Many thanks to those of you who have submitted details of new or missing enzymes, or updates to existing enzymes.
An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: (S,S)-butanediol dehydrogenase
Reaction: (2S,3S)-butane-2,3-diol + NAD+ = (S)-acetoin + NADH + H+
Other name(s): L-butanediol dehydrogenase; L-BDH; L(+)-2,3-butanediol dehydrogenase (L-acetoin forming); (S)-acetoin reductase [(S,S)-butane-2,3-diol forming]
Systematic name: (S,S)-butane-2,3-diol:NAD+ oxidoreductase
Comments: This enzyme catalyses the reversible reduction of (S)-acetoin to (S,S)-butane-2,3-diol. It can also catalyse the irreversible reduction of diacetyl to (S)-acetoin.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:
References:
1. Taylor, M.B. and Juni, E. Stereoisomeric specificities of 2,3-butanediol dehydrogenase. Biochim. Biophys. Acta 39 (1960) 448-457. [PMID: 13837186]
2. Carballo, J., Martin, R., Bernardo, A. and Gonzalez, J. Purification, characterization and some properties of diacetyl(acetoin) reductase from Enterobacter aerogenes. Eur. J. Biochem. 198 (1991) 327-332. [PMID: 2040298]
3. Takusagawa, Y., Otagiri, M., Ui, S., Ohtsuki, T., Mimura, A., Ohkuma, M. and Kudo, T. Purification and characterization of L-2,3-butanediol dehydrogenase of Brevibacterium saccharolyticum C-1012 expressed in Escherichia coli. Biosci. Biotechnol. Biochem. 65 (2001) 1876-1878. [PMID: 11577733]
Accepted name: D-arabitol-phosphate dehydrogenase
Reaction: D-arabitol 1-phosphate + NAD+ = D-xylulose 5-phosphate + NADH + H+
Other name(s): APDH; D-arabitol 1-phosphate dehydrogenase; D-arabitol 5-phosphate dehydrogenase
Systematic name: D-arabitol-phosphate:NAD+ oxidoreductase
Comments: This enzyme participates in arabitol catabolism. The enzyme also converts D-arabitol 5-phosphate to D-ribulose 5-phosphate at a lower rate [1].
References:
1. Povelainen, M., Eneyskaya, E.V., Kulminskaya, A.A., Ivanen, D.R., Kalkkinen, N., Neustroev, K.N. and Miasnikov, A.N. Biochemical and genetic characterization of a novel enzyme of pentitol metabolism: D-arabitol-phosphate dehydrogenase. Biochem. J. 371 (2003) 191-197. [PMID: 12467497]
Accepted name: 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase
Reaction: 2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate + NAD(P)+ = 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + NAD(P)H + H+
For diagram of reaction, click here
Other name(s): 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase; MjaRED; MJ0671 (gene name)
Systematic name: 2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate:NAD(P)+ oxidoreductase
Comments: The reaction proceeds in the opposite direction. A step in riboflavin biosynthesis, NADPH and NADH function equally well as reductant. Differs from EC 1.1.1.193 (5-amino-6-(5-phosphoribosylamino)uracil reductase) since it does not catalyse the reduction of 5-amino-6-ribosylaminopyrimidine-2,4(1H,3H)-dione 5'-phosphate [1].
References:
1. Graupner, M., Xu, H. and White, R.H. The pyrimidine nucleotide reductase step in riboflavin and F420 biosynthesis in archaea proceeds by the eukaryotic route to riboflavin. J. Bacteriol. 184 (2002) 1952-1957. [PMID: 11889103]
2. Chatwell, L., Krojer, T., Fidler, A., Romisch, W., Eisenreich, W., Bacher, A., Huber, R. and Fischer, M. Biosynthesis of riboflavin: structure and properties of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase of Methanocaldococcus jannaschii. J. Mol. Biol. 359 (2006) 1334-1351. [PMID: 16730025]
Accepted name: diacetyl reductase [(R)-acetoin forming]
Reaction: (R)-acetoin + NAD+ = diacetyl + NADH + H+
Other name(s): (R)-acetoin dehydrogenase
Systematic name: (R)-acetoin:NAD+ oxidoreductase
Comments: The reaction is catalysed in the reverse direction. This activity is usually associated with butanediol dehydrogenase activity (EC 1.1.1.4 or EC 1.1.1.76). While the butanediol dehydrogenase activity is reversible, diacetyl reductase activity is irreversible. This enzyme has been reported in the yeast Saccharomyces cerevisiae [1,2]. Different from EC 1.1.1.304, diacetyl reductase [(S)-acetoin forming].
References:
1. Heidlas, J. and Tressl, R. Purification and characterization of a (R)-2,3-butanediol dehydrogenase from Saccharomyces cerevisiae. Arch. Microbiol. 154 (1990) 267-273. [PMID: 2222122]
2. Gonzalez, E., Fernandez, M.R., Larroy, C., Sola, L., Pericas, M.A., Pares, X. and Biosca, J.A. Characterization of a (2R,3R)-2,3-butanediol dehydrogenase as the Saccharomyces cerevisiae YAL060W gene product. Disruption and induction of the gene. J. Biol. Chem. 275 (2000) 35876-35885. [PMID: 10938079]
Accepted name: diacetyl reductase [(S)-acetoin forming]
Reaction: (S)-acetoin + NAD+ = diacetyl + NADH + H+
Other name(s): (S)-acetoin dehydrogenase
Systematic name: ((S)-acetoin:NAD+ oxidoreductase
Comments: The reaction is catalysed in the reverse direction. This activity is usually associated with butanediol dehydrogenase activity (EC 1.1.1.4 or EC 1.1.1.76). While the butanediol dehydrogenase activity is reversible, diacetyl reductase activity is irreversible. This enzyme has been reported in the bacteria Geobacillus stearothermophilus. Enterobacter aerogenes and Klebsiella pneumoniae [1-3]. Different from EC 1.1.1.303, diacetyl reductase [(R)-acetoin forming].
References:
1. Giovannini, P.P., Medici, A., Bergamini, C.M. and Rippa, M. Properties of diacetyl (acetoin) reductase from Bacillus stearothermophilus. Bioorg. Med. Chem. 4 (1996) 1197-1201. [PMID: 8879540]
2. Carballo, J., Martin, R., Bernardo, A. and Gonzalez, J. Purification, characterization and some properties of diacetyl(acetoin) reductase from Enterobacter aerogenes. Eur. J. Biochem. 198 (1991) 327-332. [PMID: 2040298]
3. Ui, S., Okajima, Y., Mimura, A., Kanai, H., Kobayashi, T., Kudo, T. Sequence analysis of the gene for and characterization of D-acetoin forming meso-2,3-butanediol dehydrogenase of Klebsiella pneumoniae expressed in Escherichia coli. J. Ferment. Bioeng. 83 (1997) 32-37.
Accepted name: long-chain-alcohol oxidase
Reaction: a long-chain alcohol + O2 = a long-chain aldehyde + H2O2
Other name(s): long-chain fatty alcohol oxidase; fatty alcohol oxidase; fatty alcohol:oxygen oxidoreductase; long-chain fatty acid oxidase
Systematic name: long-chain-alcohol:oxygen oxidoreductase
Comments: Oxidizes long-chain fatty alcohols; best substrate is dodecyl alcohol.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 129430-50-8
References:
1. Moreau, R.A. and Huang, A.H.C. Oxidation of fatty alcohol in the cotyledons of jojoba seedlings. Arch. Biochem. Biophys. 194 (1979) 422-430. [PMID: 36040]
2. Moreau, R.A. and Huang, A.H.C. Enzymes of wax ester catabolism in jojoba. Methods Enzymol. 71 (1981) 804-813.
3. Cheng, Q., Liu, H.T., Bombelli, P., Smith, A. and Slabas, A.R. Functional identification of AtFao3, a membrane bound long chain alcohol oxidase in Arabidopsis thaliana. FEBS Lett. 574 (2004) 62-68. [PMID: 15358540]
4. Zhao, S., Lin, Z., Ma, W., Luo, D. and Cheng, Q. Cloning and characterization of long-chain fatty alcohol oxidase LjFAO1 in Lotus japonicus. Biotechnol. Prog. 24 (2008) 773-779. [PMID: 18396913]
5. Cheng, Q., Sanglard, D., Vanhanen, S., Liu, H.T., Bombelli, P., Smith, A. and Slabas, A.R. Candida yeast long chain fatty alcohol oxidase is a c-type haemoprotein and plays an important role in long chain fatty acid metabolism. Biochim. Biophys. Acta 1735 (2005) 192-203. [PMID: 16046182]
Accepted name: formate dehydrogenase-N
Reaction: formate + a quinone = CO2 + a quinol
Other name(s): Fdh-N; FdnGHI; nitrate-inducible formate dehydrogenase; formate dehydrogenase N; FDH-N; nitrate inducible Fdn; nitrate inducible formate dehydrogenase
Systematic name: formate:quinone oxidoreductase
Comments: The enzyme contains molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters and two heme b groups. Formate dehydrogenase-N oxidizes formate in the periplasm, transferring electrons via the menaquinone pool in the cytoplasmic membrane to a dissimilatory nitrate reductase (EC 1.7.5.1), which transfers electrons to nitrate in the cytoplasm. The system generates proton motive force under anaerobic conditions [3].
References:
1. Enoch, H.G. and Lester, R.L. The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli. J. Biol. Chem. 250 (1975) 6693-6705. [PMID: 1099093]
2. Jormakka, M., Tornroth, S., Byrne, B. and Iwata, S. Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Science 295 (2002) 1863-1868. [PMID: 11884747]
3. Jormakka, M., Tornroth, S., Abramson, J., Byrne, B. and Iwata, S. Purification and crystallization of the respiratory complex formate dehydrogenase-N from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 58 (2002) 160-162. [PMID: 11752799]
Accepted name: cyclic alcohol dehydrogenase (quinone)
Reaction: a cyclic alcohol + a quinone = a cyclic ketone + a quinol
Other name(s): cyclic alcohol dehydrogenase; MCAD
Systematic name: cyclic alcohol:quinone oxidoreductase
Comments: This enzyme oxidizes a wide variety of cyclic alcohols. Some minor enzyme activity is found with aliphatic secondary alcohols and sugar alcohols, but not primary alcohols. The enzyme is unable to catalyse the reverse reaction of cyclic ketones or aldehydes to cyclic alcohols. This enzyme differs from EC 1.1.5.5, alcohol dehydrogenase (quinone), which shows activity with ethanol [1].
References:
1. Moonmangmee, D., Fujii, Y., Toyama, H., Theeragool, G., Lotong, N., Matsushita, K. and Adachi, O. Purification and characterization of membrane-bound quinoprotein cyclic alcohol dehydrogenase from Gluconobacter frateurii CHM 9. Biosci. Biotechnol. Biochem. 65 (2001) 2763-2772. [PMID: 11826975]
Accepted name: formate dehydrogenase (acceptor)
Reaction: formate + acceptor = CO2 + reduced acceptor
Other name(s): FDHH; FDH-H; FDH-O; formate dehydrogenase H; formate dehydrogenase O
Systematic name: formate:acceptor oxidoreductase
Comments: Formate dehydrogenase H is a cytoplasmic enzyme that oxidizes formate without oxygen transfer, transferring electrons to a hydrogenase. The two enzymes form the formate-hydrogen lyase complex [1]. The enzyme contains an [4Fe-4S] cluster, a selenocysteine residue and a molybdopterin cofactor [1].
References:
1. Axley, M.J., Grahame, D.A. and Stadtman, T.C. Escherichia coli formate-hydrogen lyase. Purification and properties of the selenium-dependent formate dehydrogenase component. J. Biol. Chem. 265 (1990) 18213-18218. [PMID: 2211698]
2. Gladyshev, V.N., Boyington, J.C., Khangulov, S.V., Grahame, D.A., Stadtman, T.C. and Sun, P.D. Characterization of crystalline formate dehydrogenase H from Escherichia coli. Stabilization, EPR spectroscopy, and preliminary crystallographic analysis. J. Biol. Chem. 271 (1996) 8095-8100. [PMID: 8626495]
3. Khangulov, S.V., Gladyshev, V.N., Dismukes, G.C. and Stadtman, T.C. Selenium-containing formate dehydrogenase H from Escherichia coli: a molybdopterin enzyme that catalyzes formate oxidation without oxygen transfer. Biochemistry 37 (1998) 3518-3528. [PMID: 9521673]
Accepted name: 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+)
Reaction: 3,4-didehydroadipyl-CoA semialdehyde + NADP+ + H2O = 3,4-didehydroadipyl-CoA + NADPH + H+
Other name(s): BoxD; 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
Systematic name: 3,4-didehydroadipyl-CoA semialdehyde:NADP+ oxidoreductase
Comments: This enzyme catalyses a step in the aerobic benzoyl-coenzyme A catabolic pathway in Azoarcus evansii and Burkholderia xenovorans.
References:
1. Gescher, J., Ismail, W., Olgeschlager, E., Eisenreich, W., Worth, J. and Fuchs, G. Aerobic benzoyl-coenzyme A (CoA) catabolic pathway in Azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase. J. Bacteriol. 188 (2006) 2919-2927. [PMID: 16585753]
2. Bains, J. and Boulanger, M.J. Structural and biochemical characterization of a novel aldehyde dehydrogenase encoded by the benzoate oxidation pathway in Burkholderia xenovorans LB400. J. Mol. Biol. 379 (2008) 597-608. [PMID: 18462753]
Accepted name: 2-formylbenzoate dehydrogenase
Reaction: 2-formylbenzoate + NAD+ + H2O = o-phthalic acid + NADH + H+
Glossary: o-phthalic acid = benzene-1,2-dicarboxylic acid
2-formylbenzoate = 2-carboxybenzaldehyde
Other name(s): 2-carboxybenzaldehyde dehydrogenase; 2CBAL dehydrogenase; PhdK
Systematic name: 2-formylbenzoate:NAD+ oxidoreductase
Comments: The enzyme is involved in phenanthrene degradation.
References:
1. Iwabuchi, T. and Harayama, S. Biochemical and genetic characterization of 2-carboxybenzaldehyde dehydrogenase, an enzyme involved in phenanthrene degradation by Nocardioides sp. strain KP7. J. Bacteriol. 179 (1997) 6488-6494. [PMID: 9335300]
2. Kiyohara, H., Nagao, K. and Yano, K. Isolation and some properties of NAD-linked 2-carboxybenzaldehyde dehydrogenase in Alcaligenes faecalis AFK 2 grown on phenanthrene. J. Gen. Appl. Microbiol. 27 (1981) 443-455.
Accepted name: 7-chloro-L-tryptophan oxidase
Reaction: 7-chloro-L-tryptophan + O2 = 2-imino-3-(7-chloroindol-3-yl)propanoate + H2O2
For diagram of reaction, click here
Other name(s): RebO
Systematic name: 7-chloro-L-tryptophan:oxygen oxidoreductase
Comments: Contains a noncovalently bound FAD [1,2]. This enzyme catalyses a step in the biosynthesis of rebeccamycin, an indolocarbazole alkaloid produced by the Actinobacterium Lechevalieria aerocolonigenes. During catalysis, the bound FAD is reoxidized at the expense of molecular oxygen, producing one molecule of hydrogen peroxide. The enzyme shows significant preference for 7-chloro-L-tryptophan over L-tryptophan [1].
References:
1. Nishizawa, T., Aldrich, C.C. and Sherman, D.H. Molecular analysis of the rebeccamycin L-amino acid oxidase from Lechevalieria aerocolonigenes ATCC 39243. J. Bacteriol. 187 (2005) 2084-2092. [PMID: 15743957]
2. Howard-Jones, A.R. and Walsh, C.T. Enzymatic generation of the chromopyrrolic acid scaffold of rebeccamycin by the tandem action of RebO and RebD. Biochemistry 44 (2005) 15652-15663. [PMID: 16313168]
EC 1.4.5 with a quinone or similar compound as acceptor
Accepted name: D-amino acid dehydrogenase (quinone)
Reaction: a D-amino acid + H2O + a quinone = a 2-oxo acid + NH3 + a quinol
Other name(s): DadA
Systematic name: D-amino acid:quinone oxidoreductase (deaminating)
Comments: An iron-sulfur flavoprotein (FAD). This enzyme may be the same as EC 1.4.99.1.
References:
1. Olsiewski, P.J., Kaczorowski, G.J. and Walsh, C. Purification and properties of D-amino acid dehydrogenase, an inducible membrane-bound iron-sulfur flavoenzyme from Escherichia coli B. J. Biol. Chem. 255 (1980) 4487-4494. [PMID: 6102989]
2. Tanigawa, M., Shinohara, T., Saito, M., Nishimura, K., Hasegawa, Y., Wakabayashi, S., Ishizuka, M. and Nagata, Y. D. Amino acid dehydrogenase from Helicobacter pylori NCTC 11637. Amino Acids 38 (2010) 247-255. [PMID: 19212808]
Accepted name: D-proline dehydrogenase
Reaction: D-proline + oxidized acceptor + H2O = 1-pyrroline-2-carboxylate + reduced acceptor
Other name(s): D-Pro DH; D-Pro dehydrogenase; dye-linked D-proline dehydrogenase
Systematic name: D-proline:acceptor oxidoreductase
Comments: A flavoprotein (FAD). The enzyme prefers D-proline and acts on other D-amino acids with lower efficiency.
References:
1. Tani, Y., Tanaka, K., Yabutani, T., Mishima, Y., Sakuraba, H., Ohshima, T. and Motonaka, J. Development of a D-amino acids electrochemical sensor based on immobilization of thermostable D-proline dehydrogenase within agar gel membrane. Anal Chim Acta 619 (2008) 215-220. [PMID: 18558115]
2. Satomura, T., Kawakami, R., Sakuraba, H. and Ohshima, T. Dye-linked D-proline dehydrogenase from hyperthermophilic archaeon Pyrobaculum islandicum is a novel FAD-dependent amino acid dehydrogenase. J. Biol. Chem. 277 (2002) 12861-12867. [PMID: 11823469]
Accepted name: factor-independent urate hydroxylase
Reaction: urate + O2 + H2O = 5-hydroxyisourate + H2O2
For diagram of reaction, click here
Other name(s): uric acid oxidase; uricase; uricase II; urate oxidase
Systematic name: urate:oxygen oxidoreductase
Comments: This enzyme was previously thought to be a copper protein, but it is now known that the enzymes from soy bean (Glycine max), the mould Aspergillus flavus and Bacillus subtilis contains no copper nor any other transition-metal ion. The 5-hydroxyisourate formed decomposes spontaneously to form allantoin and CO2, although there is an enzyme-catalysed pathway in which EC 3.5.2.17, hydroxyisourate hydrolase, catalyses the first step. The enzyme is different from EC 1.14.13.113 (FAD-dependent urate hydroxylase).
Links to other databases: BRENDA, EXPASY, KEGG, PDB, UM-BBD, CAS registry number: 9002-12-4
References:
1. London, M. and Hudson, P.B. Purification and properties of solubilized uricase. Biochim. Biophys. Acta 21 (1956) 290-298. [PMID: 13363909]
2. Mahler, H.R., Hübscher, G. and Baum, H. Studies on uricase. I. Preparation, purification, and properties of a cuproprotein. J. Biol. Chem. 216 (1955) 625-641. [PMID: 13271340]
3. Robbins, K.C., Barnett, E.L. and Grant, N.H. Partial purification of porcine liver uricase. J. Biol. Chem. 216 (1955) 27-35. [PMID: 13252004]
4. Kahn, K. and Tipton, P.A. Spectroscopic characterization of intermediates in the urate oxidase reaction. Biochemistry 37 (1998) 11651-11659. [PMID: 9709003]
5. Colloc'h, N., el Hajji, M., Bachet, B., L'Hermite, G., Schiltz, M., Prange, T., Castro, B. and Mornon, J.-P. Crystal structure of the protein drug urate oxidase-inhibitor complex at 2.05 Å resolution. Nat. Struct. Biol. 4 (1997) 947-952. [PMID: 9360612]
6. Imhoff, R.D., Power, N.P., Borrok, M.J. and Tipton, P.A. General base catalysis in the urate oxidase reaction: evidence for a novel Thr-Lys catalytic diad. Biochemistry 42 (2003) 4094-4100. [PMID: 12680763]
EC 1.7.5 With a quinone or similar compound as acceptor
Accepted name: nitrate reductase (quinone)
Reaction: nitrate + a quinol = nitrite + a quinone + H2O
Other name(s): nitrate reductase A; nitrate reductase Z; NarGHI; quinol/nitrate oxidoreductase; quinol-nitrate oxidoreductase; quinol:nitrate oxidoreductase; NarA; NarZ; NarGHI; dissimilatory nitrate reductase
Systematic name: nitrite:quinone oxidoreductase
Comments: A membrane-bound enzyme which supports anaerobic respiration on nitrate under anaerobic conditions and in the presence of nitrate. Contains the bicyclic form of the molybdo-bis(molybdopterin guanine dinucleotide) cofactor, iron-sulfur clusters and heme b. Escherichia coli expresses two forms NarA and NarZ, both being comprised of three subunits.
References:
1. Enoch, H.G. and Lester, R.L. The role of a novel cytochrome b-containing nitrate reductase and quinone in the in vitro reconstruction of formate-nitrate reductase activity of E. coli. Biochem. Biophys. Res. Commun. 61 (1974) 1234-1241. [PMID: 4616697]
2. Bertero, M.G., Rothery, R.A., Palak, M., Hou, C., Lim, D., Blasco, F., Weiner, J.H. and Strynadka, N.C. Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat. Struct. Biol. 10 (2003) 681-687. [PMID: 12910261]
3. Lanciano, P., Magalon, A., Bertrand, P., Guigliarelli, B. and Grimaldi, S. High-stability semiquinone intermediate in nitrate reductase A (NarGHI) from Escherichia coli is located in a quinol oxidation site close to heme bD. Biochemistry 46 (2007) 5323-5329. [PMID: 17439244]
4. Bertero, M.G., Rothery, R.A., Boroumand, N., Palak, M., Blasco, F., Ginet, N., Weiner, J.H. and Strynadka, N.C. Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A. J. Biol. Chem. 280 (2005) 14836-14843. [PMID: 15615728]
5. Bonnefoy, V. and Demoss, J.A. Nitrate reductases in Escherichia coli. Antonie Van Leeuwenhoek 66 (1994) 47-56. [PMID: 7747940]
6. Guigliarelli, B., Asso, M., More, C., Augier, V., Blasco, F., Pommier, J., Giordano, G. and Bertrand, P. EPR and redox characterization of iron-sulfur centers in nitrate reductases A and Z from Escherichia coli. Evidence for a high-potential and a low-potential class and their relevance in the electron-transfer mechanism. Eur. J. Biochem. 207 (1992) 61-68. [PMID: 1321049]
Accepted name: hydrazine oxidoreductase
Reaction: hydrazine + acceptor = N2 + reduced acceptor
Other name(s): HAO (ambiguous; cf. EC 1.7.3.4 hydroxylamine oxidase)
Systematic name: hydrazine:acceptor oxidoreductase
Comments: The enzyme is involved in the pathway of anaerobic ammonium oxidation in anammox bacteria. The conversion of hydroxylamine by the enzyme from Brocadia anammoxidans results in the formation of NO and N2O [1]. Hydroxylamine is not a substrate for the enzyme from planctomycete KSU-1 [2].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9075-43-8
References:
1. Schalk, J., de Vries, S., Kuenen, J.G. and Jetten, M.S. Involvement of a novel hydroxylamine oxidoreductase in anaerobic ammonium oxidation. Biochemistry 39 (2000) 5405-5412. [PMID: 10820012]
2. Jetten, M.S., Wagner, M., Fuerst, J., van Loosdrecht, M., Kuenen, G. and Strous, M. Microbiology and application of the anaerobic ammonium oxidation ('anammox') process. Curr. Opin. Biotechnol. 12 (2001) 283-288. [PMID: 11404106]
Accepted name: glutathione amide reductase
Reaction: 2 glutathione amide + NAD+ = glutathione amide disulfide + NADH + H+
Other name(s): GAR
Systematic name: glutathione amide:NAD+ oxidoreductase
Comments: A dimeric flavoprotein (FAD). The enzyme restores glutathione amide disulfide, which is produced during the reduction of peroxide by EC 1.11.1.17 (glutathione amide-dependent peroxidase), back to glutathione amide (it catalyses the reaction in the opposite direction to that shown). The enzyme belongs to the family of flavoprotein disulfide oxidoreductases, but unlike other members of the family, which are specific for NADPH, it prefers NADH [1].
References:
1. Vergauwen, B., Pauwels, F., Jacquemotte, F., Meyer, T.E., Cusanovich, M.A., Bartsch, R.G. and Van Beeumen, J.J. Characterization of glutathione amide reductase from Chromatium gracile. Identification of a novel thiol peroxidase (Prx/Grx) fueled by glutathione amide redox cycling. J. Biol. Chem. 276 (2001) 20890-20897. [PMID: 11399772]
2. Vergauwen, B., Van Petegem, F., Remaut, H., Pauwels, F. and Van Beeumen, J.J. Crystallization and preliminary X-ray crystallographic analysis of glutathione amide reductase from Chromatium gracile. Acta Crystallogr. D Biol. Crystallogr. 58 (2002) 339-340. [PMID: 11807270]
Accepted name: glutathione amide-dependent peroxidase
Reaction: 2 glutathione amide + H2O2 = glutathione amide disulfide + 2 H2O
Systematic name: glutathione amide:hydrogen-peroxide oxidoreductase
Comments: This enzyme, which has been characterized from the proteobacterium Marichromatium gracile, is a chimeric protein, containing a peroxiredoxin-like N-terminus and a glutaredoxin-like C terminus. The enzyme has peroxidase activity towards hydrogen peroxide and several small alkyl hydroperoxides, and is thought to represent an early adaptation for fighting oxidative stress [1]. The glutathione amide disulfide produced by this enzyme can be restored to glutathione amide by EC 1.8.1.16 (glutathione amide reductase).
References:
1. Vergauwen, B., Pauwels, F., Jacquemotte, F., Meyer, T.E., Cusanovich, M.A., Bartsch, R.G. and Van Beeumen, J.J. Characterization of glutathione amide reductase from Chromatium gracile. Identification of a novel thiol peroxidase (Prx/Grx) fueled by glutathione amide redox cycling. J. Biol. Chem. 276 (2001) 20890-20897. [PMID: 11399772]
Accepted name: 1,2-dihydroxynaphthalene dioxygenase
Reaction: 1,2-dihydroxynaphthalene + O2 = 2-hydroxy-2H-chromene-2-carboxylate
For diagram of reaction, click here
Other name(s): 1,2-DHN dioxygenase; DHNDO; 1,2-dihydroxynaphthalene oxygenase
Systematic name: 1,2-dihydroxynaphthalene:oxygen oxidoreductase
Comments: This enzyme is involved in naphthalene degradation. Requires Fe2+.
References:
1. Kuhm, A.E., Stolz, A., Ngai, K.L. and Knackmuss, H.J. Purification and characterization of a 1,2-dihydroxynaphthalene dioxygenase from a bacterium that degrades naphthalenesulfonic acids. J. Bacteriol. 173 (1991) 3795-3802. [PMID: 2050635]
2. Keck, A., Conradt, D., Mahler, A., Stolz, A., Mattes, R. and Klein, J. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152 (2006) 1929-1940. [PMID: 16804169]
3. Patel, T.R. and Barnsley, E.A. Naphthalene metabolism by pseudomonads: purification and properties of 1,2-dihydroxynaphthalene oxygenase. J. Bacteriol. 143 (1980) 668-673. [PMID: 7204331]
Accepted name: dichloroarcyriaflavin A synthase
Reaction: dichlorochromopyrrolate + 3 O2 + 3 NADH + 3 H+ = dichloroarcyriaflavin A + 2 CO2 + 4 H2O + 3 NAD+
For diagram of reaction, click here
Glossary: dichloro-arcyriaflavin A = rebeccamycin aglycone
Systematic name: dichlorochromopyrrolate,NADH:oxygen 2,5-oxidoreductase (dichloroarcyriaflavin A-forming)
Comments: The conversion of dichlorochromopyrrolate to dichloroarcyriaflavin A is a complex process that involves two enzyme components. RebP is an NAD-dependent cytochrome P450 oxygenase that performs an aryl-aryl bond formation yielding the six-ring indolocarbazole scaffold [1]. Along with RebC, a flavin-dependent hydroxylase, it also catalyses the oxidative decarboxylation of both carboxyl groups. The presence of RebC ensures that the only product is the rebeccamycin aglycone dichloroarcyriaflavin A [2]. The enzymes are similar, but not identical, to StaP and StaC, which are involved in the synthesis of staurosporine [3].
References:
1. Makino, M., Sugimoto, H., Shiro, Y., Asamizu, S., Onaka, H. and Nagano, S. Crystal structures and catalytic mechanism of cytochrome P450 StaP that produces the indolocarbazole skeleton. Proc. Natl. Acad. Sci. USA 104:1159 (2007). [PMID: 17606921]
2. Howard-Jones, A.R. and Walsh, C.T. Staurosporine and rebeccamycin aglycones are assembled by the oxidative action of StaP, StaC, and RebC on chromopyrrolic acid. J. Am. Chem. Soc. 128:1228 (2006). [PMID: 16967980]
3. Sanchez, C., Zhu, L., Brana, A.F., Salas, A.P., Rohr, J., Mendez, C. and Salas, J.A. Combinatorial biosynthesis of antitumor indolocarbazole compounds. Proc. Natl. Acad. Sci. USA 102:461 (2005). [PMID: 15625109]
Accepted name: benzoyl-CoA 2,3-dioxygenase
Reaction: benzoyl-CoA + NADPH + H+ + O2 = 2,3-dihydro-2,3-dihydroxybenzoyl-CoA + NADP+
Other name(s): benzoyl-CoA dioxygenase/reductase; BoxBA; BoxA/BoxB system
Systematic name: benzoyl-CoA,NADPH:oxygen oxidoreductase (2,3-hydroxylating)
Comments: The enzyme is involved in aerobic benzoate metabolism in Azoarcus evansii. BoxB functions as the oxygenase part of benzoyl-CoA oxygenase in conjunction with BoxA, the reductase component, which upon binding of benzoyl-CoA, transfers two electrons to the ring in the course of dioxygenation. BoxA is a homodimeric 46 kDa iron-sulfur-flavoprotein (FAD), BoxB is a monomeric iron-protein [1].
References:
1. Zaar, A., Gescher, J., Eisenreich, W., Bacher, A. and Fuchs, G. New enzymes involved in aerobic benzoate metabolism in Azoarcus evansii. Mol. Microbiol. 54 (2004) 223-238. [PMID: 15458418]
2. Gescher, J., Zaar, A., Mohamed, M., Schagger, H. and Fuchs, G. Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii. J. Bacteriol. 184 (2002) 6301-6315. [PMID: 12399500]
3. Mohamed, M.E., Zaar, A., Ebenau-Jehle, C. and Fuchs, G. Reinvestigation of a new type of aerobic benzoate metabolism in the proteobacterium Azoarcus evansii. J. Bacteriol. 183 (2001) 1899-1908. [PMID: 11222587]
Accepted name: methanesulfonate monooxygenase
Reaction: methanesulfonate + NADH + H+ + O2 = formaldehyde + NAD+ + sulfite + H2O
Glossary: methanesulfonate = CH3-SO3-
formaldehyde = H-CHO
Other name(s): mesylate monooxygenase; mesylate,reduced-FMN:oxygen oxidoreductase; MsmABC; methanesulfonic acid monooxygenase; MSA monooxygenase; MSAMO; methanesulfonate,FMNH2:oxygen oxidoreductase
Systematic name: methanesulfonate,NADH:oxygen oxidoreductase
Comments: A flavoprotein. Methanesulfonate is the simplest of the sulfonates and is a substrate for the growth of certain methylotrophic microorganisms. Compared with EC 1.14.14.5, alkanesulfonate monooxygenase, this enzyme has a restricted substrate range that includes only the short-chain aliphatic sulfonates (methanesulfonate to butanesulfonate) and excludes all larger molecules, such as arylsulfonates [1]. The enzyme from the bacterium Methylosulfonomonas methylovora is a multicomponent system comprising a hydroxylase, a reductase (MsmD; EC 1.5.1.29, FMN reductase) and a ferredoxin (MsmC). The hydroxylase has both large (MsmA) and small (MsmB) subunits, with each large subunit containing a Rieske-type [2Fe-2S] centre.
References:
1. de Marco, P., Moradas-Ferreira, P., Higgins, T.P., McDonald, I., Kenna, E.M. and Murrell, J.C. Molecular analysis of a novel methanesulfonic acid monooxygenase from the methylotroph Methylosulfonomonas methylovora. J. Bacteriol. 181 (1999) 2244-2251. [PMID: 10094704]
2. Higgins, T.P., Davey, M., Trickett, J., Kelly, D.P. and Murrell, J.C. Metabolism of methanesulfonic acid involves a multicomponent monooxygenase enzyme. Microbiology 142 (1996) 251-260. [PMID: 8932698]
Accepted name: 3-epi-6-deoxocathasterone 23-monooxygenase
Reaction: (1) 3-epi-6-deoxocathasterone + NADPH + H+ + O2 = 6-deoxotyphasterol + NADP+ + H2O
(2) (22S,24R)-22-hydroxy-5α-ergostan-3-one + NADPH + H+ + O2 = 3-dehydro-6-deoxoteasterone + NADP+ + H2O
Other name(s): cytochrome P450 90C1; CYP90D1; CYP90C1
Systematic name: 3-epi-6-deoxocathasterone,NADPH:oxygen oxidoreductase (C-23-hydroxylating)
Comments: This enzyme is involved in brassinosteroid biosynthesis. C-23 hydroxylation shortcuts bypass campestanol, 6-deoxocathasterone, and 6-deoxoteasterone and lead directly from (22S,24R)-22-hydroxy-5α-ergostan-3-one and 3-epi-6-deoxocathasterone to 3-dehydro-6-deoxoteasterone and 6-deoxotyphasterol [1].
References:
1. Ohnishi, T., Szatmari, A.M., Watanabe, B., Fujita, S., Bancos, S., Koncz, C., Lafos, M., Shibata, K., Yokota, T., Sakata, K., Szekeres, M. and Mizutani, M. C-23 hydroxylation by Arabidopsis CYP90C1 and CYP90D1 reveals a novel shortcut in brassinosteroid biosynthesis. Plant Cell 18 (2006) 3275-3288. [PMID: 17138693]
Accepted name: FAD-dependent urate hydroxylase
Reaction: urate + NADH + H+ + O2 = 5-hydroxyisourate + NAD+ + H2O
Other name(s): HpxO enzyme; FAD-dependent urate oxidase; urate hydroxylase
Systematic name: urate,NADH:oxygen oxidoreductase (5-hydroxyisourate forming)
Comments: A flavoprotein. The reaction is part of the purine catabolic pathway in the bacterium Klebsiella pneumoniae. The enzyme is different from EC 1.7.3.3, factor-independent urate hydroxylase, found in most plants, which produces hydrogen peroxide. The product of the enzyme is a substrate for EC 3.5.2.17, hydroxyisourate hydrolase.
References:
1. O'Leary, S.E., Hicks, K.A., Ealick, S.E. and Begley, T.P. Biochemical characterization of the HpxO enzyme from Klebsiella pneumoniae, a novel FAD-dependent urate oxidase. Biochemistry 48 (2009) 3033-3035. [PMID: 19260710]
[EC 1.14.14.6 Transferred entry: methanesulfonate monooxygenase. Now EC 1.14.13.111, methanesulfonate monooxygenase. Formerly thought to involve FMNH2 but now shown to use NADH. (EC 1.14.14.6 created 2009, deleted 2010)]
Accepted name: steroid 15β-monooxygenase
Reaction: progesterone + reduced ferredoxin + O2 = 15β-hydroxyprogesterone + oxidized ferredoxin + H2O
Other name(s): cytochrome P-450meg; cytochrome P450meg; steroid 15β-hydroxylase; CYP106A2; BmCYP106A2
Systematic name: progesterone,reduced-ferredoxin:oxygen oxidoreductase (15β-hydroxylating)
Comments: The enzyme from Bacillus megaterium hydroxylates a variety of 3-oxo-Δ4-steroids in position 15β. Ring A-reduced, aromatic, and 3β-hydroxy-Δ4-steroids do not serve as substrates [2].
References:
1. Berg, A., Ingelman-Sundberg, M. and Gustafsson, J.A. Purification and characterization of cytochrome P-450meg. J. Biol. Chem. 254 (1979) 5264-5271. [PMID: 109432]
2. Berg, A., Gustafsson, J.A. and Ingelman-Sundberg, M. Characterization of a cytochrome P-450-dependent steroid hydroxylase system present in Bacillus megaterium. J. Biol. Chem. 251 (1976) 2831-2838. [PMID: 177422]
3. Lisurek, M., Kang, M.J., Hartmann, R.W. and Bernhardt, R. Identification of monohydroxy progesterones produced by CYP106A2 using comparative HPLC and electrospray ionisation collision-induced dissociation mass spectrometry. Biochem. Biophys. Res. Commun. 319 (2004) 677-682. [PMID: 15178459]
4. Goni, G., Zollner, A., Lisurek, M., Velazquez-Campoy, A., Pinto, S., Gomez-Moreno, C., Hannemann, F., Bernhardt, R. and Medina, M. Cyanobacterial electron carrier proteins as electron donors to CYP106A2 from Bacillus megaterium ATCC 13368. Biochim. Biophys. Acta 1794 (2009) 1635-1642. [PMID: 19635596]
5. Lisurek, M., Simgen, B., Antes, I. and Bernhardt, R. Theoretical and experimental evaluation of a CYP106A2 low homology model and production of mutants with changed activity and selectivity of hydroxylation. Chembiochem 9 (2008) 1439-1449. [PMID: 18481342]
Accepted name: ammonia monooxygenase
Reaction: ammonia + AH2 + O2 = NH2OH + A + H2O
Other name(s): AMO
Systematic name: ammonia,hydrogen-donor:oxygen oxidoreductase (hydroxylating)
Comments: Contains copper and possibly nonheme iron. The donor is membrane-bound. Electrons are derived indirectly from ubiquinol.
References:
1. Hyman, M.R., Page, C.L. and Arp, D.J. Oxidation of methyl fluoride and dimethyl ether by ammonia monooxygenase in Nitrosomonas europaea. Appl. Environ. Microbiol. 60 (1994) 3033-3035. [PMID: 8085841]
2. Bergmann, D.J. and Hooper, A.B. Sequence of the gene, amoB, for the 43-kDa polypeptide of ammonia monoxygenase of Nitrosomonas europaea. Biochem. Biophys. Res. Commun. 204 (1994) 759-762. [PMID: 7980540]
3. Holmes, A.J., Costello, A., Lidstrom, M.E. and Murrell, J.C. Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol. Lett. 132 (1995) 203-208. [PMID: 7590173]
4. Zahn, J.A., Arciero, D.M., Hooper, A.B. and DiSpirito, A.A. Evidence for an iron center in the ammonia monooxygenase from Nitrosomonas europaea. FEBS Lett. 397 (1996) 35-38. [PMID: 8941709]
5. Moir, J.W., Crossman, L.C., Spiro, S. and Richardson, D.J. The purification of ammonia monooxygenase from Paracoccus denitrificans. FEBS Lett. 387 (1996) 71-74. [PMID: 8654570]
6. Whittaker, M., Bergmann, D., Arciero, D. and Hooper, A.B. Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea. Biochim. Biophys. Acta 1459 (2000) 346-355. [PMID: 11004450]
7. Arp, D.J., Sayavedra-Soto, L.A. and Hommes, N.G. Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch. Microbiol. 178 (2002) 250-255. [PMID: 12209257]
8. Gilch, S., Meyer, O. and Schmidt, I. A soluble form of ammonia monooxygenase in Nitrosomonas europaea. Biol. Chem. 390 (2009) 863-873. [PMID: 19453274]
9. Rasche, M.E., Hicks, R.E., Hyman, M.R. and Arp, D.J. Oxidation of monohalogenated ethanes and n-chlorinated alkanes by whole cells of Nitrosomonas europaea. J. Bacteriol. 172 (1990) 5368-5373. [PMID: 2394686]
Accepted name: 5,6-dimethylbenzimidazole synthase
Reaction: FMNH2 + NADH + H+ + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + NAD+ + other product
For diagram of reaction, click here
Other name(s): BluB
Systematic name: FMNH2 oxidoreductase (5,6-dimethylbenzimidazole forming)
Comments: The C-2 of 5,6-dimethylbenzimidazole is derived from C-1' of the ribityl group of FMNH2 and 2-H from the ribityl 1'-pro-S hydrogen. The other product may be barbituric acid. For a possible mechanism click here. The stoichiometery of the reaction is not known.
References:
1. Gray, M.J. and Escalante-Semerena, J.C. Single-enzyme conversion of FMNH2 to 5,6-dimethylbenzimidazole, the lower ligand of B12. Proc. Natl. Acad. Sci. USA 104 (2007) 2921-2926. [PMID: 17301238]
2. Ealick, S.E. and Begley, T.P. Biochemistry: molecular cannibalism. Nature 446:387 (2007). [PMID: 17377573]
3. Taga, M.E., Larsen, N.A., Howard-Jones, A.R., Walsh, C.T. and Walker, G.C. BluB cannibalizes flavin to form the lower ligand of vitamin B12. Nature 446:449 (2007). [PMID: 17377583]
Accepted name: mycoredoxin
Reaction: arseno-mycothiol + mycoredoxin = arsenite + mycothiol-mycoredoxin disulfide
Other name(s): Mrx1; MrxI
Systematic name: arseno-mycothiol:mycoredoxin oxidoreductase
Comments: Reduction of arsenate is part of a defense mechanism of the cell against toxic arsenate. The substrate arseno-mycothiol is formed by EC 2.8.4.2 (arsenate:mycothiol transferase). A second mycothiol recycles mycoredoxin and forms mycothione.
References:
1. Ordonez, E., Van Belle, K., Roos, G., De Galan, S., Letek, M., Gil, J.A., Wyns, L., Mateos, L.M. and Messens, J. Arsenate reductase, mycothiol, and mycoredoxin concert thiol/disulfide exchange. J. Biol. Chem. 284 (2009) 15107-15116. [PMID: 19286650]
EC 1.22 Acting on halogen in donors
EC 1.22.1 With NAD+ or NADP+ as acceptor
Accepted name: iodotyrosine deiodinase
Reaction: (a) L-tyrosine + NADP+ + I— = 3-iodo-L-tyrosine + NADPH + H+
(b) 3-iodo-L-tyrosine + NADP+ + I— = 3,5-diiodo-L-tyrosine + NADPH + H+
Other name(s): iodotyrosine dehalogenase 1; DEHAL1
Systematic name: NADP+:L-tyrosine oxidoreductase (iodinating)
Comments: The enzyme activity has only been demonstrated in the direction of 3-deiodination. Present in a transmembrane flavoprotein. Requires FMN.
References:
1. Rosenberg, I.N. Purification of iodotyrosine deiodinase from bovine thyroid. Metabolism 19 (1970) 785-798. [PMID: 4394169]
2. Gnidehou, S., Caillou, B., Talbot, M., Ohayon, R., Kaniewski, J., Noel-Hudson, M.S., Morand, S., Agnangji, D., Sezan, A., Courtin, F., Virion, A. and Dupuy, C. Iodotyrosine dehalogenase 1 (DEHAL1) is a transmembrane protein involved in the recycling of iodide close to the thyroglobulin iodination site. FASEB J. 18 (2004) 1574-1576. [PMID: 15289438]
3. Friedman, J.E., Watson, J.A., Jr., Lam, D.W. and Rokita, S.E. Iodotyrosine deiodinase is the first mammalian member of the NADH oxidase/flavin reductase superfamily. J. Biol. Chem. 281 (2006) 2812-2819. [PMID: 16316988]
4. Thomas, S.R., McTamney, P.M., Adler, J.M., Laronde-Leblanc, N. and Rokita, S.E. Crystal structure of iodotyrosine deiodinase, a novel flavoprotein responsible for iodide salvage in thyroid glands. J. Biol. Chem. 284 (2009) 19659-19667. [PMID: 19436071]
Accepted name: homocysteine S-methyltransferase
Reaction: S-methyl-L-methionine + L-homocysteine = 2 L-methionine
Other name(s): S-adenosylmethionine homocysteine transmethylase; S-methylmethionine homocysteine transmethylase; adenosylmethionine transmethylase; methylmethionine:homocysteine methyltransferase; adenosylmethionine:homocysteine methyltransferase; homocysteine methylase; homocysteine methyltransferase; homocysteine transmethylase; L-homocysteine S-methyltransferase; S-adenosyl-L-methionine:L-homocysteine methyltransferase; S-adenosylmethionine-homocysteine transmethylase; S-adenosylmethionine:homocysteine methyltransferase
Systematic name: S-methyl-L-methionine:L-homocysteine S-methyltransferase
Comments: The enzyme uses S-adenosyl-L-methionine as methyl donor less actively than S-methyl-L-methionine.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, CAS registry number: 9012-40-2
References:
1. Balish, E. and Shapiro, S.K. Methionine biosynthesis in Escherichia coli: induction and repression of methylmethionine (or adenosylmethionine):homocysteine methyltransferase. Arch. Biochem. Biophys. 119 (1967) 62-68. [PMID: 4861151]
2. Shapiro, S.K. Adenosylmethionine-homocysteine transmethylase. Biochim. Biophys. Acta 29 (1958) 405-409. [PMID: 13572358]
3. Shapiro, S.K. and Yphantis, D.A. Assay of S-methylmethionine and S-adenosylmethionine homocysteine transmethylases. Biochim. Biophys. Acta 36 (1959) 241-244. [PMID: 14445542]
4. Mudd, S.H. and Datko, A.H. The S-Methylmethionine Cycle in Lemna paucicostata. Plant Physiol. 93 (1990) 623-630. [PMID: 16667513]
5. Ranocha, P., McNeil, S.D., Ziemak, M.J., Li, C., Tarczynski, M.C. and Hanson, A.D. The S-methylmethionine cycle in angiosperms: ubiquity, antiquity and activity. Plant J. 25 (2001) 575-584. [PMID: 11309147]
6. Ranocha, P., Bourgis, F., Ziemak, M.J., Rhodes, D., Gage, D.A. and Hanson, A.D. Characterization and functional expression of cDNAs encoding methionine-sensitive and -insensitive homocysteine S-methyltransferases from Arabidopsis. J. Biol. Chem. 275 (2000) 15962-15968. [PMID: 10747987]
7. Grue-Sorensen, G., Kelstrup, E., Kjaer, A. and Madsen, J.O.: Diastereospecific, enzymically catalysed transmethylation from S-methylL-L-methionine to L-homocysteine, a naturally occurring process. J. Chem. Soc. Perkin Trans. 1 (1984) 1091-1097.
Accepted name: demethylrebeccamycin-D-glucose O-methyltransferase
Reaction: 4'-demethylrebeccamycin + S-adenosyl-L-methionine = rebeccamycin + S-adenosyl-L-homocysteine
For diagram of reaction, click here
Other name(s): RebM
Systematic name: S-adenosyl-L-methionine:demethylrebeccamycin-D-glucose O-methyltransferase
Comments: Catalyses the last step in the biosynthesis of rebeccamycin, an indolocarbazole alkaloid produced by the Actinobacterium Lechevalieria aerocolonigenes. The enzyme is able to use a wide variety substrates, tolerating variation on the imide heterocycle, deoxygenation of the sugar moiety, and even indolocarbazole glycoside anomers [1]. The enzyme is a member of the general acid/base-dependent O-methyltransferase family [2].
References:
1. Zhang, C., Albermann, C., Fu, X., Peters, N.R., Chisholm, J.D., Zhang, G., Gilbert, E.J., Wang, P.G., Van Vranken, D.L. and Thorson, J.S. RebG- and RebM-catalyzed indolocarbazole diversification. Chembiochem 7 (2006) 795-804. [PMID: 16575939]
2. Singh, S., McCoy, J.G., Zhang, C., Bingman, C.A., Phillips, G.N., Jr. and Thorson, J.S. Structure and mechanism of the rebeccamycin sugar 4'-O-methyltransferase RebM. J. Biol. Chem. 283 (2008) 22628-22636. [PMID: 18502766]
Accepted name: methyl halide transferase
Reaction: S-adenosyl-L-methionine + iodide = S-adenosyl-L-homocysteine + methyl iodide
Other name(s): MCT; methyl chloride transferase; S-adenosyl-L-methionine:halide/bisulfide methyltransferase; AtHOL1; AtHOL2; AtHOL3; HARMLESS TO OZONE LAYER protein; HMT; S-adenosyl-L-methionine: halide ion methyltransferase; SAM:halide ion methyltransferase
Systematic name: S-adenosylmethionine:iodide methyltransferase
Comments: This enzyme contributes to the methyl halide emissions from Arabidopsis [6].
References:
1. Ni, X. and Hager, L.P. Expression of Batis maritima methyl chloride transferase in Escherichia coli. Proc. Natl. Acad. Sci. USA 96 (1999) 3611-3615. [PMID: 10097085]
2. Saxena, D., Aouad, S., Attieh, J. and Saini, H.S. Biochemical characterization of chloromethane emission from the wood-rotting fungus Phellinus pomaceus. Appl. Environ. Microbiol. 64 (1998) 2831-2835. [PMID: 9687437]
3. Attieh, J.M., Hanson, A.D. and Saini, H.S. Purification and characterization of a novel methyltransferase responsible for biosynthesis of halomethanes and methanethiol in Brassica oleracea. J. Biol. Chem. 270 (1995) 9250-9257. [PMID: 7721844]
4. Itoh, N., Toda, H., Matsuda, M., Negishi, T., Taniguchi, T. and Ohsawa, N. Involvement of S-adenosylmethionine-dependent halide/thiol methyltransferase (HTMT) in methyl halide emissions from agricultural plants: isolation and characterization of an HTMT-coding gene from Raphanus sativus (daikon radish). BMC Plant Biol. 9 (2009) 116. [PMID: 19723322]
5. Ohsawa, N., Tsujita, M., Morikawa, S. and Itoh, N. Purification and characterization of a monohalomethane-producing enzyme S-adenosyl-L-methionine: halide ion methyltransferase from a marine microalga, Pavlova pinguis. Biosci. Biotechnol. Biochem. 65 (2001) 2397-2404. [PMID: 11791711]
6. Nagatoshi, Y.and Nakamura, T. Characterization of three halide methyltransferases in Arabidopsis thaliana. Plant Biotechnol 24 (2007) 503-506.
Accepted name: mycothiol synthase
Reaction: desacetylmycothiol + acetyl-CoA = mycothiol + coenzyme-A
For diagram of reaction, click here
Glossary: desacetylmycothiol = 1-O-[2-(L-cysteinamido)-2-deoxy-α-D-glucopyranosyl]-1D-myo-inositol
mycothiol = 1-O-[2-(N2-acetyl-L-cysteinamido)-2-deoxy-α-D-glucopyranosyl]-1D-myo-inositol
Other name(s): MshD
Systematic name: acetyl-CoA:desacetylmycothiol O-acetyltransferase
Comments: This enzyme catalyses the last step in the biosynthesis of mycothiol, the major thiol in most actinomycetes, including Mycobacterium [1]. The enzyme is a member of a large family of GCN5-related N-acetyltransferases (GNATs) [2]. The enzyme has been purified from Mycobacterium tuberculosis H37Rv. Acetyl-CoA is the preferred CoA thioester but propionyl-CoA is also a substrate [3].
References:
1. Spies, H.S. and Steenkamp, D.J. Thiols of intracellular pathogens. Identification of ovothiol A in Leishmania donovani and structural analysis of a novel thiol from Mycobacterium bovis. Eur. J. Biochem. 224 (1994) 203-213. [PMID: 8076641]
2. Koledin, T., Newton, G.L. and Fahey, R.C. Identification of the mycothiol synthase gene (mshD) encoding the acetyltransferase producing mycothiol in actinomycetes. Arch. Microbiol. 178 (2002) 331-337. [PMID: 12375100]
3. Vetting, M.W., Roderick, S.L., Yu, M. and Blanchard, J.S. Crystal structure of mycothiol synthase (Rv0819) from Mycobacterium tuberculosis shows structural homology to the GNAT family of N-acetyltransferases. Protein Sci. 12 (2003) 1954-1959. [PMID: 12930994]
Accepted name: acetoin dehydrogenase
Reaction: acetoin + coenzyme A + NAD+ = acetaldehyde + acetyl-CoA + NADH + H+
Other name(s): acetoin dehydrogenase complex;acetoin dehydrogenase enzyme system;AoDH ES
Systematic name: acetyl-CoA:acetoin O-acetyltransferase
Comments: Requires thiamine diphosphate. This enzyme, which belongs to the family of 2-oxo acid dehydrogenase complexes, catalyses the oxidative-hydrolytic cleavage of acetoin to acetaldehyde and acetyl-CoA in many bacterial strains, both aerobic and anaerobic. The enzyme is composed of multiple copies of three enzymatic components:acetoin oxidoreductase (E1), dihydrolipoamide acetyltransferase (E2) and dihydrolipoyl dehydrogenase (E3).
References:
1. Priefert, H., Hein, S., Kruger, N., Zeh, K., Schmidt, B. and Steinbuchel, A. Identification and molecular characterization of the Alcaligenes eutrophus H16 aco operon genes involved in acetoin catabolism. J. Bacteriol. 173 (1991) 4056-4071. [PMID: 2061286]
2. Oppermann, F.B. and Steinbuchel, A. Identification and molecular characterization of the aco genes encoding the Pelobacter carbinolicus acetoin dehydrogenase enzyme system. J. Bacteriol. 176 (1994) 469-485. [PMID: 8110297]
3. Kruger, N., Oppermann, F.B., Lorenzl, H. and Steinbuchel, A. Biochemical and molecular characterization of the Clostridium magnum acetoin dehydrogenase enzyme system. J. Bacteriol. 176 (1994) 3614-3630. [PMID: 8206840]
4. Huang, M., Oppermann, F.B. and Steinbuchel, A. Molecular characterization of the Pseudomonas putida 2,3-butanediol catabolic pathway. FEMS Microbiol. Lett. 124 (1994) 141-150. [PMID: 7813883]
5. Huang, M., Oppermann-Sanio, F.B. and Steinbuchel, A. Biochemical and molecular characterization of the Bacillus subtilis acetoin catabolic pathway. J. Bacteriol. 181 (1999) 3837-3841. [PMID: 10368162]
Accepted name: D-inositol-3-phosphate glycosyltransferase
Reaction: UDP-N-acetyl-D-glucosamine + 1D-myo-inositol 3-phosphate = 1-O-(2-acetamido-2-deoxy-α-D-glucopyranosyl)-1D-myo-inositol 3-phosphate + UDP
For diagram of reaction, click here
Other name(s): mycothiol glycosyltransferases; MshA
Systematic name: UDP-N-acetyl-D-glucosamine:1D-myo-inositol 3-phosphate α-D-glycosyltransferase
Comments: The enzyme, which belongs to the GT-B fold superfamily, catalyses the first dedicated reaction in the biosynthesis of mycothiol [1]. The substrate was initially believed to be inositol, but eventually shown to be D-myo-inositol 3-phosphate [2]. A substantial conformational change occurs upon UDP binding, which generates the binding site for D-myo-inositol 3-phosphate [3]
References:
1. Newton, G.L., Koledin, T., Gorovitz, B., Rawat, M., Fahey, R.C. and Av-Gay, Y. The glycosyltransferase gene encoding the enzyme catalyzing the first step of mycothiol biosynthesis (mshA). J. Bacteriol. 185 (2003) 3476-3479. [PMID: 12754249]
2. Newton, G.L., Ta, P., Bzymek, K.P. and Fahey, R.C. Biochemistry of the initial steps of mycothiol biosynthesis. J. Biol. Chem. 281 (2006) 33910-33920. [PMID: 16940050]
3. Vetting, M.W., Frantom, P.A. and Blanchard, J.S. Structural and enzymatic analysis of MshA from Corynebacterium glutamicum: substrate-assisted catalysis. J. Biol. Chem. 283 (2008) 15834-15844. [PMID: 18390549]
Accepted name: UDP-D-xylose:β-D-glucoside α-1,3-D-xylosyltransferase
Reaction: UDP-D-xylose + Glcβ-Ser53-EGF-like domain of bovine factor IX(45-87) = UDP + Xylα(1-3)Glcβ-Ser53-EGF-like domain of bovine factor IX(45-87)
Other name(s): β-glucoside α-1,3-xylosyltransferase
Systematic name: UDP-D-xylose:β-D-glucoside α-1,3-D-xylosyltransferase
Comments: The enzyme is involved in the biosynthesis of the Xylα(1-3)Xylα(1-3)Glcβ-1-O-Ser on epidermal growth factor-like domains [1].
References:
1. Ishimizu, T., Sano, K., Uchida, T., Teshima, H., Omichi, K., Hojo, H., Nakahara, Y. and Hase, S. Purification and substrate specificity of UDP-D-xylose:β-D-glucoside α-1,3-D-xylosyltransferase involved in the biosynthesis of the Xyl α1-3Xyl α1-3Glc β1-O-Ser on epidermal growth factor-like domains. J. Biochem. 141 (2007) 593-600. [PMID: 17317689]
2. Omichi, K., Aoki, K., Minamida, S. and Hase, S. Presence of UDP-D-xylose: β-D-glucoside α-1,3-D-xylosyltransferase involved in the biosynthesis of the Xyl α 1-3Glc β-Ser structure of glycoproteins in the human hepatoma cell line HepG2. Eur. J. Biochem. 245 (1997) 143-146. [PMID: 9128735]
Accepted name: 4-dimethylallyltryptophan synthase
Reaction: dimethylallyl diphosphate + L-tryptophan = diphosphate + 4-(3-methylbut-2-enyl)-L-tryptophan
Other name(s): dimethylallylpyrophosphate:L-tryptophan dimethylallyltransferase; dimethylallyltryptophan synthetase; dimethylallylpyrophosphate:tryptophan dimethylallyl transferase; DMAT synthetase; 4-(γ,γ-dimethylallyl)tryptophan synthase; tryptophan dimethylallyltransferase
Systematic name: dimethylallyl-diphosphate:L-tryptophan 4-dimethylallyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 55127-01-0
References:
1. Lee, S.L., Floss, H.G. and Heinstein, P. Purification and properties of dimethylallylpyrophosphate:tryptophan dimethylallyl transferase, the first enzyme of ergot alkaloid biosynthesis in Claviceps sp. SD 58. Arch. Biochem. Biophys. 177 (1976) 84-94. [PMID: 999297]
Accepted name: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase
Reaction: 5-amino-6-(D-ribitylamino)uracil + 3-(4-hydroxyphenyl)pyruvate + 2 S-adenosyl-L-methionine + H2O = 7,8-didemethyl-8-hydroxy-5-deazariboflavin + 2 L-methionine + 2 5'-deoxyadenosine + oxalate + NH3
For diagram of reaction, click here
Glossary: 5-amino-6-(D-ribitylamino)uracil = 5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione
Other name(s): FO synthase
Systematic name: 5-amino-6-(D-ribitylamino)uracil:4-hydroxyphenylpyruvate, 4-methylphenol transferase
Comments: Binds a 4Fe-4S cluster. The cluster is coordinated by 3 cysteines and an exchangeable AdoMet molecule. The first stage of catalysis is reduction of the 2 AdoMet to produce give 2 methionine and 2 5'-deoxyadenosin-5-yl radicals that extracts a hydrogen from each of the substrates permitting the condensation of the two [1]. The overall reaction catalysed is the transfer of the hydroxybenzyl group from 4-hydroxyphenylpyruvate (HPP) to 5-amino-6-ribitylaminopyrimidine-2,4(1H,3H)-dione to form 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO). 7,8-Didemethyl-8-hydroxy-5-deazariboflavin is the chromophore of the hydride carrier coenzyme F420 [1].
References:
1. Graham, D.E., Xu, H. and White, R.H. Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F420 biosynthesis. Arch. Microbiol. 180 (2003) 455-464. [PMID: 14593448]
2. Choi, K.P., Kendrick, N. and Daniels, L. Demonstration that fbiC is required by Mycobacterium bovis BCG for coenzyme F420 and FO biosynthesis. J. Bacteriol. 184 (2002) 2420-2428. [PMID: 11948155]
Accepted name: 6,7-dimethyl-8-ribityllumazine synthase
Reaction: 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
For reaction click here
Glossary: 5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione = 5-amino-6-(1-D-ribitylamino)-2,4-dihydroxypyrimidine = 6-(1-D-ribitylamino)-5-amino-2,4-dihydroxypyrimidine = 6-(1-D-ribitylamino)-5-aminouracil = 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
6,7-dimethyl-8-(1-D-ribityl)lumazine = 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol
(S)-2-hydroxy-3-oxobutyl dihydrogen phosphate = (3S)-3-hydroxy-4-(phosphonooxy)butan-2-one = (2S)-2-hydroxy-3-oxobutyl phosphate = L-3,4-dihydroxybutan-2-one 4-phosphate = (S)-3-hydroxy-4-(phosphonooxy)-2-butanone
Other name(s): lumazine synthase, 6,7-dimethyl-8-ribityllumazine synthase 2; 6,7-dimethyl-8-ribityllumazine synthase 1; lumazine synthase 2; lumazine synthase 1; type I lumazine synthase; type II lumazine synthase; RIB4; MJ0303; RibH; Pbls; MbtLS; RibH1 protein; RibH2 protein; RibH1; RibH2
Systematic name: 5-amino-6-(D-ribitylamino)uracil butanedionetransferase
Comments: Involved in riboflavin biosynthesis.
References:
1. Kis, K., Volk, R. and Bacher, A. Biosynthesis of riboflavin. Studies on the reaction mechanism of 6,7-dimethyl-8-ribityllumazine synthase. Biochemistry 34 (1995) 2883-2892. [PMID: 7893702]
2. Garcia-Ramirez, J.J., Santos, M.A. and Revuelta, J.L. The Saccharomyces cerevisiae RIB4 gene codes for 6,7-dimethyl-8-ribityllumazine synthase involved in riboflavin biosynthesis. Molecular characterization of the gene and purification of the encoded protein. J. Biol. Chem. 270 (1995) 23801-23807. [PMID: 7559556]
3. Bacher, A., Fischer, M., Kis, K., Kugelbrey, K., Mörtl, S., Scheuring, J., Weinkauf, S., Eberhardt, S., Schmidt-Bäse, K., Huber, R., Ritsert, K., Cushman, M., Ladenstein, R. Biosynthesis of riboflavin: structure and mechanism of lumazine synthase. Biochem. Soc. Trans. 24 (1996) 89-94. [PMID: 8674771]
4. Mortl, S., Fischer, M., Richter, G., Tack, J., Weinkauf, S. and Bacher, A. Biosynthesis of riboflavin. Lumazine synthase of Escherichia coli. J. Biol. Chem. 271 (1996) 33201-33207. [PMID: 8969176]
5. Bacher, A., Eberhardt, S., Fischer, M., Mortl, S., Kis, K., Kugelbrey, K., Scheuring, J. and Schott, K. Biosynthesis of riboflavin: lumazine synthase and riboflavin synthase. Methods Enzymol. 280 (1997) 389-399. [PMID: 9211334]
6. Goldbaum, F.A., Velikovsky, C.A., Baldi, P.C., Mortl, S., Bacher, A. and Fossati, C.A. The 18-kDa cytoplasmic protein of Brucella species - an antigen useful for diagnosis- is a lumazine synthase. J Med Microbiol 48 (1999) 833-839. [PMID: 10482294]
7. Jordan, D.B., Bacot, K.O., Carlson, T.J., Kessel, M. and Viitanen, P.V. Plant riboflavin biosynthesis. Cloning, chloroplast localization, expression, purification, and partial characterization of spinach lumazine synthase. J. Biol. Chem. 274 (1999) 22114-22121. [PMID: 10419541]
8. Zhang, X., Meining, W., Fischer, M., Bacher, A. and Ladenstein, R. X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 Å resolution: determinants of thermostability revealed from structural comparisons. J. Mol. Biol. 306 (2001) 1099-1114. [PMID: 11237620]
9. Fischer, M., Haase, I., Feicht, R., Richter, G., Gerhardt, S., Changeux, J.P., Huber, R. and Bacher, A. Biosynthesis of riboflavin: 6,7-dimethyl-8-ribityllumazine synthase of Schizosaccharomyces pombe. Eur. J. Biochem. 269 (2002) 519-526. [PMID: 11856310]
10. Cushman, M., Yang, D., Gerhardt, S., Huber, R., Fischer, M., Kis, K. and Bacher, A. Design, synthesis, and evaluation of 6-carboxyalkyl and 6-phosphonoxyalkyl derivatives of 7-oxo-8-ribitylaminolumazines as inhibitors of riboflavin synthase and lumazine synthase. J. Org. Chem. 67 (2002) 5807-5816. [PMID: 12153285]
11. Haase, I., Mortl, S., Kohler, P., Bacher, A. and Fischer, M. Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii. Eur. J. Biochem. 270 (2003) 1025-1032. [PMID: 12603336]
12. Morgunova, E., Meining, W., Illarionov, B., Haase, I., Jin, G., Bacher, A., Cushman, M., Fischer, M. and Ladenstein, R. Crystal structure of lumazine synthase from Mycobacterium tuberculosis as a target for rational drug design: binding mode of a new class of purinetrione inhibitors. Biochemistry 44 (2005) 2746-2758. [PMID: 15723519]
Accepted name: thermospermine synthase
Reaction: S-adenosylmethioninamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+
Glossary: thermospermine = N1-[3-(3-aminopropylamino)propyl]butane-1,4-diamine
Other name(s): TSPMS; ACL5; SAC51
Systematic name: S-adenosylmethioninamine:spermidine 3-aminopropyltransferase (thermospermine synthesizing)
Comments: This enzyme is required for correct xylem specification through regulation of the lifetime of the xylem elements [3].
References:
1. Romer, P., Faltermeier, A., Mertins, V., Gedrange, T., Mai, R. and Proff, P. Investigations about N-aminopropyl transferases probably involved in biomineralization. J. Physiol. Pharmacol. 59 Suppl 5 (2008) 27-37. [PMID: 19075322]
2. Knott, J.M., Romer, P. and Sumper, M. Putative spermine synthases from Thalassiosira pseudonana and Arabidopsis thaliana synthesize thermospermine rather than spermine. FEBS Lett. 581 (2007) 3081-3086. [PMID: 17560575]
3. Muniz, L., Minguet, E.G., Singh, S.K., Pesquet, E., Vera-Sirera, F., Moreau-Courtois, C.L., Carbonell, J., Blazquez, M.A. and Tuominen, H. ACAULIS5 controls Arabidopsis xylem specification through the prevention of premature cell death. Development 135 (2008) 2573-2582. [PMID: 18599510]
Accepted name: 7-dimethylallyltryptophan synthase
Reaction: dimethylallyl diphosphate + L-tryptophan = diphosphate + 7-(3-methylbut-2-enyl)-L-tryptophan
Other name(s): 7-DMATS
Systematic name: dimethylallyl-diphosphate:L-tryptophan 7-dimethylallyltransferase
Comments: This enzyme is more flexible towards the aromatic substrate than EC 2.5.1.34 (4-dimethylallyltryptophan synthase), but similar to that enzyme, accepts only dimethylallyl diphosphate as the prenyl donor.
References:
1. Kremer, A. and Li, S.M. Potential of a 7-dimethylallyltryptophan synthase as a tool for production of prenylated indole derivatives. Appl. Microbiol. Biotechnol. 79 (2008) 951-961. [PMID: 18481055]
2. Kremer, A., Westrich, L. and Li, S.M. A 7-dimethylallyltryptophan synthase from Aspergillus fumigatus: overproduction, purification and biochemical characterization. Microbiology 153 (2007) 3409-3416. [PMID: 17906140]
Accepted name: glycerate 2-kinase
Reaction: ATP + (R)-glycerate = ADP + 2-phospho-(R)-glycerate
Other name(s): D-glycerate-2-kinase; glycerate kinase (2-phosphoglycerate forming)
Systematic name: ATP:(R)-glycerate 2-phosphotransferase
Comments: A key enzyme in the nonphosphorylative Entner-Doudoroff pathway in archaea [1,2]. In Hyphomicrobium methylovorum GM2 the enzyme is involved in formaldehyde assimilation I (serine pathway) [5]. In Escherichia coli the enzyme is involved in D-glucarate/D-galactarate degradation [6]. The enzyme requires a divalent metal ion [1].
References:
1. Liu, B., Wu, L., Liu, T., Hong, Y., Shen, Y. and Ni, J. A MOFRL family glycerate kinase from the thermophilic crenarchaeon, Sulfolobus tokodaii, with unique enzymatic properties. Biotechnol. Lett. 31 (2009) 1937-1941. [PMID: 19690808]
2. Reher, M., Bott, M. and Schonheit, P. Characterization of glycerate kinase (2-phosphoglycerate forming), a key enzyme of the nonphosphorylative Entner-Doudoroff pathway, from the thermoacidophilic euryarchaeon Picrophilus torridus. FEMS Microbiol. Lett. 259 (2006) 113-119. [PMID: 16684110]
3. Liu, B., Hong, Y., Wu, L., Li, Z., Ni, J., Sheng, D. and Shen, Y. A unique highly thermostable 2-phosphoglycerate forming glycerate kinase from the hyperthermophilic archaeon Pyrococcus horikoshii: gene cloning, expression and characterization. Extremophiles 11 (2007) 733-739. [PMID: 17563835]
4. Noh, M., Jung, J.H. and Lee, S.B. Purification and characterization of glycerate kinase from the thermoacidophilic archaeon Thermoplasma acidophilum: an enzyme belonging to the second glycerate kinase family. Biotechnol. Bioprocess Eng. 11 (2006) 344-350.
5. Yoshida, T., Fukuta, K., Mitsunaga, T., Yamada, H. and Izumi, Y. Purification and characterization of glycerate kinase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2. Eur. J. Biochem. 210 (1992) 849-854. [PMID: 1336459]
6. Hubbard, B.K., Koch, M., Palmer, D.R., Babbitt, P.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry 37 (1998) 14369-14375. [PMID: 9772162]
Accepted name: 2-phospho-L-lactate guanylyltransferase
Reaction: (2S)-2-phospholactate + GTP = (2S)-lactyl-2-diphospho-5'-guanosine + diphosphate
Glossary: (2S)-2-phospholactate = (2S)-2-(phosphonooxy)propanoate
Other name(s): CofC; MJ0887
Systematic name: GTP:2-phospho-L-lactate guanylyltransferase
Comments: This enzyme is involved in the biosynthesis of coenzyme F420, a redox-active cofactor found in all methanogenic archaea, as well as some eubacteria.
References:
1. Grochowski, L.L., Xu, H. and White, R.H. Identification and characterization of the 2-phospho-L-lactate guanylyltransferase involved in coenzyme F420 biosynthesis. Biochemistry 47 (2008) 3033-3037. [PMID: 18260642]
Accepted name: 2-phospho-L-lactate transferase
Reaction: (2S)-lactyl-2-diphospho-5'-guanosine + 7,8-didemethyl-8-hydroxy-5-deazariboflavin = guanosine 5'-phosphate + coenzyme F420-0
Other name(s): LPPG:Fo 2-phospho-L-lactate transferase; LPPG:7,8-didemethyl-8-hydroxy-5-deazariboflavin 2-phospho-L-lactate transferase; MJ1256, lactyl-2-diphospho-(5')guanosine:Fo 2-phospho-L-lactate transferase; CofD
Systematic name: (2S)-lactyl-2-diphospho-5'-guanosine:7,8-didemethyl-8-hydroxy-5-deazariboflavin 2-phospho-L-lactate transferase
Comments: This enzyme is involved in the biosynthesis of coenzyme F420, a redox-active cofactor found in all methanogenic archaea, as well as some eubacteria.
References:
1. Graupner, M., Xu, H. and White, R.H. Characterization of the 2-phospho-L-lactate transferase enzyme involved in coenzyme F420 biosynthesis in Methanococcus jannaschii. Biochemistry 41 (2002) 3754-3761. [PMID: 11888293]
2. Forouhar, F., Abashidze, M., Xu, H., Grochowski, L.L., Seetharaman, J., Hussain, M., Kuzin, A., Chen, Y., Zhou, W., Xiao, R., Acton, T.B., Montelione, G.T., Galinier, A., White, R.H. and Tong, L. Molecular insights into the biosynthesis of the F420 coenzyme. J. Biol. Chem. 283 (2008) 11832-11840. [PMID: 18252724]
Accepted name: arsenate-mycothiol transferase
Reaction: arsenate + mycothiol = arseno-mycothiol + H2O
Other name(s): ArsC1; ArsC2; mycothiol:arsenate transferase
Systematic name: mycothiol:arsenate S-arsenotransferase
Comments: Reduction of arsenate is part of a defence mechanism of the cell against toxic arsenate. The product arseno-mycothiol is reduced by EC 1.20.4.3 (mycoredoxin) to arsenite and mycothiol-mycoredoxin disulfide. Finally, a second mycothiol recycles mycoredoxin and forms mycothione.
References:
1. Ordonez, E., Van Belle, K., Roos, G., De Galan, S., Letek, M., Gil, J.A., Wyns, L., Mateos, L.M. and Messens, J. Arsenate reductase, mycothiol, and mycoredoxin concert thiol/disulfide exchange. J. Biol. Chem. 284 (2009) 15107-15116. [PMID: 19286650]
Accepted name: cocaine esterase
Reaction: cocaine + H2O = ecgonine methyl ester + benzoate
Other name(s): CocE; hCE2; hCE-2; human carboxylesterase 2
Systematic name: cocaine benzoylhydrolase
Comments: Rhodococcus sp. strain MB1 and Pseudomonas maltophilia strain MB11L can utilize cocaine as sole source of carbon and energy [2,3].
References:
1. Gao, D., Narasimhan, D.L., Macdonald, J., Brim, R., Ko, M.C., Landry, D.W., Woods, J.H., Sunahara, R.K. and Zhan, C.G. Thermostable variants of cocaine esterase for long-time protection against cocaine toxicity. Mol. Pharmacol. 75 (2009) 318-323. [PMID: 18987161]
2. Bresler, M.M., Rosser, S.J., Basran, A. and Bruce, N.C. Gene cloning and nucleotide sequencing and properties of a cocaine esterase from Rhodococcus sp. strain MB1. Appl. Environ. Microbiol. 66 (2000) 904-908. [PMID: 10698749]
3. Britt, A.J., Bruce, N.C. and Lowe, C.R. Identification of a cocaine esterase in a strain of Pseudomonas maltophilia. J. Bacteriol. 174 (1992) 2087-2094. [PMID: 1551831]
4. Larsen, N.A., Turner, J.M., Stevens, J., Rosser, S.J., Basran, A., Lerner, R.A., Bruce, N.C. and Wilson, I.A. Crystal structure of a bacterial cocaine esterase. Nat. Struct. Biol. 9 (2002) 17-21. [PMID: 11742345]
5. Pindel, E.V., Kedishvili, N.Y., Abraham, T.L., Brzezinski, M.R., Zhang, J., Dean, R.A. and Bosron, W.F. Purification and cloning of a broad substrate specificity human liver carboxylesterase that catalyzes the hydrolysis of cocaine and heroin. J. Biol. Chem. 272 (1997) 14769-14775. [PMID: 9169443]
Accepted name: 2,3-bisphosphoglycerate 3-phosphatase
Reaction: 2,3-bisphospho-D-glycerate + H2O = 2-phospho-D-glycerate + phosphate
Other name(s): MIPP1; 2,3-BPG 3-phosphatase
Systematic name: 2,3-bisphospho-D-glycerate 3-phosphohydrolase
Comments: This reaction is a shortcut in the Rapoport-Luebering shunt. It bypasses the reactions of EC 3.1.3.13/EC 5.4.2.1 (bisphosphoglycerate phosphatase/phosphoglycerate mutase) and directly forms 2-phospho-D-glycerate by removing the 3-phospho-group of 2,3-diphospho-D-glycerate [1]. The MIPP1 protein also catalyses the reaction of EC 3.1.3.62 (multiple inositol-polyphosphate phosphatase).
References:
1. Cho, J., King, J.S., Qian, X., Harwood, A.J. and Shears, S.B. Dephosphorylation of 2,3-bisphosphoglycerate by MIPP expands the regulatory capacity of the Rapoport-Luebering glycolytic shunt. Proc. Natl. Acad. Sci. USA 105 (2008) 5998-6003. [PMID: 18413611]
Accepted name: exoribonuclease H
Reaction: 3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Comments: This is a secondary reaction to the RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end performed by EC 3.1.26.13 (retroviral ribonuclease H).
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:
References:
1. Schatz, O., Mous, J. and Le Grice, S.F. HIV-1 RT-associated ribonuclease H displays both endonuclease and 3'—5' exonuclease activity. EMBO J. 9 (1990) 1171-1176. [PMID: 1691093]
Accepted name: ribonuclease H
Reaction: Endonucleolytic cleavage to 5'-phosphomonoester
Other name(s): endoribonuclease H (calf thymus); RNase H; RNA*DNA hybrid ribonucleotidohydrolase; hybrid ribonuclease; hybridase; hybridase (ribonuclease H); ribonuclease H; hybrid nuclease; calf thymus ribonuclease H
Comments: Acts on RNA-DNA hybrids.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9050-76-4
References:
1. Haberkern, R.C. and Cantoni, G.L. Studies on a calf thymus ribonuclease specific for ribonucleic acid-deoxyribonucleic acid hybrids. Biochemistry 12 (1973) 2389-2395. [PMID: 4709937]
2. Stavrianopoulos, J.G. and Chargaff, E. Purification and properties of ribonuclease H of calf thymus. Proc. Natl. Acad. Sci. USA 70 (1973) 1959-1963. [PMID: 4516197]
Accepted name: 2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase
Reaction: 2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + H2O = 2,5-diamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + formate
Other name(s): ArfB
Systematic name: 2-amino-5-formylamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate amidohydrolase
Comments: The enzyme catalyses the second step in archaeal riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin biosynthesis. The first step is catalysed by EC 3.5.4.29 (GTP cyclohydrolase IIa). The bacterial enzyme, EC 3.5.4.25 (GTP cyclohydrolase II) catalyses both reactions.
References:
1. Grochowski, L.L., Xu, H. and White, R.H. An iron(II) dependent formamide hydrolase catalyzes the second step in the archaeal biosynthetic pathway to riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin. Biochemistry 48 (2009) 4181-4188. [PMID: 19309161]
Accepted name: N-acetyl-1D-myo-inositol-2-amino-2-deoxy-α-D-glucopyranoside deacetylase
Reaction: 1-(2-acetamido-2-deoxy-α-D-glucopyranosyl)-1D-myo-inositol + H2O = 1-(2-amino-2-deoxy-α-D-glucopyranoside)-1D-myo-inositol + acetate
For diagram of reaction, click here
Other name(s): MshB
Systematic name: 1-(2-acetamido-2-deoxy-α-D-glucopyranosyl)-1D-myo-inositol acetylhydrolase
Comments: This enzyme is considered the key enzyme and rate limiting step in the mycothiol biosynthesis pathway [1]. In addition to acetylase activity, the enzyme possesses weak mycothiol conjugate amidase activity, and shares sequence similarity with mycothiol S-conjugate amidase [2]. The enzyme requires a divalent transition metal ion for activity, believed to be Zn2+ [3].
References:
1. Rawat, M., Kovacevic, S., Billman-Jacobe, H. and Av-Gay, Y. Inactivation of mshB, a key gene in the mycothiol biosynthesis pathway in Mycobacterium smegmatis. Microbiology 149 (2003) 1341-1349. [PMID: 12724395]
2. Newton, G.L., Av-Gay, Y. and Fahey, R.C. N-Acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside deacetylase (MshB) is a key enzyme in mycothiol biosynthesis. J. Bacteriol. 182 (2000) 6958-6963. [PMID: 11092856]
3. Maynes, J.T., Garen, C., Cherney, M.M., Newton, G., Arad, D., Av-Gay, Y., Fahey, R.C. and James, M.N. The crystal structure of 1-D-myo-inosityl 2-acetamido-2-deoxy-α-D-glucopyranoside deacetylase (MshB) from Mycobacterium tuberculosis reveals a zinc hydrolase with a lactate dehydrogenase fold. J. Biol. Chem. 278 (2003) 47166-47170. [PMID: 12958317]
Accepted name: benzoyl-CoA-dihydrodiol lyase
Reaction: 2,3-dihydro-2,3-dihydroxybenzoyl-CoA + H2O = 3,4-didehydroadipyl-CoA semialdehyde + formate
Other name(s): 2,3-dihydro-2,3-dihydroxybenzoyl-CoA lyase/hydrolase (deformylating); BoxC; dihydrodiol transforming enzyme; benzoyl-CoA oxidation component C
Systematic name: 2,3-dihydro-2,3-dihydroxybenzoyl-CoA 3,4-didehydroadipyl-CoA semialdehyde-lyase (formate-forming)
Comments: The enzyme is involved in the aerobic benzoyl-CoA catabolic pathway in Azoarcus evansii. In a previous step benzoyl-CoA is oxidized to 2,3-dihydro-2,3-dihydroxybenzoyl-CoA (benzoyl-CoA dihydrodiol) by EC 1.14.12.21 (benzoyl-CoA 2,3-dioxygenase) in the presence of molecular oxygen [1].
References:
1. Gescher, J., Eisenreich, W., Worth, J., Bacher, A. and Fuchs, G. Aerobic benzoyl-CoA catabolic pathway in Azoarcus evansii: studies on the non-oxygenolytic ring cleavage enzyme. Mol. Microbiol. 56 (2005) 1586-1600. [PMID: 15916608]
Accepted name: trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
Reaction: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate + H2O = 2-hydroxybenzaldehyde + pyruvate
For diagram of reaction, click here
Glossary: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate = (E)-2'-hydroxybenzylidenepyruvate
Other name(s): 2'-hydroxybenzalpyruvate aldolase; NsaE; tHBPA hydratase-aldolase
Systematic name: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate hydro-lyase
Comments: This enzyme is involved in naphthalene degradation. The enzyme catalyses a retro-aldol reaction in vitro, and it accepts a broad range of aldehydes and 4-substituted 2-oxobut-3-enoates as substrates [4].
References:
1. Kuhm, A.E., Knackmuss, H.J. and Stolz, A. Purification and properties of 2'-hydroxybenzalpyruvate aldolase from a bacterium that degrades naphthalenesulfonates. J. Biol. Chem. 268 (1993) 9484-9489. [PMID: 8486638]
2. Keck, A., Conradt, D., Mahler, A., Stolz, A., Mattes, R. and Klein, J. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152 (2006) 1929-1940. [PMID: 16804169]
3. Eaton, R.W. Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J. Bacteriol. 176 (1994) 7757-7762. [PMID: 8002605]
4. Eaton, R.W. trans-o-Hydroxybenzylidenepyruvate hydratase-aldolase as a biocatalyst. Appl. Environ. Microbiol. 66 (2000) 2668-2672. [PMID: 10831455]
Accepted name: chromopyrrolate synthase
Reaction: 2 2-imino-3-(7-chloroindol-3-yl)propanoate = dichlorochromopyrrolate + NH3
For diagram of reaction, click here
Other name(s): RebD; chromopyrrolic acid synthase
Systematic name: 2-imino-3-(7-chloroindol-3-yl)propanoate ammonia-lyase (dichlorochromopyrrolate-forming)
Comments: This enzyme catalyses a step in the biosynthesis of rebeccamycin, an indolocarbazole alkaloid produced by the Actinobacterium Lechevalieria aerocolonigenes. The enzyme is a dimeric heme-protein oxidase that catalyses the oxidative dimerization of two L-tryptophan-derived molecules to form dichlorochromopyrrolic acid, the precursor for the fused six-ring indolocarbazole scaffold of rebeccamycin [1]. Contains one molecule of heme b per monomer, as well as non-heme iron that is not part of an iron-sulfur center [2]. The enzyme also possesses catalase activity.
References:
1. Nishizawa, T., Gruschow, S., Jayamaha, D.H., Nishizawa-Harada, C. and Sherman, D.H. Enzymatic assembly of the bis-indole core of rebeccamycin. J. Am. Chem. Soc. 128 (2006) 724-725. [PMID: 16417354]
2. Howard-Jones, A.R. and Walsh, C.T. Enzymatic generation of the chromopyrrolic acid scaffold of rebeccamycin by the tandem action of RebO and RebD. Biochemistry 44 (2005) 15652-15663. [PMID: 16313168]
Accepted name: 4'-demethylrebeccamycin synthase
Reaction: 4'-O-demethylrebeccamycin + H2O = dichloro-arcyriaflavin A + β-D-glucose
For diagram of reaction, click here
Glossary: dichloro-arcyriaflavin A = rebeccamycin aglycone
Other name(s): arcyriaflavin A N-glycosyltransferase; RebG
Systematic name: 4'-demethylrebeccamycin D-glucose-lyase
Comments: This enzyme catalyses a step in the biosynthesis of rebeccamycin, an indolocarbazole alkaloid produced by the Actinobacterium Lechevalieria aerocolonigenes. The enzyme is a glycosylase, and acts in the reverse direction to that shown. It has a wide substrate range, and was shown to glycosylate several substrates, including the staurosporine aglycone, EJG-III-108A, J-104303, 6-N-methyl-arcyriaflavin C and indolo-[2,3-a]-carbazole [1,2].
References:
1. Ohuchi, T., Ikeda-Araki, A., Watanabe-Sakamoto, A., Kojiri, K., Nagashima, M., Okanishi, M. and Suda, H. Cloning and expression of a gene encoding N-glycosyltransferase (ngt) from Saccharothrix aerocolonigenes ATCC39243. J. Antibiot. (Tokyo) 53 (2000) 393-403. [PMID: 10866221]
2. Zhang, C., Albermann, C., Fu, X., Peters, N.R., Chisholm, J.D., Zhang, G., Gilbert, E.J., Wang, P.G., Van Vranken, D.L. and Thorson, J.S. RebG- and RebM-catalyzed indolocarbazole diversification. Chembiochem 7 (2006) 795-804. [PMID: 16575939]
Accepted name: 2-hydroxychromene-2-carboxylate isomerase
Reaction: 2-hydroxy-2H-chromene-2-carboxylate = (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate
For diagram of reaction, click here
Other name(s): HCCA isomerase; 2HC2CA isomerase; 2-hydroxychromene-2-carboxylic acid isomerase
Systematic name: 2-hydroxy-2H-chromene-2-carboxylate—(3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate isomerase
Comments: This enzyme is involved in naphthalene degradation.
References:
1. Ohmoto, T., Kinoshita, T., Moriyoshi, K., Sakai, K., Hamada, N. and Ohe, T. Purification and some properties of 2-hydroxychromene-2-carboxylate isomerase from naphthalenesulfonate-assimilating Pseudomonas sp. TA-2. J. Biochem. 124 (1998) 591-597. [PMID: 9722670]
2. Keck, A., Conradt, D., Mahler, A., Stolz, A., Mattes, R. and Klein, J. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152 (2006) 1929-1940. [PMID: 16804169]
3. Eaton, R.W. Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J. Bacteriol. 176 (1994) 7757-7762. [PMID: 8002605]
4. Thompson, L.C., Ladner, J.E., Codreanu, S.G., Harp, J., Gilliland, G.L. and Armstrong, R.N. 2-Hydroxychromene-2-carboxylic acid isomerase: a kappa class glutathione transferase from Pseudomonas putida. Biochemistry 46 (2007) 6710-6722. [PMID: 17508726]
Accepted name: coenzyme F420-0:L-glutamate ligase
Reaction: GTP + coenzyme F420-0 + L-glutamate = GDP + phosphate + coenzyme F420-1
For diagram of reaction, click here
Other name(s): CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-0 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to cofactor F420 by two distinct and independent reactions. In the reaction described here the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction (EC 6.3.2.34, coenzyme F420-1—γ-L-glutamate ligase) it catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
References:
1. Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771-9778. [PMID: 12911320]
2. Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456-469. [PMID: 17669425]
Accepted name: coenzyme γ-F420-2:α-L-glutamate ligase
Reaction: ATP + coenzyme γ-F420-2 + L-glutamate = ADP + phosphate + coenzyme α-F420-3
For diagram of reaction, click here
Other name(s): MJ1001; CofF protein; γ-F420-2:α-L-glutamate ligase
Systematic name: L-glutamate:coenzyme γ-F420-2 (ADP-forming)
Comments: The enzyme caps the γ-glutamyl tail of the hydride carrier coenzyme F420 [1].
References:
1. Li, H., Xu, H., Graham, D.E. and White, R.H. Glutathione synthetase homologs encode α-L-glutamate ligases for methanogenic coenzyme F420 and tetrahydrosarcinapterin biosyntheses. Proc. Natl. Acad. Sci. USA 100 (2003) 9785-9790. [PMID: 12909715]
Accepted name: tetrahydrosarcinapterin synthase
Reaction: ATP + tetrahydromethanopterin + L-glutamate = ADP + phosphate + 5,6,7,8-tetrahydrosarcinapterin
Other name(s): H4MPT:α-L-glutamate ligase; MJ0620; MptN protein
Systematic name: tetrahydromethanopterin:α-L-glutamate ligase (ADP-forming)
Comments: This enzyme catalyses the biosynthesis of 5,6,7,8-tetrahydrosarcinapterin, a modified form of tetrahydromethanopterin found in the Methanosarcinales. It does not require K+, and does not discriminate between ATP and GTP [1].
References:
1. Li, H., Xu, H., Graham, D.E. and White, R.H. Glutathione synthetase homologs encode α-L-glutamate ligases for methanogenic coenzyme F420 and tetrahydrosarcinapterin biosyntheses. Proc. Natl. Acad. Sci. USA 100 (2003) 9785-9790. [PMID: 12909715]
Accepted name: coenzyme F420-1:γ-L-glutamate ligase
Reaction: GTP + coenzyme F420-1 + L-glutamate = GDP + phosphate + coenzyme γ-F420-2
For diagram of reaction, click here
Other name(s): F420:γ-glutamyl ligase; CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-1 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to cofactor F420 by two distinct and independent reactions. In the first reaction (EC 6.3.2.31, coenzyme F420-0—L-glutamate ligase) the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction, which is described here, the enzyme catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
References:
1. Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771-9778. [PMID: 12911320]
2. Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456-469. [PMID: 17669425]