroxyquinoline and 2,4-dihydroxyquinoline. 2-Heptyl-4-hydroxyquinoline is a signal molecule, that is involved in regulation of virulence factor production and biofilm formation. The enzyme shows a broad specificity and is involved in the synthesis of a wide array of additional 2-alkyl-4(1H)-quinolones synthesized by the organism.
References:
1. Zhang, Y.M., Frank, M.W., Zhu, K., Mayasundari, A. and Rock, C.O. PqsD is responsible for the synthesis of 2,4-dihydroxyquinoline, an extracellular metabolite produced by Pseudomonas aeruginosa. J. Biol. Chem. 283 (2008) 28788-28794. [PMID: 18728009]
2. Bera, A.K., Atanasova, V., Robinson, H., Eisenstein, E., Coleman, J.P., Pesci, E.C. and Parsons, J.F. Structure of PqsD, a Pseudomonas quinolone signal biosynthetic enzyme, in complex with anthranilate. Biochemistry 48 (2009) 8644-8655. [PMID: 19694421]
3. Pistorius, D., Ullrich, A., Lucas, S., Hartmann, R.W., Kazmaier, U. and Muller, R. Biosynthesis of 2-alkyl-4(1H)-quinolones in Pseudomonas aeruginosa: potential for therapeutic interference with pathogenicity. Chembiochem 12 (2011) 850-853. [PMID: 21425231]
4. Storz, M.P., Maurer, C.K., Zimmer, C., Wagner, N., Brengel, C., de Jong, J.C., Lucas, S., Musken, M., Haussler, S., Steinbach, A. and Hartmann, R.W. Validation of PqsD as an anti-biofilm target in Pseudomonas aeruginosa by development of small-molecule inhibitors. J. Am. Chem. Soc. 134 (2012) 16143-16146. [PMID: 22992202]
EC 2.3.1.231
Accepted name: tRNAPhe {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methoxycarbonyltransferase
Reaction: S-adenosyl-L-methionine + 7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37 in tRNAPhe + CO2 = S-adenosyl-L-homocysteine + wybutosine37 in tRNAPhe
For diagram of reaction, click here
Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW4 (ambiguous); tRNA-yW synthesizing enzyme-4 (ambiguous)
Systematic name: S-adenosyl-L-methionine:tRNAPhe {7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methyltransferase (carbon dioxide-adding)
Comments: The enzyme is found only in eukaryotes, where it is involved in the biosynthesis of wybutosine, a hypermodified tricyclic base found at position 37 of certain tRNAs. The modification is important for translational reading-frame maintenance. In some species that produce hydroxywybutosine the enzyme uses 7-[2-hydroxy-3-amino-3-(methoxycarbonyl)propyl]wyosine37 in tRNAPhe as substrate. The enzyme also has the activity of EC 2.1.1.290, tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase [2].
References:
1. Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142-2154. [PMID: 16642040]
2. Suzuki, Y., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. 37 (2009) 2910-2925. [PMID: 19287006]
3. Kato, M., Araiso, Y., Noma, A., Nagao, A., Suzuki, T., Ishitani, R. and Nureki, O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res. 39 (2011) 1576-1585. [PMID: 20972222]
*EC 2.4.1.161
Accepted name: oligosaccharide 4-α-D-glucosyltransferase
Reaction: Transfers the non-reducing terminal α-D-glucose residue from a (1→4)-α-D-glucan to the 4-position of a free glucose or of a glucosyl residue at the non-reducing terminus of a (1→4)-α-D-glucan, thus bringing about the rearrangement of oligosaccharides
Other name(s): amylase III; 1,4-α-glucan:1,4-α-glucan 4-α-glucosyltransferase; 1,4-α-D-glucan:1,4-α-D-glucan 4-α-D-glucosyltransferase; α-1,4-transglucosylase
Systematic name: (1→4)-α-D-glucan:(1→4)-α-D-glucan 4-α-D-glucosyltransferase
Comments: The enzyme acts on amylose, amylopectin, glycogen and maltooligosaccharides. No detectable free glucose is formed, indicating the enzyme does not act as a hydrolase. The enzyme from the bacterium Cellvibrio japonicus has the highest activity with maltotriose as a donor, and also accepts maltose [3], while the enzyme from amoeba does not accept maltose [1,2]. Oligosaccharides with 1→6 linkages cannot function as donors, but can act as acceptors [3]. Unlike EC 2.4.1.25, 4-α-glucanotransferase, this enzyme can transfer only a single glucosyl residue.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
CAS registry number: 9000-92-4
References:
1. Nebinger, P. Separation and characterization of four different amylases of Entamoeba histolytica. I. Purification and properties. Biol. Chem. Hoppe-Seyler 367 (1986) 161-167. [PMID: 2423097]
2. Nebinger, P. Separation and characterization of four different amylases of Entamoeba histolytica. II. Characterization of amylases. Biol. Chem. Hoppe-Seyler 367 (1986) 169-176. [PMID: 2423098]
3. Larsbrink, J., Izumi, A., Hemsworth, G.R., Davies, G.J. and Brumer, H. Structural enzymology of Cellvibrio japonicus Agd31B protein reveals α-transglucosylase activity in glycoside hydrolase family 31. J. Biol. Chem. 287 (2012) 43288-43299. [PMID: 23132856]
EC 2.4.1.310
Accepted name: vancomycin aglycone glucosyltransferase
Reaction: UDP-α-D-glucose + vancomycin aglycone = UDP + desvancoaminyl-vancomycin
For diagram of reaction, click here
Glossary: desvancoaminyl-vancomycin = vancomycin pseudoaglycone
Other name(s): GtfB (ambiguous)
Systematic name: UDP-α-D-glucose:vancomycin aglycone 48-O-β-glucosyltransferase
Comments: The enzyme from the bacterium Amycolatopsis orientalis is involved in the biosynthesis of the glycopeptide antibiotic chloroeremomycin.
References:
1. Losey, H.C., Peczuh, M.W., Chen, Z., Eggert, U.S., Dong, S.D., Pelczer, I., Kahne, D. and Walsh, C.T. Tandem action of glycosyltransferases in the maturation of vancomycin and teicoplanin aglycones: novel glycopeptides. Biochemistry 40 (2001) 4745-4755. [PMID: 11294642]
2. Mulichak, A.M., Losey, H.C., Walsh, C.T. and Garavito, R.M. Structure of the UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics. Structure 9 (2001) 547-557. [PMID: 11470430]
EC 2.4.1.311
Accepted name: chloroorienticin B synthase
Reaction: dTDP-β-L-4-epi-vancosamine + desvancosaminyl-vancomycin = dTDP + chloroorienticin B
For diagram of reaction, click here
Glossary: dTDP-β-L-4-epi-vancosamine = dTDP-3-amino-2,3,6-trideoxy-3-methyl-β-L-arabino-hexopyranose
Other name(s): GtfA
Systematic name: dTDP-L-4-epi-vancosamine:desvancosaminyl-vancomycin vancosaminyltransferase
Comments: The enzyme from the bacterium Amycolatopsis orientalis is involved in the biosynthesis of the glycopeptide antibiotic chloroeremomycin.
References:
1. Mulichak, A.M., Losey, H.C., Lu, W., Wawrzak, Z., Walsh, C.T. and Garavito, R.M. Structure of the TDP-epi-vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway. Proc. Natl. Acad. Sci. USA 100 (2003) 9238-9243. [PMID: 12874381]
2. Lu, W., Oberthur, M., Leimkuhler, C., Tao, J., Kahne, D. and Walsh, C.T. Characterization of a regiospecific epivancosaminyl transferase GtfA and enzymatic reconstitution of the antibiotic chloroeremomycin. Proc. Natl. Acad. Sci. USA 101 (2004) 4390-4395. [PMID: 15070728]
EC 2.4.1.312
Accepted name: protein O-mannose β-1,4-N-acetylglucosaminyltransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + 3-O-(α-D-mannosyl)-L-threonyl-[protein] = UDP + 3-O-[N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl]-L-threonyl-[protein]
Other name(s): GTDC2 (gene name); POMGNT2
Systematic name: UDP-N-acetyl-α-D-glucosamine:α-D-mannosyl-threonyl-[protein] 4-β-N-acetyl-D-glucosaminyltransferase
Comments: The human protein is involved in the formation of a phosphorylated trisaccharide on a threonine residue of α-dystroglycan, an extracellular peripheral glycoprotein that acts as a receptor for extracellular matrix proteins containing laminin-G domains.
References:
1. Yoshida-Moriguchi, T., Willer, T., Anderson, M.E., Venzke, D., Whyte, T., Muntoni, F., Lee, H., Nelson, S.F., Yu, L. and Campbell, K.P. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. Science 341 (2013) 896-899. [PMID: 23929950]
EC 2.4.1.313
Accepted name: protein O-mannose β-1,3-N-acetylgalactosaminyltransferase
Reaction: UDP-N-acetyl-α-D-galactosamine + 3-O-[N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl]-L-threonyl-[protein] = UDP + 3-O-[N-acetyl-β-D-galactosaminyl-(1→3)-N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl]-L-threonyl-[protein]
Other name(s): B3GALNT2
Systematic name: UDP-N-acetyl-α-D-galactosamine:N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl-threonyl-[protein] 3-β-N-acetyl-D-galactosaminyltransferase
Comments: The human protein is specific for UDP-N-acetyl-α-D-galactosamine as donor [1]. The enzyme is involved in the formation of a phosphorylated trisaccharide on a threonine residue of α-dystroglycan, an extracellular peripheral glycoprotein that acts as a receptor for extracellular matrix proteins containing laminin-G domains.
References:
1. Hiruma, T., Togayachi, A., Okamura, K., Sato, T., Kikuchi, N., Kwon, Y.D., Nakamura, A., Fujimura, K., Gotoh, M., Tachibana, K., Ishizuka, Y., Noce, T., Nakanishi, H. and Narimatsu, H. A novel human β1,3-N-acetylgalactosaminyltransferase that synthesizes a unique carbohydrate structure, GalNAcβ1-3GlcNAc. J. Biol. Chem. 279 (2004) 14087-14095. [PMID: 14724282]
2. Yoshida-Moriguchi, T., Willer, T., Anderson, M.E., Venzke, D., Whyte, T., Muntoni, F., Lee, H., Nelson, S.F., Yu, L. and Campbell, K.P. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. Science 341 (2013) 896-899. [PMID: 23929950]
EC 2.4.1.314
Accepted name: ginsenoside Rd glucosyltransferase
Reaction: UDP-α-D-glucose + ginsenoside Rd = UDP + ginsenoside Rb1
Glossary: ginsenoside Rd = 20-(β-D-glucopyranosyl)oxy-3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
Other name(s): UDPG:ginsenoside Rd glucosyltransferase; UDP-glucose:ginsenoside Rd glucosyltransferase; UGRdGT
Systematic name: UDP-glucose:ginsenoside-Rd β-1,6-glucosyltransferase
Comments: The glucosyl group forms a 1→6 bond to the glucosyloxy moiety at C-20 of ginsenoside Rd. Isolated from sanchi ginseng (Panax notoginseng).
References:
1. Yue, C.-J. and Zhong J.-J. Purification and characterization of UDPG:ginsenoside Rd glucosyltransferase from suspended cells of Panax notoginseng. Process Biochem. 40 (2005) 3742-3748.
EC 2.4.2.55
Accepted name: nicotinate D-ribonucleotide:phenol phospho-D-ribosyltransferase
Reaction: nicotinate D-ribonucleotide + phenol = nicotinate + phenyl 5-phospho-α-D-ribofuranoside
Other name(s): ArsAB
Systematic name: nicotinate D-ribonucleotide:phenol phospho-D-ribosyltransferase
Comments: The enzyme is involved in the biosynthesis of phenolic cobamides in the Gram-positive bacterium Sporomusa ovata. It can also transfer the phospho-D-ribosyl group to 4-methylphenol and 5,6-dimethylbenzimidazole. The related EC 2.4.2.21, nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase, also transfers the phospho-D-ribosyl group from nicotinate D-ribonucleotide to 5,6-dimethylbenzimidazole, but shows no activity with 4-methylphenol or phenol.
References:
1. Chan, C.H. and Escalante-Semerena, J.C. ArsAB, a novel enzyme from Sporomusa ovata activates phenolic bases for adenosylcobamide biosynthesis. Mol. Microbiol. 81 (2011) 952-967. [PMID: 21696461]
EC 2.4.2.56
Accepted name: kaempferol 3-O-xylosyltransferase
Reaction: UDP-α-D-xylose + kaempferol = UDP + kaempferol 3-O-β-D-xyloside
For diagram of reaction, click here
Other name(s): F3XT; UDP-D-xylose:flavonol 3-O-xylosyltransferase; flavonol 3-O-xylosyltransferase
Systematic name: UDP-α-D-xylose:kaempferol 3-O-D-xylosyltransferase
Comments: The enzyme from the plant Euonymus alatus also catalyses the 3-O-D-xylosylation of other flavonols (e.g. quercetin, isorhamnetin, rhamnetin, myricetin, fisetin) with lower activity.
References:
1. Ishikura, N. and Yang, Z.Q. UDP-D-xylose: flavonol 3-O-xylosyltransferase from young leaves of Euonymus alatus f. ciliato-dentatus. Z. Naturforsch. C: Biosci. 46 (1991) 1003-1010.
*EC 2.5.1.27
Accepted name: adenylate dimethylallyltransferase
Reaction: dimethylallyl diphosphate + AMP = diphosphate + N6-(dimethylallyl)adenosine 5′-phosphate
For diagram of reaction, click here
Other name(s): cytokinin synthase (ambiguous); isopentenyltransferase (ambiguous); 2-isopentenyl-diphosphate:AMP Δ2-isopentenyltransferase; adenylate isopentenyltransferase (ambiguous); IPT; adenylate dimethylallyltransferase
Systematic name: dimethylallyl-diphosphate:AMP dimethylallyltransferase
Comments: Involved in the biosynthesis of cytokinins in plants. Some isoforms from the plant Arabidopsis thaliana are specific for AMP while others also have the activity of EC 2.5.1.112, adenylate dimethylallyltransferase (ADP/ATP-dependent).
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
CAS registry number: 72840-95-0
References:
1. Chen, C.-M. and Melitz, D.K. Cytokinin biosynthesis in a cell-free system from cytokinin-autotrophic tobacco tissue cultures. FEBS Lett. 107 (1979) 15-20. [PMID: 499537]
2. Takei, K., Sakakibara, H. and Sugiyama, T. Identification of genes encoding adenylate isopentenyltransferase, a cytokinin biosynthesis enzyme, in Arabidopsis thaliana. J. Biol. Chem. 276 (2001) 26405-26410. [PMID: 11313355]
3. Sakano, Y., Okada, Y., Matsunaga, A., Suwama, T., Kaneko, T., Ito, K., Noguchi, H. and Abe, I. Molecular cloning, expression, and characterization of adenylate isopentenyltransferase from hop (Humulus lupulus L.). Phytochemistry 65 (2004) 2439-2446. [PMID: 15381407]
EC 2.5.1.112
Accepted name: adenylate dimethylallyltransferase (ADP/ATP-dependent)
Reaction: (1) dimethylallyl diphosphate + ADP = diphosphate + N6-(dimethylallyl)adenosine 5′-diphosphate
For diagram of reaction, click here
Other name(s): cytokinin synthase (ambiguous); isopentenyltransferase (ambiguous); 2-isopentenyl-diphosphate:ADP/ATP Δ2-isopentenyltransferase; adenylate isopentenyltransferase (ambiguous); dimethylallyl diphosphate:ATP/ADP isopentenyltransferase: IPT
Systematic name: dimethylallyl-diphosphate:ADP/ATP dimethylallyltransferase
Comments: Involved in the biosynthesis of cytokinins in plants. The IPT4 isoform from the plant Arabidopsis thaliana is specific for ADP and ATP [1]. Other isoforms, such as IPT1 from Arabidopsis thaliana [1,2] and the enzyme from the common hop, Humulus lupulus [3], also have a lower activity with AMP (cf. EC 2.5.1.27, adenylate dimethylallyltransferase).
References:
1. Kakimoto, T. Identification of plant cytokinin biosynthetic enzymes as dimethylallyl diphosphate:ATP/ADP isopentenyltransferases. Plant Cell Physiol 42 (2001) 677-685. [PMID: 11479373]
2. Takei, K., Sakakibara, H. and Sugiyama, T. Identification of genes encoding adenylate isopentenyltransferase, a cytokinin biosynthesis enzyme, in Arabidopsis thaliana. J. Biol. Chem. 276 (2001) 26405-26410. [PMID: 11313355]
3. Sakano, Y., Okada, Y., Matsunaga, A., Suwama, T., Kaneko, T., Ito, K., Noguchi, H. and Abe, I. Molecular cloning, expression, and characterization of adenylate isopentenyltransferase from hop (Humulus lupulus L.). Phytochemistry 65 (2004) 2439-2446. [PMID: 15381407]
EC 2.5.1.113
Accepted name: [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase
Reaction: O-phospho-L-serine + [CysO sulfur-carrier protein]-Gly-NH-CH2-C(O)SH = [CysO sulfur-carrier protein]-Gly-NH-CH2-C(O)-S-L-cysteine + phosphate
Other name(s): CysM
Systematic name: O-phospho-L-serine:thiocarboxylated [CysO sulfur-carrier protein] 2-amino-2-carboxyethyltransferase
Comments: A pyridoxal-phosphate protein. The enzyme participates in an alternative pathway for L-cysteine biosynthesis that involves a protein-bound thiocarboxylate as the sulfide donor. The enzyme from the bacterium Mycobacterium tuberculosis also has very low activity with O3-acetyl-L-serine (cf. EC 2.5.1.65, O-phosphoserine sulfhydrylase).
References:
1. O'Leary, S.E., Jurgenson, C.T., Ealick, S.E. and Begley, T.P. O-Phospho-L-serine and the thiocarboxylated sulfur carrier protein CysO-COSH are substrates for CysM, a cysteine synthase from Mycobacterium tuberculosis. Biochemistry 47 (2008) 11606-11615. [PMID: 18842002]
2. Jurgenson, C.T., Burns, K.E., Begley, T.P. and Ealick, S.E. Crystal structure of a sulfur carrier protein complex found in the cysteine biosynthetic pathway of Mycobacterium tuberculosis. Biochemistry 47 (2008) 10354-10364. [PMID: 18771296]
3. Ågren, D., Schnell, R., Oehlmann, W., Singh, M. and Schneider, G. Cysteine synthase (CysM) of Mycobacterium tuberculosis is an O-phosphoserine sulfhydrylase: evidence for an alternative cysteine biosynthesis pathway in mycobacteria. J. Biol. Chem. 283 (2008) 31567-31574. [PMID: 18799456]
4. Ågren, D., Schnell, R. and Schneider, G. The C-terminal of CysM from Mycobacterium tuberculosis protects the aminoacrylate intermediate and is involved in sulfur donor selectivity. FEBS Lett 583 (2009) 330-336. [PMID: 19101553]
EC 2.5.1.114
Accepted name: tRNAPhe (4-demethylwyosine37-C7) aminocarboxypropyltransferase
Reaction: S-adenosyl-L-methionine + 4-demethylwyosine37 in tRNAPhe = S-methyl-5′-thioadenosine + 7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine37 in tRNAPhe
For diagram of reaction, click here
Glossary: 4-demethylwyosine = imG-14 = 6-methyl-3-(β-D-ribofuranosyl)-3,5-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW2; tRNA-yW synthesizing enzyme-2; TRM12 (gene name); taw2 (gene name)
Systematic name: S-adenosyl-L-methionine:tRNAPhe (4-demethylwyosine37-C7)-[(3S)-3-amino-3-carboxypropyl]transferase
Comments: The enzyme, which is found in all eukaryotes and in the majority of Euryarchaeota (but not in the Crenarchaeota), is involved in the hypermodification of the guanine nucleoside at position 37 of tRNA leading to formation of assorted wye bases. This modification is essential for translational reading-frame maintenance.The eukaryotic enzyme is involved in biosynthesis of the tricyclic base wybutosine, which is found only in tRNAPhe.
References:
1. Umitsu, M., Nishimasu, H., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Proc. Natl. Acad. Sci. USA 106 (2009) 15616-15621. [PMID: 19717466]
2. Rodriguez, V., Vasudevan, S., Noma, A., Carlson, B.A., Green, J.E., Suzuki, T. and Chandrasekharappa, S.C. Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA. PLoS One 7 (2012) e39297. [PMID: 22761755]
3. de Crecy-Lagard, V., Brochier-Armanet, C., Urbonavicius, J., Fernandez, B., Phillips, G., Lyons, B., Noma, A., Alvarez, S., Droogmans, L., Armengaud, J. and Grosjean, H. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol Biol Evol 27 (2010) 2062-2077. [PMID: 20382657]
EC 2.6.1.103
Accepted name: (S)-3,5-dihydroxyphenylglycine transaminase
Reaction: (S)-3,5-dihydroxyphenylglycine + 2-oxoglutarate = 2-(3,5-dihydroxyphenyl)-2-oxoacetate + L-glutamate
Glossary: (S)-3,5-dihydroxyphenylglycine = (2S)-2-amino-2-(3,5-dihydroxyphenyl)acetic acid
Other name(s): HpgT
Systematic name: (S)-3,5-dihydroxyphenylglycine:2-oxoglutarate aminotransferase
Comments: A pyridoxal-5′-phosphate protein. The enzyme from the bacterium Amycolatopsis orientalis catalyses the reaction in the reverse direction as part of the biosynthesis of the (S)-3,5-dihydroxyphenylglycine constituent of the glycopeptide antibiotic chloroeremomycin.
References:
1. Sandercock, A.M., Charles, E.H., Scaife, W., Kirkpatrick, P.N., O'Brien, S.W., Papageorgiou, E.A., Spencer, J.B. and Williams, D.H. Biosynthesis of the di-meta-hydroxyphenylglycine constituent of the vancomycin-group antibiotic chloroeremomycin. Chem. Comm. (2001) 1252-1253.
*EC 2.7.1.107
Accepted name: diacylglycerol kinase (ATP)
Reaction: ATP + 1,2-diacyl-sn-glycerol = ADP + 1,2-diacyl-sn-glycerol 3-phosphate
Glossary: 1,2-diacyl-sn-glycerol 3-phosphate = phosphatidate
Other name(s): diglyceride kinase (ambiguous); 1,2-diacylglycerol kinase (phosphorylating) (ambiguous); 1,2-diacylglycerol kinase (ambiguous); sn-1,2-diacylglycerol kinase (ambiguous); DG kinase (ambiguous); DGK (ambiguous); ATP:diacylglycerol phosphotransferase; arachidonoyl-specific diacylglycerol kinase; diacylglycerol:ATP kinase; ATP:1,2-diacylglycerol 3-phosphotransferase; diacylglycerol kinase (ATP dependent)
Systematic name: ATP:1,2-diacyl-sn-glycerol 3-phosphotransferase
Comments: Involved in synthesis of membrane phospholipids and the neutral lipid triacylglycerol. Activity is stimulated by certain phospholipids [4,7]. In plants and animals the product 1,2-diacyl-sn-glycerol 3-phosphate is an important second messenger. cf. EC 2.7.1.174, diacylglycerol kinase (CTP).
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
PDB,
CAS registry number: 60382-71-0
References:
1. Hokin, L.E. and Hokin, M.R. Diglyceride kinase and other pathways for phosphatidic acid synthesis in the erythrocyte membrane. Biochim. Biophys. Acta 67 (1963) 470-484. [PMID: 13961253]
2. Weissbach, H., Thomas, E. and Kaback, H.R. Studies on the metabolism of ATP by isolated bacterial membranes: formation and metabolism of membrane-bound phosphatidic acid. Arch. Biochem. Biophys. 147 (1971) 249-254. [PMID: 4940043]
3. Daleo, G.R., Piras, M.M. and Piras, R. Diglyceride kinase activity of microtubules. Characterization and comparison with the protein kinase and ATPase activities associated with vinblastine-isolated tubulin of chick embryonic muscles. Eur. J. Biochem. 68 (1976) 339-346. [PMID: 185051]
4. Walsh, J.P. and Bell, R.M. sn-1,2-Diacylglycerol kinase of Escherichia coli. Structural and kinetic analysis of the lipid cofactor dependence. J. Biol. Chem. 261 (1986) 15062-15069. [PMID: 3021764]
5. Russ, E., Kaiser, U. and Sandermann, H., Jr. Lipid-dependent membrane enzymes. Purification to homogeneity and further characterization of diacylglycerol kinase from Escherichia coli. Eur. J. Biochem. 171 (1988) 335-342. [PMID: 2828054]
6. Walsh, J.P. and Bell, R.M. Diacylglycerol kinase from Escherichia coli. Methods Enzymol. 209 (1992) 153-162. [PMID: 1323028]
7. Wissing, J.B. and Wagner, K.G. Diacylglycerol kinase from suspension cultured plant cells : characterization and subcellular localization. Plant Physiol. 98 (1992) 1148-1153. [PMID: 16668739]
*EC 2.7.1.174
Accepted name: diacylglycerol kinase (CTP)
Reaction: CTP + 1,2-diacyl-sn-glycerol = CDP + 1,2-diacyl-sn-glycerol 3-phosphate
Glossary: 1,2-diacyl-sn-glycerol 3-phosphate = phosphatidate
Other name(s): DAG kinase; CTP-dependent diacylglycerol kinase; diglyceride kinase (ambiguous); DGK1 (gene name); diacylglycerol kinase (CTP dependent)
Systematic name: CTP:1,2-diacyl-sn-glycerol 3-phosphotransferase
Comments: Requires Ca2+ or Mg2+ for activity. Involved in synthesis of membrane phospholipids and the neutral lipid triacylglycerol. Unlike the diacylglycerol kinases from bacteria, plants, and animals [cf. EC 2.7.1.107, diacylglycerol kinase (ATP)], the enzyme from Saccharomyces cerevisiae utilizes CTP. The enzyme can also use dCTP, but not ATP, GTP or UTP.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc
References:
1. Han, G.S., O'Hara, L., Carman, G.M. and Siniossoglou, S. An unconventional diacylglycerol kinase that regulates phospholipid synthesis and nuclear membrane growth. J. Biol. Chem. 283 (2008) 20433-20442. [PMID: 18458075]
2. Han, G.S., O'Hara, L., Siniossoglou, S. and Carman, G.M. Characterization of the yeast DGK1-encoded CTP-dependent diacylglycerol kinase. J. Biol. Chem. 283 (2008) 20443-20453. [PMID: 18458076]
3. Fakas, S., Konstantinou, C. and Carman, G.M. DGK1-encoded diacylglycerol kinase activity is required for phospholipid synthesis during growth resumption from stationary phase in Saccharomyces cerevisiae. J. Biol. Chem. 286 (2011) 1464-1474. [PMID: 21071438]
EC 2.7.1.180
Accepted name: FAD:protein FMN transferase
Reaction: FAD + [protein]-L-threonine = [protein]-FMN-L-threonine + AMP
Glossary: FMN = flavin mononucleotide = riboflavin-5′-phosphate
Other name(s): flavin transferase; apbE (gene name)
Systematic name: FAD:protein riboflavin-5′-phosphate transferase
Comments: The enzyme catalyses the transfer of the FMN portion of FAD and its covalent binding to the hydroxyl group of an L-threonine residue in a target flavin-binding protein such as the B and C subunits of EC 1.6.5.8, NADH:ubiquinone reductase (Na+-transporting). Requires Mg2+.
References:
1. Bertsova, Y.V., Fadeeva, M.S., Kostyrko, V.A., Serebryakova, M.V., Baykov, A.A. and Bogachev, A.V. Alternative pyrimidine biosynthesis protein ApbE is a flavin transferase catalyzing covalent attachment of FMN to a threonine residue in bacterial flavoproteins. J. Biol. Chem. 288 (2013) 14276-14286. [PMID: 23558683]
*EC 2.7.4.21
Accepted name: inositol-hexakisphosphate kinase
Reaction: (1) ATP + 1D-myo-inositol hexakisphosphate = ADP + 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate
Other name(s): ATP:1D-myo-inositol-hexakisphosphate phosphotransferase; IP6K
Systematic name: ATP:1D-myo-inositol-hexakisphosphate 5-phosphotransferase
Comments: Three mammalian isoforms are known to exist.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
CAS registry number: 176898-37-6
References:
1. Saiardi, A., Erdjument-Bromage, H., Snowman, A.M., Tempst, P. and Snyder, S.H. Synthesis of diphosphoinositol pentakisphosphate by a newly identified family of higher inositol polyphosphate kinases. Curr. Biol. 9 (1999) 1323-1326. [PMID: 10574768]
2. Schell, M.J., Letcher, A.J., Brearley, C.A., Biber, J., Murer, H. and Irvine, R.F. PiUS (Pi uptake stimulator) is an inositol hexakisphosphate kinase. FEBS Lett. 461 (1999) 169-172. [PMID: 10567691]
3. Albert, C., Safrany, S.T., Bembenek, M.E., Reddy, K.M., Reddy, K.K., Falck, J.-R., Bröcker, M., Shears, S.B. and Mayr, G.W. Biological variability in the structures of diphosphoinositol polyphosphates in Dictyostelium discoideum and mammalian cells. Biochem. J. 327 (1997) 553-560. [PMID: 9359429]
4. Lin, H., Fridy, P.C., Ribeiro, A.A., Choi, J.H., Barma, D.K., Vogel, G., Falck, J.R., Shears, S.B., York, J.D. and Mayr, G.W. Structural analysis and detection of biological inositol pyrophosphates reveal that the family of VIP/diphosphoinositol pentakisphosphate kinases are 1/3-kinases. J. Biol. Chem. 284 (2009) 1863-1872. [PMID: 18981179]
5. Wang, H., Falck, J.R., Hall, T.M. and Shears, S.B. Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat. Chem. Biol. 8 (2012) 111-116. [PMID: 22119861]
EC 2.8.3.19
Accepted name: CoA:oxalate CoA-transferase
Reaction: acetyl-CoA + oxalate = acetate + oxalyl-CoA
Other name(s): acetyl-coenzyme A transferase; acetyl-CoA oxalate CoA-transferase; ACOCT; YfdE; UctC
Systematic name: acetyl-CoA:oxalate CoA-transferase
Comments: The enzymes characterized from the bacteria Escherichia coli and Acetobacter aceti can also use formyl-CoA and oxalate (EC 2.8.3.16, formyl-CoA transferase) or formyl-CoA and acetate, with significantly reduced specific activities.
References:
1. Mullins, E.A., Sullivan, K.L. and Kappock, T.J. Function and X-Ray crystal structure of Escherichia coli YfdE. PLoS One 8 (2013) e67901. [PMID: 23935849]
*EC 3.1.3.16
Accepted name: protein-serine/threonine phosphatase
Reaction: [a protein]-serine/threonine phosphate + H2O = [a protein]-serine/threonine + phosphate
Other name(s): phosphoprotein phosphatase (ambiguous); protein phosphatase-1; protein phosphatase-2A; protein phosphatase-2B; protein phosphatase-2C; protein D phosphatase; phosphospectrin phosphatase; casein phosphatase; Aspergillus awamori acid protein phosphatase; calcineurin; phosphatase 2A; phosphatase 2B; phosphatase II; phosphatase IB; phosphatase C-II; polycation modulated (PCM-) phosphatase; phosphopyruvate dehydrogenase phosphatase; phosphatase SP; branched-chain α-keto acid dehydrogenase phosphatase; BCKDH phosphatase; 3-hydroxy 3-methylglutaryl coenzymeA reductase phosphatase; HMG-CoA reductase phosphatase; phosphatase H-II; phosphatase III; phosphatase I; protein phosphatase; phosphatase IV; phosphoprotein phosphohydrolase
Systematic name: protein-serine/threonine-phosphate phosphohydrolase
Comments: A group of enzymes removing the serine- or threonine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes that have been phosphorylated under the action of a kinase (cf. EC 3.1.3.48 protein-tyrosine-phosphatase). The spleen enzyme also acts on phenolic phosphates and phosphamides (cf. EC 3.9.1.1, phosphoamidase).
Links to other databases:
BRENDA,
EXPASY,
KEGG,
Metacyc,
PDB,
CAS registry number: 9025-75-6
References:
1. Deutscher, J., Kessler, U. and Hengstenberg, W. Streptococcal phosphoenolpyruvate: sugar phosphotransferase system: purification and characterization of a phosphoprotein phosphatase which hydrolyzes the phosphoryl bond in seryl-phosphorylated histidine-containing protein. J. Bacteriol. 163 (1985) 1203-1209. [PMID: 2993239]
2. Ingebritsen, T.S. and Cohen, P. The protein phosphatases involved in cellular regulation. 1. Classification and substrate specificities. Eur. J. Biochem. 132 (1983) 255-261. [PMID: 6301824]
3. Sundarajan, T.A. and Sarma, P.S. Substrate specificity of phosphoprotein phosphatase from spleen. Biochem. J. 71 (1959) 537-544. [PMID: 13638262]
4. Tonks, N.K. and Cohen, P. The protein phosphatases involved in cellular regulation. Identification of the inhibitor-2 phosphatases in rabbit skeletal muscle. Eur. J. Biochem. 145 (1984) 65-70. [PMID: 6092084]
EC 3.2.1.187
Accepted name: (Ara-f)3-Hyp β-L-arabinobiosidase
Reaction: 4-O-(β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H2O = 4-O-(β-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranose
Glossary: 4-O-(β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline = (Ara-f)3-Hyp
Other name(s): hypBA2 (gene name); β-L-arabinobiosidase
Systematic name: 4-O-(β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranose hydrolase
Comments: The enzyme, which was identified in the bacterium Bifidobacterium longum JCM1217, is specific for (Ara-f)3-Hyp, a sugar chain found in hydroxyproline-rich glyoproteins such as extensin and lectin. The enzyme was not able to accept (Ara-f)2-Hyp or (Ara-f)4-Hyp as substrates. In the presence of 1-alkanols, the enzyme demonstrates transglycosylation activity, retaining the anomeric configuration of the arabinofuranose residue.
References:
1. Fujita, K., Sakamoto, S., Ono, Y., Wakao, M., Suda, Y., Kitahara, K. and Suganuma, T. Molecular cloning and characterization of a β-L-Arabinobiosidase in Bifidobacterium longum that belongs to a novel glycoside hydrolase family. J. Biol. Chem. 286 (2011) 5143-5150. [PMID: 21149454]
EC 3.2.1.188
Accepted name: avenacosidase
Reaction: avenacoside B + H2O = 26-desgluco-avenacoside B + D-glucose
For diagram of reaction, click here
Glossary: avenacoside B = (22S,25S)-3β-{β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-[α-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranosyloxy}-26-(β-D-glucopyranosyloxy)-22,25-epoxyfurost-5-ene
Other name(s): As-P60
Systematic name: avenacoside B 26-β-D-glucohydrolase
Comments: Isolated from oat (Avena sativa) seedlings. The product acts as a defense system against fungal infection. Also acts on avenacoside A.
References:
1. Gus-Mayer, S., Brunner, H., Schneider-Poetsch, H.A. and Rudiger, W. Avenacosidase from oat: purification, sequence analysis and biochemical characterization of a new member of the BGA family of β-glucosidases. Plant Mol. Biol. 26 (1994) 909-921. [PMID: 8000004]
2. Gus-Mayer, S., Brunner, H., Schneider-Poetsch, H.A., Lottspeich, F., Eckerskorn, C., Grimm, R. and Rudiger, W. The amino acid sequence previously attributed to a protein kinase or a TCP1-related molecular chaperone and co-purified with phytochrome is a β-glucosidase. FEBS Lett 347 (1994) 51-54. [PMID: 8013661]
EC 3.2.1.189
Accepted name: dioscin glycosidase (diosgenin-forming)
Reaction: 3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin + 3 H2O = D-glucose + 2 L-rhamnose + diosgenin
For diagram of reaction, click here
Glossary: 3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin = (3β,25R)-spirost-5-en-3-yl 6-deoxy-α-L-mannopyranosyl-(1→2)-[6-deoxy-α-L-mannopyranosyl-(1→4)]-β-D-glucopyranoside = dioscin
Other name(s): dioscin glycosidase (aglycone-forming)
Systematic name: 3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin hydrolase (diosgenin-forming)
Comments: The enzyme is involved in degradation of the steroid saponin dioscin by some fungi of the Absidia genus. The enzyme can also hydrolyse 3-O-[α-L-Ara-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin into diosgenin and free sugars as the final products. cf EC 3.2.1.190, dioscin glycosidase (3-O-β-D-Glc-diosgenin-forming).
References:
1. Fu, Y., Yu, H., Tang, S.H., Hu, X., Wang, Y., Liu, B., Yu, C. and Jin, F. New dioscin-glycosidase hydrolyzing multi-glycosides of dioscin from Absidia strain. J Microbiol Biotechnol 20 (2010) 1011-1017. [PMID: 20622501]
EC 3.2.1.190
Accepted name: dioscin glycosidase (3-O-β-D-Glc-diosgenin-forming)
Reaction: 3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin + 2 H2O = 2 L-rhamnopyranose + diosgenin 3-O-β-D-glucopyranoside
Glossary: 3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin = (3β,25R)-spirost-5-en-3-yl 6-deoxy-α-L-mannopyranosyl-(1→2)-[6-deoxy-α-L-mannopyranosyl-(1→4)]-β-D-glucopyranoside = dioscin
Other name(s): dioscin-α-L-rhamnosidase
Systematic name: 3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin (3-O-β-D-Glc-diosgenin-forming)
Comments: The enzyme is involved in the hydrolysis of the steroid saponin dioscin by the digestive system of Sus scrofa (pig). cf. EC 3.2.1.189, dioscin glycosidase (diosgenin-forming).
References:
1. Qian, S., Yu, H., Zhang, C., Lu, M., Wang, H. and Jin, F. Purification and characterization of dioscin-α-L-rhamnosidase from pig liver. Chem Pharm Bull (Tokyo) 53 (2005) 911-914. [PMID: 16079518]
*EC 3.2.2.5
Accepted name: NAD+ glycohydrolase
Reaction: NAD+ + H2O = ADP-D-ribose + nicotinamide
Glossary: ADP-D-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)
Other name(s): NAD glycohydrolase; nicotinamide adenine dinucleotide glycohydrolase; β-NAD+ glycohydrolase; DPNase (ambiguous); NAD hydrolase (ambiguous); diphosphopyridine nucleosidase (ambiguous); nicotinamide adenine dinucleotide nucleosidase (ambiguous); NAD nucleosidase (ambiguous); DPN hydrolase (ambiguous); NADase (ambiguous); nga (gene name)
Systematic name: NAD+ glycohydrolase
Comments: This enzyme catalyses the hydrolysis of NAD+, without associated ADP-ribosyl transferase or ADP-ribosyl cyclase activities (unlike the metazoan enzyme EC 3.2.2.6, bifunctional ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase). The enzyme from Group A streptococci has been implicated in the pathogenesis of diseases such as streptococcal toxic shock-like syndrome (STSS) and necrotizing fasciitis. The enzyme from the venom of the snake Agkistrodon acutus also catalyses EC 3.6.1.5, apyrase [3].
Links to other databases:
BRENDA,
EXPASY,
GTD,
KEGG,
Metacyc,
CAS registry number: 9025-46-1
References:
1. Fehrenbach, F.J. Reinigung und Kristallisation der NAD-Glykohydrolase aus C-Streptokokken. Eur. J. Biochem. 18 (1971) 94-102. [PMID: 4322210]
2. Grushoff, P.S., Shany, S. and Bernheimer, A.W. Purification and properties of streptococcal nicotinamide adenine dinucleotide glycohydrolase. J. Bacteriol. 122 (1975) 599-605. [PMID: 236282]
3. Zhang, L., Xu, X., Luo, Z., Shen, D. and Wu, H. Identification of an unusual AT(D)Pase-like activity in multifunctional NAD glycohydrolase from the venom of Agkistrodon acutus. Biochimie 91 (2009) 240-251. [PMID: 18952139]
4. Ghosh, J., Anderson, P.J., Chandrasekaran, S. and Caparon, M.G. Characterization of Streptococcus pyogenes β-NAD+ glycohydrolase: re-evaluation of enzymatic properties associated with pathogenesis. J. Biol. Chem. 285 (2010) 5683-5694. [PMID: 20018886]
5. Smith, C.L., Ghosh, J., Elam, J.S., Pinkner, J.S., Hultgren, S.J., Caparon, M.G. and Ellenberger, T. Structural basis of Streptococcus pyogenes immunity to its NAD+ glycohydrolase toxin. Structure 19 (2011) 192-202. [PMID: 21300288]
EC 3.3.2.13
Accepted name: chorismatase
Reaction: chorismate + H2O = (4R,5R)-4,5-dihydroxycyclohexa-1(6),2-diene-1-carboxylate + pyruvate
For diagram of reaction, click here
Glossary: chorismate = (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylate
Other name(s): chorismate/3,4-dihydroxycyclohexa-1,5-dienoate synthase; fkbO (gene name); rapK (gene name)
Systematic name: chorismate pyruvate-hydrolase
Comments: The enzyme found in several bacterial species is involved in the biosynthesis of macrocyclic polyketides.
References:
1. Andexer, J.N., Kendrew, S.G., Nur-e-Alam, M., Lazos, O., Foster, T.A., Zimmermann, A.S., Warneck, T.D., Suthar, D., Coates, N.J., Koehn, F.E., Skotnicki, J.S., Carter, G.T., Gregory, M.A., Martin, C.J., Moss, S.J., Leadlay, P.F. and Wilkinson, B. Biosynthesis of the immunosuppressants FK506, FK520, and rapamycin involves a previously undescribed family of enzymes acting on chorismate. Proc. Natl. Acad. Sci. USA 108 (2011) 4776-4781. [PMID: 21383123]
2. Juneja, P., Hubrich, F., Diederichs, K., Welte, W. and Andexer, J.N. Mechanistic implications for the chorismatase FkbO based on the crystal structure. J. Mol. Biol. (2013) . [PMID: 24036425]
EC 3.4.21.121
Accepted name: Lys-Lys/Arg-Xaa endopeptidase
Reaction: Cleavage of -Lys-Lys┼ and -Lys-Arg┼ bonds.
Other name(s): ASP (Aeromonas sobria)-type peptidase; Aeromonas extracellular serine protease
Comments: The enzyme is a serine peptidase, which has been shown to cleave prothrombin and prekallikrein. It hydrolyses the complement component C5 releasing complement component C5a.
References:
1. Kobayashi, H., Utsunomiya, H., Yamanaka, H., Sei, Y., Katunuma, N., Okamoto, K. and Tsuge, H. Structural basis for the kexin-like serine protease from Aeromonas sobria as sepsis-causing factor. J. Biol. Chem. 284 (2009) 27655-27663. [PMID: 19654332]
2. Nitta, H., Kobayashi, H., Irie, A., Baba, H., Okamoto, K. and Imamura, T. Activation of prothrombin by ASP, a serine protease released from Aeromonas sobria. FEBS Lett 581 (2007) 5935-5939. [PMID: 18067862]
3. Kobayashi, H., Takahashi, E., Oguma, K., Fujii, Y., Yamanaka, H., Negishi, T., Arimoto-Kobayashi, S., Tsuji, T. and Okamoto, K. Cleavage specificity of the serine protease of Aeromonas sobria, a member of the kexin family of subtilases. FEMS Microbiol. Lett. 256 (2006) 165-170. [PMID: 16487335]
4. Imamura, T., Nitta, H., Wada, Y., Kobayashi, H. and Okamoto, K. Impaired plasma clottability induction through fibrinogen degradation by ASP, a serine protease released from Aeromonas sobria. FEMS Microbiol. Lett. 284 (2008) 35-42. [PMID: 18462393]
5. Nitta, H., Imamura, T., Wada, Y., Irie, A., Kobayashi, H., Okamoto, K. and Baba, H. Production of C5a by ASP, a serine protease released from Aeromonas sobria. J. Immunol. 181 (2008) 3602-3608. [PMID: 18714034]
*EC 3.5.1.14
Accepted name: N-acyl-aliphatic-L-amino acid amidohydrolase
Reaction: (1) an N-acyl-aliphatic-L-amino acid + H2O = an aliphatic L-amino acid + a carboxylate
Glossary: N-acetyl-L-cysteine-S-conjugate = mercapturic acid
Other name(s): aminoacylase 1; aminoacylase I; dehydropeptidase II; histozyme; hippuricase; benzamidase; acylase I; hippurase; amido acid deacylase; L-aminoacylase; acylase; aminoacylase; L-amino-acid acylase; α-N-acylaminoacid hydrolase; long acyl amidoacylase; short acyl amidoacylase; ACY1 (gene name); N-acyl-L-amino-acid amidohydrolase
Systematic name: N-acyl-aliphatic-L-amino acid amidohydrolase (carboxylate-forming)
Comments: Contains Zn2+. The enzyme is found in animals and is involved in the hydrolysis of N-acylated or N-acetylated amino acids (except L-aspartate). It acts on mercapturic acids (S-conjugates of N-acetyl-L-cysteine) and neutral aliphatic N-acyl-α-amino acids .Some bacterial aminoacylases demonstrate substrate specificity of both EC 3.5.1.14 and EC 3.5.1.114. cf. EC 3.5.1.15, aspartoacylase and EC 3.5.1.114, N-acyl-aromatic-L-amino acid amidohydrolase.
Links to other databases:
BRENDA,
EXPASY,
GTD,
KEGG,
Metacyc,
PDB,
CAS registry number: 9012-37-7
References:
1. Birnbaum, S.M., Levintow, L., Kingsley, R.B. and Greenstein, J.P. Specificity of amino acid acylases. J. Biol. Chem. 194 (1952) 455-470. [PMID: 14927637]
2. Fones, W.S. and Lee, M. Hydrolysis of N-acyl derivatives of alanine and phenylalanine by acylase I and carboxypeptidase. J. Biol. Chem. 201 (1953) 847-856. [PMID: 13061423]
3. Henseling, J. and Rohm, K.H. Aminoacylase I from hog kidney: anion effects and the pH dependence of kinetic parameters. Biochim. Biophys. Acta 959 (1988) 370-377. [PMID: 3355856]
4. Heese, D., Berger, S. and Rohm, K.H. Nuclear magnetic relaxation studies of the role of the metal ion in Mn2+-substituted aminoacylase I. Eur. J. Biochem. 188 (1990) 175-180. [PMID: 2318199]
5. Palm, G.J. and Rohm, K.H. Aminoacylase I from porcine kidney: identification and characterization of two major protein domains. J. Protein Chem. 14 (1995) 233-240. [PMID: 7662111]
6. Uttamsingh, V., Keller, D.A. and Anders, M.W. Acylase I-catalyzed deacetylation of N-acetyl-L-cysteine and S-alkyl-N-acetyl-L-cysteines. Chem. Res. Toxicol. 11 (1998) 800-809. [PMID: 9671543]
7. Lindner, H., Hopfner, S., Tafler-Naumann, M., Miko, M., Konrad, L. and Rohm, K.H. The distribution of aminoacylase I among mammalian species and localization of the enzyme in porcine kidney. Biochimie 82 (2000) 129-137. [PMID: 10727768]
EC 3.5.1.114
Accepted name: N-acyl-aromatic-L-amino acid amidohydrolase
Reaction: (1) an N-acyl-aromatic-L-amino acid + H2O = an aromatic-L-amino acid + a carboxylate
Glossary: N-acetyl-L-cysteine-S-conjugate = mercapturic acid
Other name(s): aminoacylase 3; aminoacylase III; ACY3 (gene name)
Systematic name: N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)
Comments: This enzyme is found in animals and is involved in the hydrolysis of N-acylated or N-acetylated amino acids (except L-aspartate). It preferentially deacetylates Nα-acetylated aromatic amino acids and mercapturic acids (S-conjugates of N-acetyl-L-cysteine) that are usually not deacetylated by EC 3.5.1.14, N-acyl-aliphatic-L-amino acid amidohydrolase. The enzyme is significantly activated by Co2+ and Ni2+ [3]. Some bacterial aminoacylases demonstrate substrate specificity for both EC 3.5.1.14 and EC 3.5.1.114. cf. EC 3.5.1.14, N-acyl-aliphatic-L-amino acid amidohydrolase and EC 3.5.1.15, aspartoacylase.
References:
1. Pushkin, A., Carpenito, G., Abuladze, N., Newman, D., Tsuprun, V., Ryazantsev, S., Motemoturu, S., Sassani, P., Solovieva, N., Dukkipati, R. and Kurtz, I. Structural characterization, tissue distribution, and functional expression of murine aminoacylase III. Am. J. Physiol. Cell Physiol. 286 (2004) C848-C856. [PMID: 14656720]
2. Newman, D., Abuladze, N., Scholz, K., Dekant, W., Tsuprun, V., Ryazantsev, S., Bondar, G., Sassani, P., Kurtz, I. and Pushkin, A. Specificity of aminoacylase III-mediated deacetylation of mercapturic acids. Drug Metab. Dispos. 35 (2007) 43-50. [PMID: 17012540]
3. Tsirulnikov, K., Abuladze, N., Newman, D., Ryazantsev, S., Wolak, T., Magilnick, N., Koag, M.C., Kurtz, I. and Pushkin, A. Mouse aminoacylase 3: a metalloenzyme activated by cobalt and nickel. Biochim. Biophys. Acta 1794 (2009) 1049-1057. [PMID: 19362172]
4. Hsieh, J.M., Tsirulnikov, K., Sawaya, M.R., Magilnick, N., Abuladze, N., Kurtz, I., Abramson, J. and Pushkin, A. Structures of aminoacylase 3 in complex with acetylated substrates. Proc. Natl. Acad. Sci. USA 107 (2010) 17962-17967. [PMID: 20921362]
5. Tsirulnikov, K., Abuladze, N., Bragin, A., Faull, K., Cascio, D., Damoiseaux, R., Schibler, M.J. and Pushkin, A. Inhibition of aminoacylase 3 protects rat brain cortex neuronal cells from the toxicity of 4-hydroxy-2-nonenal mercapturate and 4-hydroxy-2-nonenal. Toxicol. Appl. Pharmacol. 263 (2012) 303-314. [PMID: 22819785]
EC 3.5.1.115
Accepted name: mycothiol S-conjugate amidase
Reaction: a mycothiol S-conjugate + H2O = an N-acetyl L-cysteine-S-conjugate + 1-O-(2-amino-2-deoxy-α-D-glucopyranosyl)-1D-myo-inositol
Glossary: mycothiol = 1-O-[2-(N2-acetyl-L-cysteinamido)-2-deoxy-α-D-glucopyranosyl]-1D-myo-inositol
Other name(s): MCA
Systematic name: mycothiol S-conjugate 1D-myo-inositol 2-amino-2-deoxy-α-D-glucopyranosyl-hydrolase
Comments: The enzyme that is found in actinomycetes is involved in the detoxification of oxidizing agents and electrophilic antibiotics. The enzyme has low activity with 1-O-(2-acetamido-2-deoxy-α-D-glucopyranosyl)-1D-myo-inositol as substrate (cf. EC 3.5.1.103, N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-α-D-glucopyranoside deacetylase) [2].
References:
1. Newton, G.L., Av-Gay, Y. and Fahey, R.C. A novel mycothiol-dependent detoxification pathway in mycobacteria involving mycothiol S-conjugate amidase. Biochemistry 39 (2000) 10739-10746. [PMID: 10978158]
2. Steffek, M., Newton, G.L., Av-Gay, Y. and Fahey, R.C. Characterization of Mycobacterium tuberculosis mycothiol S-conjugate amidase. Biochemistry 42 (2003) 12067-12076. [PMID: 14556638]
EC 3.5.3.26
Accepted name: (S)-ureidoglycine aminohydrolase
Reaction: (S)-2-ureidoglycine + H2O = (S)-ureidoglycolate + NH3
Other name(s): UGlyAH; UGHY; ylbA (gene name)
Systematic name: (S)-ureidoglycine aminohydrolase
Comments: Binds Mn2+. This enzyme, found in plants and bacteria, is part of the ureide pathway, which enables the recycling of the nitrogen in purine compounds. In plants it is localized in the endoplasmic reticulum.
References:
1. Serventi, F., Ramazzina, I., Lamberto, I., Puggioni, V., Gatti, R. and Percudani, R. Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria. ACS Chem. Biol. 5 (2010) 203-214. [PMID: 20038185]
2. Werner, A.K., Romeis, T. and Witte, C.P. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat. Chem. Biol. 6 (2010) 19-21. [PMID: 19935661]
3. Shin, I., Percudani, R. and Rhee, S. Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana. J. Biol. Chem. 287 (2012) 18796-18805. [PMID: 22493446]
EC 3.6.1.66
Accepted name: XTP/dITP diphosphatase
Reaction: (1) XTP + H2O = XMP + diphosphate
Other name(s): hypoxanthine/xanthine dNTP pyrophosphatase; rdgB (gene name)
Systematic name: XTP/dITP diphosphohydrolase (diphosphate-forming)
Comments: The enzymes from the bacterium Escherichia coli and the archaea Methanococcus jannaschii and Archaeoglobus fulgidus are highly specific for XTP and dITP. The activity is dependent on divalent cations, Mg2+ is preferred.
References:
1. Chung, J.H., Back, J.H., Park, Y.I. and Han, Y.S. Biochemical characterization of a novel hypoxanthine/xanthine dNTP pyrophosphatase from Methanococcus jannaschii. Nucleic Acids Res. 29 (2001) 3099-3107. [PMID: 11452035]
2. Chung, J.H., Park, H.Y., Lee, J.H. and Jang, Y. Identification of the dITP- and XTP-hydrolyzing protein from Escherichia coli. J. Biochem. Mol. Biol. 35 (2002) 403-408. [PMID: 12297000]
EC 4.1.3.45
Accepted name: 3-hydroxybenzoate synthase
Reaction: chorismate = 3-hydroxybenzoate + pyruvate
For diagram of reaction, click here
Glossary: chorismate = (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylate
Other name(s): chorismatase/3-hydroxybenzoate synthase; hyg5 (gene name); bra8 (gene name); XanB2
Systematic name: chorismate pyruvate-lyase (3-hydroxybenzoate-forming)
Comments: The enzyme, found in several bacterial species is involved in biosynthesis of secondary products. The enzyme from the bacterium Xanthomonas campestris pv. campestris also has the activity of EC 4.1.3.40, chorismate lyase [3].
References:
1. Andexer, J.N., Kendrew, S.G., Nur-e-Alam, M., Lazos, O., Foster, T.A., Zimmermann, A.S., Warneck, T.D., Suthar, D., Coates, N.J., Koehn, F.E., Skotnicki, J.S., Carter, G.T., Gregory, M.A., Martin, C.J., Moss, S.J., Leadlay, P.F. and Wilkinson, B. Biosynthesis of the immunosuppressants FK506, FK520, and rapamycin involves a previously undescribed family of enzymes acting on chorismate. Proc. Natl. Acad. Sci. USA 108 (2011) 4776-4781. [PMID: 21383123]
2. Jiang, Y., Wang, H., Lu, C., Ding, Y., Li, Y. and Shen, Y. Identification and characterization of the cuevaene A biosynthetic gene cluster in Streptomyces sp. LZ35. ChemBioChem. 14 (2013) 1468-1475. [PMID: 23824670]
3. Zhou, L., Wang, J.Y., Wang, J., Poplawsky, A., Lin, S., Zhu, B., Chang, C., Zhou, T., Zhang, L.H. and He, Y.W. The diffusible factor synthase XanB2 is a bifunctional chorismatase that links the shikimate pathway to ubiquinone and xanthomonadins biosynthetic pathways. Mol. Microbiol. 87 (2013) 80-93. [PMID: 23113660]
EC 4.3.1.29
Accepted name: D-glucosaminate-6-phosphate ammonia lyase
Reaction: 6-phospho-D-glucosaminate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + NH3
Other name(s): DgaE
Systematic name: D-glucosaminate-6-phosphate ammonia-lyase (2-dehydro-3-deoxy-6-phospho-D-gluconate-forming)
Comments: The enzyme, from the bacterium Salmonella typhimurium, is involved in the degradation pathway of D-glucosaminate.
References:
1. Miller, K.A., Phillips, R.S., Mrazek, J. and Hoover, T.R. Salmonella utilizes D-glucosaminate via a mannose family phosphotransferase system permease and associated enzymes. J. Bacteriol. 195 (2013) 4057-4066. [PMID: 23836865]
EC 5.1.3.27
Accepted name: dTDP-4-dehydro-6-deoxy-D-glucose 3-epimerase
Reaction: dTDP-4-dehydro-6-deoxy-α-D-glucose = dTDP-4-dehydro-6-deoxy-α-D-gulose
For diagram of reaction, click here
Glossary: dTDP-4-dehydro-6-deoxy-α-D-gulose = dTDP-4-dehydro-6-deoxy-α-D-allose
Other name(s): dTDP-deoxyglucose 3-epimerase; dTDP-4-keto-6-deoxy-D-glucose 3-epimerase; dTDP-4-keto-6-deoxyglucose 3-epimerase; gerF (gene name); tylJ (gene name); chmJ (gene name); mydH (gene name)
Systematic name: dTDP-4-dehydro-6-deoxy-α-D-glucose 3-epimerase
Comments: The enzyme is involved in the biosynthetic pathway of dTDP-6-deoxy-α-D-allose, which is converted to mycinose after attachment to the aglycones of several macrolide antibiotics, including tylosin, chalcomycin, dihydrochalcomycin, and mycinamicin II.
References:
1. Sohng, J.K., Kim, H.J., Nam, D.H., Lim, D.O., Han, J.M., Lee, H.J. and Yoo, J.C. Cloning, expression, and biological function of a dTDP-deoxyglucose epimerase (gerF) gene from Streptomyces sp. GERI-155. Biotechnol. Lett. 26 (2004) 185-191. [PMID: 15049360]
2. Thuy, T.T., Liou, K., Oh, T.J., Kim, D.H., Nam, D.H., Yoo, J.C. and Sohng, J.K. Biosynthesis of dTDP-6-deoxy-β-D-allose, biochemical characterization of dTDP-4-keto-6-deoxyglucose reductase (GerKI) from Streptomyces sp. KCTC 0041BP. Glycobiology 17 (2007) 119-126. [PMID: 17053005]
3. Kubiak, R.L., Phillips, R.K., Zmudka, M.W., Ahn, M.R., Maka, E.M., Pyeatt, G.L., Roggensack, S.J. and Holden, H.M. Structural and functional studies on a 3′-epimerase involved in the biosynthesis of dTDP-6-deoxy-D-allose. Biochemistry 51 (2012) 9375-9383. [PMID: 23116432]
*EC 5.3.1.3
Accepted name: D-arabinose isomerase
Reaction: D-arabinose = D-ribulose
Other name(s): D-arabinose(L-fucose) isomerase; L-fucose isomerase; D-arabinose ketol-isomerase; arabinose isomerase (misleading)
Systematic name: D-arabinose aldose-ketose-isomerase
Comments: Requires a divalent metal ion (the enzyme from the bacterium Escherichia coli prefers Mn2+). The enzyme binds the closed form of the sugar and catalyses ring opening to generate a form of open-chain conformation that facilitates the isomerization reaction, which proceeds via an ene-diol mechanism [3]. The enzyme catalyses the aldose-ketose isomerization of several sugars. Most enzymes also catalyse the reaction of EC 5.3.1.25, L-fucose isomerase [3]. The enzyme from the bacterium Falsibacillus pallidus also converts D-altrose to D-psicose [4]. cf. EC 5.3.1.4, L-arabinose isomerase.
Links to other databases:
BRENDA,
EXPASY,
GTD,
KEGG,
Metacyc,
CAS registry number: 9023-81-8
References:
1. Cohen, S.S. Studies on D-ribulose and its enzymatic conversion to D-arabinose. J. Biol. Chem. 201 (1953) 71-84. [PMID: 13044776]
2. Green, M. and Cohen, S.S. Enzymatic conversion of L-fucose to L-fuculose. J. Biol. Chem. 219 (1956) 557-568. [PMID: 13319278]
3. Seemann, J.E. and Schulz, G.E. Structure and mechanism of L-fucose isomerase from Escherichia coli. J. Mol. Biol. 273 (1997) 256-268. [PMID: 9367760]
4. Takeda, K., Yoshida, H., Izumori, K. and Kamitori, S. X-ray structures of Bacillus pallidus D-arabinose isomerase and its complex with L-fucitol. Biochim. Biophys. Acta 1804 (2010) 1359-1368. [PMID: 20123133]
EC 5.5.1.24
Accepted name: tocopherol cyclase
Reaction: (1) δ-tocopherol = 2-methyl-6-phytylbenzene-1,4-diol
For diagram of tocopherol biosynthesis, click here or tocotrienol biosynthesis click here
Other name(s): VTE1 (gene name); SXD1 (gene name)
Systematic name: δ/γ-tocopherol lyase (decyclizing)
Comments: The enzyme has been described from plants and cyanobacteria. It has similar activity with all four listed benzoquinol substrates. Involved in the biosynthesis of vitamin E tocopherols and tocotrienols.
References:
1. Porfirova, S., Bergmuller, E., Tropf, S., Lemke, R. and Dormann, P. Isolation of an Arabidopsis mutant lacking vitamin E and identification of a cyclase essential for all tocopherol biosynthesis. Proc. Natl. Acad. Sci. USA 99 (2002) 12495-12500. [PMID: 12213958]
2. Sattler, S.E., Cahoon, E.B., Coughlan, S.J. and DellaPenna, D. Characterization of tocopherol cyclases from higher plants and cyanobacteria. Evolutionary implications for tocopherol synthesis and function. Plant Physiol. 132 (2003) 2184-2195. [PMID: 12913173]
(2) linoleate + O2 = (8E,10S,12Z)-10-hydroperoxyoctadeca-8,12-dienoate
(3) α-linolenate + O2 = (8E,10S,12Z,15Z)-10-hydroperoxyoctadeca-8,12,15-trienoate
(2) (25R)-cholest-5-ene-3β,26-diol + NADPH + H+ + O2 = (25R)-cholest-5-ene-3β,7α,26-triol + NADP+ + H2O
protopanaxadiol = dammar-24-ene-3β,12β,20-triol
protopanaxatriol = dammar-24-ene-3β,6α,12β,20-tetrol
wybutosine = yW = 7-[(3S)-3-(methoxycarbonyl)-3-(methoxycarbonylamino)propyl]-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
(2) S-adenosyl-L-methionine + (R)-reticuline = S-adenosyl-L-homocysteine + (R)-laudanine
(R)-reticuline = (1R)-1-[(3-hydroxy-4-methoxyphenyl)methyl]-6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-ol
(S)-laudanine = 5-[((1S)-6,7-dimethoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-1-yl)methyl]-2-methoxyphenol
(R)-laudanine = 5-[((1R)-6,7-dimethoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-1-yl)methyl]-2-methoxyphenol
carminomycin = (1S,3S)-3-acetyl-3,5,10,12-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranoside = (1S,3S)-3-acetyl-3,5,10,12-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydronaphthacen-1-yl 3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranoside
carubicin = (1S,3S)-3-acetyl-3,5,12-trihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranoside
= (8S,10S)-8-acetyl-10-[(3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranosyl)oxy]-6,8,11-trihydroxy-1-methoxy-7,8,9,10-tetrahydronaphthacene-5,12-dione
tryprostatin A = (3S,8aS)-3-{[6-methoxy-2-(3-methylbut-2-en-1-yl)-1H-indol-3-yl]methyl}hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
(2) malonyl-CoA + anthraniloyl-CoA = 2 CoA + 4-hydroxy-2(1H)-quinolone + CO2
2-heptyl-4(1H)-quinolone = 2-heptyl-4-hydroxyquinoline
anthraniloyl-CoA = 2-aminobenzoyl-CoA
wybutosine = yW = 7-{(3S)-3-(methoxycarbonyl)-3-(methoxycarbonylamino)propyl}-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
desvancosaminyl-vancomycin = vanomycin pseudoaglycone
ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
(2) dimethylallyl diphosphate + ATP = diphosphate + N6-(dimethylallyl)adenosine 5′-triphosphate
7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine = yW-89
(2) ATP + 1D-myo-inositol 1-diphosphate pentakisphosphate = ADP + 1D-myo-inositol 1,5-bis(diphosphate) 2,3,4,6-tetrakisphosphate
26-desgluco-avenacoside B = (22S,25S)-3β-{β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-[α-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranosyloxy}-22,25-epoxyfurost-5-en-26-ol
diosgenin = (3β,25R)-spirost-5-en-3-ol
diosgenin = (3β,25R)-spirost-5-en-3-ol
(2) an N-acetyl-L-cysteine-S-conjugate + H2O = an L-cysteine-S-conjugate + acetate
(2) an N-acetyl-L-cysteine-S-conjugate + H2O = an L-cysteine-S-conjugate + acetate
N-acetyl L-cysteine-S-conjugate = mercapturic acid
(2) dITP + H2O = dIMP + diphosphate
(2) γ-tocopherol = 2,3-dimethyl-6-phytylbenzene-1,4-diol
(3) δ-tocotrienol = 6-geranylgeranyl-2-methylbenzene-1,4-diol
(4) γ-tocotrienol = 6-geranylgeranyl-2,3-dimethylbenzene-1,4-diol
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