An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: dihydropyrimidine dehydrogenase (NAD+)
Reaction: (1) 5,6-dihydrouracil + NAD+ = uracil + NADH + H+
(2) 5,6-dihydrothymine + NAD+ = thymine + NADH + H+
Other name(s): dihydropyrimidine dehydrogenase; dihydrothymine dehydrogenase; pyrimidine reductase; thymine reductase; uracil reductase; dihydrouracil dehydrogenase (NAD+)
Systematic name: 5,6-dihydropyrimidine:NAD+ oxidoreductase
Comments: An iron-sulfur flavoenzyme. The enzyme was originally discovered in the uracil-fermenting bacterium, Clostridium uracilicum, which utilizes uracil and thymine as nitrogen and carbon sources for growth [1]. Since then the enzyme was found in additional organisms including Alcaligenes eutrophus [2], Pseudomonas strains [3,4] and Escherichia coli [5,6].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9026-89-5
References:
1. Campbell, L.L. Reductive degradation of pyrimidines. III. Purificaion and properties of dihydrouracil dehydrogenase. J. Biol. Chem. 227 (1957) 693-700. [PMID: 13462991]
2. Schmitt, U., Jahnke, K., Rosenbaum, K., Cook, P.F. and Schnackerz, K.D. Purification and characterization of dihydropyrimidine dehydrogenase from Alcaligenes eutrophus. Arch. Biochem. Biophys. 332 (1996) 175-182. [PMID: 8806723]
3. Kim, S. and West, T.P. Pyrimidine catabolism in Pseudomonas aeruginosa. FEMS Microbiol. Lett. 61 (1991) 175-179. [PMID: 1903745]
4. West, T.P. Pyrimidine base catabolism in Pseudomonas putida biotype B. Antonie Van Leeuwenhoek 80 (2001) 163-167. [PMID: 11759049]
5. West, T.P. Isolation and characterization of an Escherichia coli B mutant strain defective in uracil catabolism. Can. J. Microbiol. 44 (1998) 1106-1109. [PMID: 10030006]
6. Hidese, R., Mihara, H., Kurihara, T. and Esaki, N. Escherichia coli dihydropyrimidine dehydrogenase is a novel NAD-dependent heterotetramer essential for the production of 5,6-dihydrouracil. J. Bacteriol. 193 (2011) 989-993. [PMID: 21169495]
Accepted name: 9,9'-dicis-ζ-carotene desaturase
Reaction: 9,9'-dicis-ζ-carotene + 2 quinone = 7,9,7',9'-tetracis-lycopene + 2 quinol (overall reaction)
(1a) 9,9'-dicis-ζ-carotene + a quinone = 7,9,9'-tricis-neurosporene + a quinol
(1b) 7,9,9'-tricis-neurosporene + a quinone = 7,9,7',9'-tetracis-lycopene + a quinol
For diagram of reaction click here.
Glossary: 7,9,7',9'-tetracis-lycopene = prolycopene
Other name(s): ζ-carotene desaturase; ZDS
Systematic name: 9,9'-dicis-ζ-corotene:quinone oxidoreductase
Comments: This enzyme is involved in carotenoid biosynthesis in plants and cyanobacteria.
References:
1. Albrecht, M., Linden, H. and Sandmann, G. Biochemical characterization of purified ζ-carotene desaturase from Anabaena PCC 7120 after expression in E. coli. Eur. J. Biochem. 236 (1996) 115-120. [PMID: 8617254]
2. Josse, E.M., Simkin, A.J., Gaffe, J., Laboure, A.M., Kuntz, M. and Carol, P. A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol. 123 (2000) 1427-1436. [PMID: 10938359]
3. Breitenbach, J., Kuntz, M., Takaichi, S. and Sandmann, G. Catalytic properties of an expressed and purified higher plant type ζ-carotene desaturase from Capsicum annuum. Eur. J. Biochem. 265 (1999) 376-383. [PMID: 10491195]
4. Breitenbach, J. and Sandmann, G. ζ-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta 220 (2005) 785-793. [PMID: 15503129]
Accepted name: benzoyl-CoA reductase
Reaction: cyclohexa-1,5-diene-1-carbonyl-CoA + oxidized ferredoxin + 2 ADP + 2 phosphate = benzoyl-CoA + reduced ferredoxin + 2 ATP + 2 H2O
Other name(s): benzoyl-CoA reductase (dearomatizing)
Systematic name: cyclohexa-1,5-diene-1-carbonyl-CoA:ferredoxin oxidoreductase (aromatizing, ATP-forming)
Comments: An iron-sulfur protein. Requires Mg2+ or Mn2+. Inactive towards aromatic acids that are not CoA esters but will also catalyse the reaction: ammonia + acceptor + 2 ADP + 2 phosphate = hydroxylamine + reduced acceptor + 2 ATP + H2O. In the presence of reduced acceptor, but in the absence of oxidizable substrate, the enzyme catalyses the hydrolysis of ATP to ADP plus phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, UM-BBD, CAS registry number: 176591-18-7
References:
1. Boll, M. and Fuchs, G. Benzoyl-coenzyme A reductase (dearomatizing), a key enzyme of anaerobic aromatic metabolism. ATP dependence of the reaction, purification and some properties of the enzyme from Thauera aromatica strain K172. Eur. J. Biochem. 234 (1995) 921-933. [PMID: 8575453]
2. Kung, J.W., Baumann, S., von Bergen, M., Muller, M., Hagedoorn, P.L., Hagen, W.R. and Boll, M. Reversible biological Birch reduction at an extremely low redox potential. J. Am. Chem. Soc. 132 (2010) 9850-9856. [PMID: 20578740]
Accepted name: all-trans-ζ-carotene desaturase
Reaction: all-trans-ζ-carotene + 2 acceptor = all-trans-lycopene + 2 reduced acceptor (overall reaction)
(1a) all-trans-ζ-carotene + acceptor = all-trans-neurosporene + reduced acceptor
(1b) all-trans-neurosporene + acceptor = all-trans-lycopene + reduced acceptor
For diagram of reaction click here.
Other name(s): Crtlb; phytoene desaturase (ambiguous); 2-step phytoene desaturase (ambiguous); two-step phytoene desaturase (ambiguous); CrtI (ambiguous)
Systematic name: all-trans-ζ-carotene:acceptor oxidoreductase
Comments: This enzyme is involved in carotenoid biosynthesis.
References:
1. Iniesta, A.A., Cervantes, M. and Murillo, F.J. Cooperation of two carotene desaturases in the production of lycopene in Myxococcus xanthus. FEBS J. 274 (2007) 4306-4314. [PMID: 17662111]
Accepted name: 1-hydroxycarotenoid 3,4-desaturase
Reaction: 1-hydroxy-1,2-dihydrolycopene + acceptor = 1-hydroxy-3,4-didehydro-1,2-dihydrolycopene + reduced acceptor
Other name(s): CrtD; hydroxyneurosporene desaturase; carotenoid 3,4-dehydrogenase; 1-hydroxy-carotenoid 3,4-dehydrogenase
Systematic name: 1-hydroxy-1,2-dihydrolycopene:acceptor oxidoreductase
Comments: The enzymes from Rubrivivax gelatinosus and Rhodobacter sphaeroides prefer the acyclic carotenoids (e.g. 1-hydroxy-1,2-dihydroneurosporene, 1-hydroxy-1,2-dihydrolycopene) as substrates. The conversion rate for the 3,4-desaturation of the monocyclic 1'-hydroxy-1',2'-dihydro-γ-carotene is lower [2,3]. The enzyme from the marine bacterium strain P99-3 shows high activity with the monocyclic carotenoid 1'-hydroxy-1',2'-dihydro-γ-carotene [1]. The enzyme from Rhodobacter sphaeroides utilizes molecular oxygen as the electron acceptor in vitro [3]. However, oxygen is unlikely to be the natural electron acceptor under anaerobic conditions.
References:
1. Teramoto, M., Rahlert, N., Misawa, N. and Sandmann, G. 1-Hydroxy monocyclic carotenoid 3,4-dehydrogenase from a marine bacterium that produces myxol. FEBS Lett. 570 (2004) 184-188. [PMID: 15251462]
2. Steiger, S., Astier, C. and Sandmann, G. Substrate specificity of the expressed carotenoid 3,4-desaturase from Rubrivivax gelatinosus reveals the detailed reaction sequence to spheroidene and spirilloxanthin. Biochem. J. 349 (2000) 635-640. [PMID: 10880364]
3. Albrecht, M., Ruther, A. and Sandmann, G. Purification and biochemical characterization of a hydroxyneurosporene desaturase involved in the biosynthetic pathway of the carotenoid spheroidene in Rhodobacter sphaeroides. J. Bacteriol. 179 (1997) 7462-7467. [PMID: 9393712]
Accepted name: phytoene desaturase (neurosporene-forming)
Reaction: 15-cis-phytoene + 3 acceptor = all-trans-neurosporene + 3 reduced acceptor (overall reaction)
(1a) 15-cis-phytoene + acceptor = all-trans-phytofluene + reduced acceptor
(1b) all-trans-phytofluene + acceptor = all-trans-ζ-carotene + reduced acceptor
(1c) all-trans-ζ-carotene + acceptor = all-trans-neurosporene + reduced acceptor
For diagram of reaction click here.
Other name(s): 3-step phytoene desaturase; three-step phytoene desaturase; phytoene desaturase (ambiguous); CrtI (ambiguous)
Systematic name: 15-cis-phytoene:acceptor oxidoreductase (neurosporene-forming)
Comments: This enzyme is involved in carotenoid biosynthesis and catalyses up to three desaturation steps (cf. EC 1.3.99.29 [phytoene desaturase (ζ-carotene-forming)], EC 1.3.99.30 [phytoene desaturase (3,4-didehydrolycopene-forming)], EC 1.3.99.31 [phytoene desaturase (lycopene-forming)]). The enzyme is activated by FAD. NAD+, NADP+ or ATP show no activating effect [1].
References:
1. Raisig, A., Bartley, G., Scolnik, P. and Sandmann, G. Purification in an active state and properties of the 3-step phytoene desaturase from Rhodobacter capsulatus overexpressed in Escherichia coli. J. Biochem. 119 (1996) 559-564. [PMID: 8830054]
2. Wang, C.W. and Liao, J.C. Alteration of product specificity of Rhodobacter sphaeroides phytoene desaturase by directed evolution. J. Biol. Chem. 276 (2001) 41161-41164. [PMID: 11526111]
Accepted name: phytoene desaturase (ζ-carotene-forming)
Reaction: 15-cis-phytoene + 2 acceptor = all-trans-ζ-carotene + 2 reduced acceptor (overall reaction)
(1a) 15-cis-phytoene + acceptor = all-trans-phytofluene + reduced acceptor
(1b) all-trans-phytofluene + acceptor = all-trans-ζ-carotene + reduced acceptor
For diagram of reaction click here.
Other name(s): CrtIa; 2-step phytoene desaturase (ambiguous); two-step phytoene desaturase (ambiguous)
Systematic name: 15-cis-phytoene:acceptor oxidoreductase (ζ-carotene-forming)
Comments: The enzyme is involved in carotenoid biosynthesis and catalyses up to two desaturation steps (cf. EC 1.3.99.28 [phytoene desaturase (neurosporene-forming)], EC 1.3.99.30 [phytoene desaturase (3,4-didehydrolycopene-forming)] and EC 1.3.99.31 [phytoene desaturase (lycopene-forming)]).
References:
1. Iniesta, A.A., Cervantes, M. and Murillo, F.J. Cooperation of two carotene desaturases in the production of lycopene in Myxococcus xanthus. FEBS J. 274 (2007) 4306-4314. [PMID: 17662111]
Accepted name: phytoene desaturase (3,4-didehydrolycopene-forming)
Reaction: 15-cis-phytoene + 5 acceptor = all-trans-3,4-didehydrolycopene + 5 reduced acceptor (overall reaction)
(1a) 15-cis-phytoene + acceptor = all-trans-phytofluene + reduced acceptor
(1b) all-trans-phytofluene + acceptor = all-trans-ζ-carotene + reduced acceptor
(1c) all-trans-ζ-carotene + acceptor = all-trans-neurosporene + reduced acceptor
(1d) all-trans-neurosporene + acceptor = all-trans-lycopene + reduced acceptor
(1e) all-trans-lycopene + acceptor = all-trans-3,4-didehydrolycopene + reduced acceptor
For diagram of reaction click here.
Other name(s): 5-step phytoene desaturase; five-step phytoene desaturase; phytoene desaturase (ambiguous); Al-1
Systematic name: 15-cis-phytoene:acceptor oxidoreductase (3,4-didehydrolycopene-forming)
Comments: This enzyme is involved in carotenoid biosynthesis and catalyses up to five desaturation steps (cf. EC 1.3.99.28 [phytoene desaturase (neurosporene-forming)], EC 1.3.99.29 [phytoene desaturase (ζ-carotene-forming)] and EC 1.3.99.31 [phytoene desaturase (lycopene-forming)]).
References:
1. Hausmann, A. and Sandmann, G. A single five-step desaturase is involved in the carotenoid biosynthesis pathway to β-carotene and torulene in Neurospora crassa. Fungal Genet. Biol. 30 (2000) 147-153. [PMID: 11017770]
2. Estrada, A.F., Maier, D., Scherzinger, D., Avalos, J. and Al-Babili, S. Novel apocarotenoid intermediates in Neurospora crassa mutants imply a new biosynthetic reaction sequence leading to neurosporaxanthin formation. Fungal Genet. Biol. 45 (2008) 1497-1505. [PMID: 18812228]
Accepted name: phytoene desaturase (lycopene-forming)
Reaction: 15-cis-phytoene + 4 acceptor = all-trans-lycopene + 4 reduced acceptor (overall reaction)
(1a) 15-cis-phytoene + acceptor = all-trans-phytofluene + reduced acceptor
(1b) all-trans-phytofluene + acceptor = all-trans-ζ-carotene + reduced acceptor
(1c) all-trans-ζ-carotene + acceptor = all-trans-neurosporene + reduced acceptor
(1d) all-trans-neurosporene + acceptor = all-trans-lycopene + reduced acceptor
For diagram of reaction click here.
Other name(s): 4-step phytoene desaturase; four-step phytoene desaturase; phytoene desaturase (ambiguous); CrtI (ambiguous)
Systematic name: 15-cis-phytoene:acceptor oxidoreductase (lycopene-forming)
Comments: Requires FAD. The enzyme is involved in carotenoid biosynthesis and catalyses up to four desaturation steps (cf. EC 1.3.99.28 [phytoene desaturase (neurosporene-forming)], EC 1.3.99.29 [phytoene desaturase (ζ-carotene-forming)] and EC 1.3.99.30 [phytoene desaturase (3,4-didehydrolycopene-forming)]).
References:
1. Fraser, P.D., Misawa, N., Linden, H., Yamano, S., Kobayashi, K. and Sandmann, G. Expression in Escherichia coli, purification, and reactivation of the recombinant Erwinia uredovora phytoene desaturase. J. Biol. Chem. 267 (1992) 19891-19895. [PMID: 1400305]
Accepted name: flavin reductase (NADPH)
Reaction: reduced riboflavin + NADP+ = riboflavin + NADPH + H+
Other name(s): NADPH:flavin oxidoreductase; riboflavin mononucleotide (reduced nicotinamide adenine dinucleotide phosphate) reductase; flavin mononucleotide reductase; flavine mononucleotide reductase; FMN reductase (NADPH); NADPH-dependent FMN reductase; NADPH-flavin reductase; NADPH-FMN reductase; NADPH-specific FMN reductase; riboflavin mononucleotide reductase; riboflavine mononucleotide reductase; NADPH2 dehydrogenase (flavin); NADPH2:riboflavin oxidoreductase
Systematic name: reduced-riboflavin:NADP+ oxidoreductase
Comments: The enzyme from Entamoeba histolytica reduces riboflavin and galactoflavin, and, more slowly, FMN and FAD. NADH is oxidized more slowly than NADPH.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 56626-29-0
References:
1. Lo, H.-S. and Reeves, R.E. Purification and properties of NADPH:flavin oxidoreductase from Entamoeba histolytica. Mol. Biochem. Parasitol. 2 (1980) 23-30. [PMID: 6258069]
2. Yubisui, T., Tamura, M. and Takeshita, M. Characterization of a second form of NADPH-flavin reductase purified from human erythrocytes. Biochem. Int. 15 (1987) 1-8. [PMID: 3453680]
Accepted name: flavin reductase (NADH)
Reaction: reduced flavin + NAD+ = flavin + NADH + H+
Other name(s): NADH-dependent flavin reductase; flavin:NADH oxidoreductase
Systematic name: flavin:NAD+ oxidoreductase
Comments: The enzyme from Escherichia coli W catalyses the reduction of free flavins by NADH. The enzyme has similar affinity to FAD, FMN and riboflavin. Activity with NADPH is more than 2 orders of magnitude lower than activity with NADH.
References:
1. Galan, B., Diaz, E., Prieto, M.A. and Garcia, J.L. Functional analysis of the small component of the 4-hydroxyphenylacetate 3-monooxygenase of Escherichia coli W: a prototype of a new Flavin:NAD(P)H reductase subfamily. J. Bacteriol. 182 (2000) 627-636. [PMID: 10633095]
Accepted name: thiol oxidase
Reaction: 2 R'C(R)SH + O2 = R'C(R)S-S(R)CR' + H2O2
Other name(s): sulfhydryl oxidase
Systematic name: thiol:oxygen oxidoreductase
Comments: R may be =S or =O, or a variety of other groups. The enzyme is not specific for R'.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, UM-BBD, CAS registry number: 9029-39-4
References:
1. Aurbach, G.D. and Jakoby, W.B. The multiple functions of thiooxidase. J. Biol. Chem. 237 (1962) 565-568. [PMID: 13863296]
2. Neufeld, H.A., Green, L.F., Latterell, F.M. and Weintraub, R.L. Thiooxidase, a new sulfhydryl-oxidizing enzyme from Piricularia oryzae and Polyporus vesicolor. J. Biol. Chem. 232 (1958) 1093-1099. [PMID: 13549489]
3. Ostrowski, M.C. and Kistler, W.S. Properties of a flavoprotein sulfhydryl oxidase from rat seminal vesicle secretion. Biochemistry 19 (1980) 2639-2645. [PMID: 7397095]
4. Hoober, K.L., Joneja, B., White, H.B., 3rd and Thorpe, C. A sulfhydryl oxidase from chicken egg white. J. Biol. Chem. 271 (1996) 30510-30516. [PMID: 8940019]
5. Jaje, J., Wolcott, H.N., Fadugba, O., Cripps, D., Yang, A.J., Mather, I.H. and Thorpe, C. A flavin-dependent sulfhydryl oxidase in bovine milk. Biochemistry 46 (2007) 13031-13040. [PMID: 17944490]
6. Sevier, C.S., Cuozzo, J.W., Vala, A., Aslund, F. and Kaiser, C.A. A flavoprotein oxidase defines a new endoplasmic reticulum pathway for biosynthetic disulphide bond formation. Nat. Cell Biol. 3 (2001) 874-882. [PMID: 11584268]
7. Dabir, D.V., Leverich, E.P., Kim, S.K., Tsai, F.D., Hirasawa, M., Knaff, D.B. and Koehler, C.M. A role for cytochrome c and cytochrome c peroxidase in electron shuttling from Erv1. EMBO J. 26 (2007) 4801-4811. [PMID: 17972915]
8. Farrell, S.R. and Thorpe, C. Augmenter of liver regeneration: a flavin-dependent sulfhydryl oxidase with cytochrome c reductase activity. Biochemistry 44 (2005) 1532-1541. [PMID: 15683237]
9. Gross, E., Sevier, C.S., Heldman, N., Vitu, E., Bentzur, M., Kaiser, C.A., Thorpe, C. and Fass, D. Generating disulfides enzymatically: reaction products and electron acceptors of the endoplasmic reticulum thiol oxidase Ero1p. Proc. Natl. Acad. Sci. USA 103 (2006) 299-304. [PMID: 16407158]
10. de la Motte, R.S. and Wagner, F.W. Aspergillus niger sulfhydryl oxidase. Biochemistry 26 (1987) 7363-7371. [PMID: 3427078]
11. Riemer, J., Bulleid, N. and Herrmann, J.M. Disulfide formation in the ER and mitochondria: two solutions to a common process. Science 324 (2009) 1284-1287. [PMID: 19498160]
Accepted name: L-ascorbate peroxidase
Reaction: 2 L-ascorbate + H2O2 + 2 H+ = L-ascorbate + L-dehydroascorbate + 2 H2O (overall reaction)
(1a) 2 L-ascorbate + H2O2 + 2 H+ = 2 monodehydroascorbate + 2 H2O
(1b) 2 monodehydroascorbate = L-ascorbate + L-dehydroascorbate (spontaneous)
Glossary: monodehydroascorbate = ascorbate radical
Other name(s): L-ascorbic acid peroxidase; L-ascorbic acid-specific peroxidase; ascorbate peroxidase; ascorbic acid peroxidase
Systematic name: L-ascorbate:hydrogen-peroxide oxidoreductase
Comments: A heme protein. Oxidizes ascorbate and low molecular weight aromatic substrates. The monodehydroascorbate radical produced is either directly reduced back to ascorbate by EC 1.6.5.4 [monodehydroascorbate reductase (NADH)] or undergoes non-enzymatic disproportionation to ascorbate and dehydroascorbate.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 72906-87-7
References:
1. Shigeoka, S., Nakano, Y. and Kitaoka, S. Purification and some properties of L-ascorbic-acid-specific peroxidase in Euglena gracilis. Z. Arch. Biochem. Biophys. 201 (1980) 121-127. [PMID: 6772104]
2. Shigeoka, S., Nakano, Y. and Kitaoka, S. Metabolism of hydrogen peroxide in Euglena gracilis Z by L-ascorbic acid peroxidase. Biochem. J. 186 (1980) 377-380. [PMID: 6768357]
3. Nakano, Y and Asada, K. Purification of ascorbate peroxidase in spinach chloroplasts; its inactivation in ascorbate-depleted medium and reactivation by monodehydroascorbate radical. Plant Cell Physiol. 28 (1987) 131-140.
4. Patterson, W.R. and Poulos, T.L. Crystal structure of recombinant pea cytosolic ascorbate peroxidase. Biochemistry 34 (1995) 4331-4341. [PMID: 7703247]
5. Sharp, K.H., Moody, P.C., Brown, K.A. and Raven, E.L. Crystal structure of the ascorbate peroxidase-salicylhydroxamic acid complex. Biochemistry 43 (2004) 8644-8651. [PMID: 15236572]
6. Macdonald, I.K., Badyal, S.K., Ghamsari, L., Moody, P.C. and Raven, E.L. Interaction of ascorbate peroxidase with substrates: a mechanistic and structural analysis. Biochemistry 45 (2006) 7808-7817. [PMID: 16784232]
[EC 1.14.99.30 Transferred entry: carotene 7,8-desaturase. Now EC 1.3.5.6, 9,9'-dicis-ζ-carotene desaturase. (EC 1.14.99.30 created 1999, deleted 2011)]
Accepted name: ferric-chelate reductase (NADH)
Reaction: 2 Fe(II) + NAD+ + H+ = 2 Fe(III) + NADH
Other name(s): ferric chelate reductase (ambigous); iron chelate reductase (ambigous); NADH:Fe3+-EDTA reductase; NADH2:Fe3+ oxidoreductase
Systematic name: Fe(II):NAD+ oxidoreductase
Comments: Involved in the transport of iron across plant plasma membranes.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 120720-17-4
References:
1. Askerlund, P., Larrson, C. and Widell, S. Localization of donor and acceptor sites of NADH dehydrogenase activities using inside-out and right-side-out plasma membrane vesicles from plants. FEBS Lett. 239 (1988) 23-28.
2. Brüggemann, W. and Moog, P.R. NADH-dependent Fe3+ EDTA and oxygen reduction by plasma membrane vesicles from barley roots. Physiol. Plant. 75 (1989) 245-254.
3. Brüggemann, W., Moog, P.R., Nakagawa, H., Janiesch, P. and Kuiper, P.J.C. Plasma membrane-bound NADH:Fe3+-EDTA reductase and iron deficiency in tomato (Lycopersicon esculentum). Is there a Turbo reductase ? Physiol. Plant. 79 (1990) 339-346.
4. Buckhout, T.J. and Hrubec, T.C. Pyridine nucleotide-dependent ferricyanide reduction associated with isolated plasma membranes of maize (Zea mays L.) roots. Protoplasma 135 (1986) 144-154.
5. Sandelius, A.S., Barr, R., Crane, F.L. and Morré, D.J. Redox reactions of plasma membranes isolated from soybean hypocotyls by phase partition. Plant Sci. 48 (1986) 1-10.
6. Mazoch, J., Tesarik, R., Sedlacek, V., Kucera, I. and Turanek, J. Isolation and biochemical characterization of two soluble iron(III) reductases from Paracoccus denitrificans. Eur. J. Biochem. 271 (2004) 553-562. [PMID: 14728682]
Accepted name: ferric-chelate reductase (NADPH)
Reaction: 2 Fe(II) + NADP+ + H+ = 2 Fe(III) + NADPH
Other name(s): ferric chelate reductase (ambigous); iron chelate reductase (ambigous); NADPH:Fe3+-EDTA reductase; ferric reductase, NADPH-dependent; yqjH (gene name)
Systematic name: Fe(II):NADP+ oxidoreductase
Comments: Contains FAD. The enzyme plays a role in iron homeostasis.
References:
1. Bamford, V.A., Armour, M., Mitchell, S.A., Cartron, M., Andrews, S.C. and Watson, K.A. Preliminary X-ray diffraction analysis of YqjH from Escherichia coli: a putative cytoplasmic ferri-siderophore reductase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 792-796. [PMID: 18765906]
2. Wang, S., Wu, Y. and Outten, F.W. Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli. J. Bacteriol. 193 (2011) 563-574. [PMID: 21097627]
Accepted name: rubredoxin—NAD(P)+ reductase
Reaction: 2 reduced rubredoxin + NAD(P)+ + H+ = 2 oxidized rubredoxin + NAD(P)H
Glossary: benzyl viologen = 1,1'-dibenzyl-4,4'-bipyridinium
2,6-dichloroindophenol = 4-(2,6-dichloro-4-hydroxyphenylimino)cyclohexa-2,5-dien-1-one
menadione = 2-methyl-1,4-naphthoquinone
rubredoxin
Other name(s): rubredoxin-nicotinamide adenine dinucleotide (phosphate) reductase; rubredoxin-nicotinamide adenine; dinucleotide phosphate reductase; NAD(P)+-rubredoxin oxidoreductase; NAD(P)H-rubredoxin oxidoreductase
Systematic name: rubredoxin:NAD(P)+ oxidoreductase
Comments: The enzyme from Pyrococcus furiosus requires FAD. It reduces a number of electron carriers, including benzyl viologen, menadione and 2,6-dichloroindophenol, but rubredoxin is the most efficient. Ferredoxin is not utilized.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 80237-97-4
References:
1. Petitdemange, H., Blusson, H. and Gay, R. Detection of NAD(P)H-rubredoxin oxidoreductases in Clostridia. Anal. Biochem. 116 (1981) 564-570. [PMID: 6274224]
2. Ma, K. and Adams, M.W.W. A hyperactive NAD(P)H:rubredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 181 (1999) 5530-5533. [PMID: 10464233]
Accepted name: photosystem I
Reaction: reduced plastocyanin + oxidized ferredoxin + hν = oxidized plastocyanin + reduced ferredoxin
Systematic name: plastocyanin:ferredoxin oxidoreductase (light-dependent)
Comments: Contains chlorophyll, phylloquinones, carotenoids and [4Fe-4S] clusters. Cytochrome c6 can act as an alternative electron donor, and flavodoxin as an alternative acceptor in some species.
References:
1. Takabe, T., Iwasaki, Y., Hibino, T. and Ando, T. Subunit composition of photosystem I complex that catalyzes light-dependent transfer of electrons from plastocyanin to ferredoxin. J. Biochem. 110 (1991) 622-627. [PMID: 1778985]
2. van Thor, J.J., Geerlings, T.H., Matthijs, H.C. and Hellingwerf, K.J. Kinetic evidence for the PsaE-dependent transient ternary complex photosystem I/Ferredoxin/Ferredoxin:NADP+ reductase in a cyanobacterium. Biochemistry 38 (1999) 12735-12746. [PMID: 10504244]
3. Chitnis, P.R. Photosystem I: function and physiology. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52 (2001) 593-626. [PMID: 11337410]
4. Amunts, A., Toporik, H., Borovikova, A. and Nelson, N. Structure determination and improved model of plant photosystem I. J. Biol. Chem. 285 (2010) 3478-3486. [PMID: 19923216]
Accepted name: tRNA (guanosine18-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanosine18 in tRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine18 in tRNA
Other name(s): tRNA (Gm18) 2'-O-methyltransferase; tRNA (Gm18) methyltransferase; TrmH; SpoU
Systematic name: S-adenosyl-L-methionine:tRNA (guanosine18-2'-O)-methyltransferase
Comments: The enzyme catalyses the methylation of guanosine18 in tRNA.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 37257-01-5
References:
1. Gefter, M.L. The in vitro synthesis of 2'-O-methylguanosine and 2-methylthio 6N (γ,γ-dimethylallyl) adenosine in transfer RNA of Escherichia coli. Biochem. Biophys. Res. Commun. 36 (1969) 435-441. [PMID: 4898378]
2. Kumagai, I., Watanabe, K. and Oshima, T. Thermally induced biosynthesis of 2'-O-methylguanosine in tRNA from an extreme thermophile, Thermus thermophilus HB27. Proc. Natl. Acad. Sci. USA 77 (1980) 1922-1926. [PMID: 6990416]
3. Hori, H., Yamazaki, N., Matsumoto, T., Watanabe, Y., Ueda, T., Nishikawa, K., Kumagai, I. and Watanabe, K. Substrate recognition of tRNA (guanosine-2'-)-methyltransferase from Thermus thermophilus HB27. J. Biol. Chem. 273 (1998) 25721-25727. [PMID: 9748240]
4. Pleshe, E., Truesdell, J. and Batey, R.T. Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 61 (2005) 722-728. [PMID: 16511140]
5. Ochi, A., Makabe, K., Kuwajima, K. and Hori, H. Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes. J. Biol. Chem. 285 (2010) 9018-9029. [PMID: 20053984]
Accepted name: 23S rRNA (uridine2479-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + uridine2479 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methyluridine2479 in 23S rRNA
Other name(s): AviRb
Systematic name: S-adenosyl-L-methionine:23S rRNA (uridine2479-2'-O)-methyltransferase
Comments: Streptomyces viridochromogenes produces the antibiotic avilamycin A which binds to the 50S ribosomal subunit to inhibit protein synthesis. To protect itself from the antibiotic, Streptomyces viridochromogenes utilizes two methyltransferases, 23S rRNA (uridine2479-2'-O)-methyltransferase and EC 2.1.1.209 [23S rRNA (guanine2535-N1)-methyltransferase], whose actions confer avilamycin resistance to the RNA.
References:
1. Mosbacher, T.G., Bechthold, A. and Schulz, G.E. Structure and function of the antibiotic resistance-mediating methyltransferase AviRb from Streptomyces viridochromogenes. J. Mol. Biol. 345 (2005) 535-545. [PMID: 15581897]
2. Treede, I., Jakobsen, L., Kirpekar, F., Vester, B., Weitnauer, G., Bechthold, A. and Douthwaite, S. The avilamycin resistance determinants AviRa and AviRb methylate 23S rRNA at the guanosine 2535 base and the uridine 2479 ribose. Mol. Microbiol. 49 (2003) 309-318. [PMID: 12828631]
3. Weitnauer, G., Gaisser, S., Trefzer, A., Stockert, S., Westrich, L., Quiros, L.M., Mendez, C., Salas, J.A. and Bechthold, A. An ATP-binding cassette transporter and two rRNA methyltransferases are involved in resistance to avilamycin in the producer organism Streptomyces viridochromogenes Tu57. Antimicrob. Agents Chemother. 45 (2001) 690-695. [PMID: 11181344]
Accepted name: 23S rRNA (guanine2535-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine2535 in 23S rRNA = S-adenosyl-L-homocysteine + N1-methylguanine2535 in 23S rRNA
Other name(s): AviRa
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine2535-N1)-methyltransferase
Comments: Streptomyces viridochromogenes produces the antibiotic avilamycin A which binds to the 50S ribosomal subunit to inhibit protein synthesis. To protect itself from the antibiotic, Streptomyces viridochromogenes utilizes two methyltransferases, 23S rRNA (guanine2535-N1)-methyltransferase and EC 2.1.1.208 [23S rRNA (uridine2479-2-O)-methyltransferase], whose actions confer avilamycin resistance to the RNA.
References:
1. Treede, I., Jakobsen, L., Kirpekar, F., Vester, B., Weitnauer, G., Bechthold, A. and Douthwaite, S. The avilamycin resistance determinants AviRa and AviRb methylate 23S rRNA at the guanosine 2535 base and the uridine 2479 ribose. Mol. Microbiol. 49 (2003) 309-318. [PMID: 12828631]
2. Weitnauer, G., Gaisser, S., Trefzer, A., Stockert, S., Westrich, L., Quiros, L.M., Mendez, C., Salas, J.A. and Bechthold, A. An ATP-binding cassette transporter and two rRNA methyltransferases are involved in resistance to avilamycin in the producer organism Streptomyces viridochromogenes Tu57. Antimicrob. Agents Chemother. 45 (2001) 690-695. [PMID: 11181344]
3. Mosbacher, T.G., Bechthold, A. and Schulz, G.E. Crystal structure of the avilamycin resistance-conferring methyltransferase AviRa from Streptomyces viridochromogenes. J. Mol. Biol. 329 (2003) 147-157. [PMID: 12742024]
Accepted name: demethylspheroidene O-methyltransferase
Reaction: S-adenosyl-L-methionine + demethylspheroidene = S-adenosyl-L-homocysteine + spheroidene
Other name(s): 1-hydroxycarotenoid O-methylase; 1-hydroxycarotenoid methylase; 1-HO-carotenoid methylase; CrtF
Systematic name: S-adenosyl-L-methionine:demethylspheroidene O-methyltransferase
Comments: In Rhodopseudomonas capsulata and Rubrivivax gelatinosus the enzyme is involved in biosynthesis of spheroidene [1,2,3]. In Rubrivivax gelatinosus the enzyme also catalyses the methylation of demethylspirilloxanthin to spirilloxanthin and the methylation of 3,4-didehydrorhodopin to anhydrorhodovibrin [2].
References:
1. Badenhop, F., Steiger, S., Sandmann, M. and Sandmann, G. Expression and biochemical characterization of the 1-HO-carotenoid methylase CrtF from Rhodobacter capsulatus. FEMS Microbiol. Lett. 222 (2003) 237-242. [PMID: 12770713]
2. Pinta, V., Ouchane, S., Picaud, M., Takaichi, S., Astier, C. and Reiss-Husson, F. Characterization of unusual hydroxy- and ketocarotenoids in Rubrivivax gelatinosus: involvement of enzyme CrtF or CrtA. Arch. Microbiol. 179 (2003) 354-362. [PMID: 12664193]
3. Scolnik, P.A., Walker, M.A. and Marrs, B.L. Biosynthesis of carotenoids derived from neurosporene in Rhodopseudomonas capsulata. J. Biol. Chem. 255 (1980) 2427-2432. [PMID: 7358679]
Accepted name: D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphosphoundecaprenol 2-β-glucuronyltransferase
Reaction: UDP-glucuronate + D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol = UDP + D-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol
Other name(s): GumK
Systematic name: UDP-glucuronate:D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol β-1,2-glucuronyltransferase
Comments: The enzyme is involved in the biosynthesis of the exopolysaccharides xanthan (in the bacterium Xanthomonas campestris) and acetan (in the bacterium Gluconacetobacter xylinus).
References:
1. Katzen, F., Ferreiro, D.U., Oddo, C.G., Ielmini, M.V., Becker, A., Puhler, A. and Ielpi, L. Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence. J. Bacteriol. 180 (1998) 1607-1617. [PMID: 9537354]
2. Ielpi, L., Couso, R.O. and Dankert, M.A. Sequential assembly and polymerization of the polyprenol-linked pentasaccharide repeating unit of the xanthan polysaccharide in Xanthomonas campestris. J. Bacteriol. 175 (1993) 2490-2500. [PMID: 7683019]
3. Kim, S.Y., Kim, J.G., Lee, B.M. and Cho, J.Y. Mutational analysis of the gum gene cluster required for xanthan biosynthesis in Xanthomonas oryzae pv oryzae. Biotechnol. Lett. 31 (2009) 265-270. [PMID: 18854951]
4. Barreras, M., Bianchet, M.A. and Ielpi, L. Crystallization and preliminary crystallographic characterization of GumK, a membrane-associated glucuronosyltransferase from Xanthomonas campestris required for xanthan polysaccharide synthesis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (2006) 880-883. [PMID: 16946469]
5. Barreras, M., Salinas, S.R., Abdian, P.L., Kampel, M.A. and Ielpi, L. Structure and mechanism of GumK, a membrane-associated glucuronosyltransferase. J. Biol. Chem. 283 (2008) 25027-25035. [PMID: 18596046]
6. Vojnov, A.A., Bassi, D.E., Daniels, M.J. and Dankert, M.A. Biosynthesis of a substituted cellulose from a mutant strain of Xanthomonas campestris. Carbohydr. Res. 337 (2002) 315-326. [PMID: 11841812]
7. Barreras, M., Abdian, P.L. and Ielpi, L. Functional characterization of GumK, a membrane-associated β-glucuronosyltransferase from Xanthomonas campestris required for xanthan polysaccharide synthesis. Glycobiology 14 (2004) 233-241. [PMID: 14736729]
Accepted name: Dol-P-Glc:Glc1Man9GlcNAc2-PP-Dol α-1,3-glucosyltransferase
Reaction: dolichyl β-D-glucosyl phosphate + D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = D-Glc-α-(1→3)-D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate
For diagram of reaction click here.
Other name(s): ALG8
Systematic name: dolichyl β-D-glucosyl phosphate:D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,3-glucosyltransferase
Comments: The successive addition of three glucose residues by EC 2.4.1.267 (Dol-P-Glc:Man9GlcNAc2-PP-Dol -1,3-glucosyltransferase), EC 2.4.1.265 and EC 2.4.1.256 (Dol-P-Glc:Glc2Man9GlcNAc2-PP-Dol 1,2-glucosyltransferase) represents the final stage of the lipid-linked oligosaccharide assembly.
References:
1. Stagljar, I., te Heesen, S. and Aebi, M. New phenotype of mutations deficient in glucosylation of the lipid-linked oligosaccharide: cloning of the ALG8 locus. Proc. Natl. Acad. Sci. USA 91 (1994) 5977-5981. [PMID: 8016100]
2. Runge, K.W. and Robbins, P.W. A new yeast mutation in the glucosylation steps of the asparagine-linked glycosylation pathway. Formation of a novel asparagine-linked oligosaccharide containing two glucose residues. J. Biol. Chem. 261 (1986) 15582-15590. [PMID: 3536907]
3. Chantret, I., Dancourt, J., Dupre, T., Delenda, C., Bucher, S., Vuillaumier-Barrot, S., Ogier de Baulny, H., Peletan, C., Danos, O., Seta, N., Durand, G., Oriol, R., Codogno, P. and Moore, S.E. A deficiency in dolichyl-P-glucose:Glc1Man9GlcNAc2-PP-dolichyl α3-glucosyltransferase defines a new subtype of congenital disorders of glycosylation. J. Biol. Chem. 278 (2003) 9962-9971. [PMID: 12480927]
Accepted name: glucosyl-3-phosphoglycerate synthase
Reaction: NDP-glucose + 3-phospho-D-glycerate = NDP + 2-O-(α-D-glucopyranosyl)-3-phospho-D-glycerate
Other name(s): GpgS protein; GPG synthase; glucosylphosphoglycerate synthase
Systematic name: NDP-glucose:3-phospho-D-glycerate 2-α-D-glucosyltransferase
Comments: The enzyme is involved in biosynthesis of 2-O-(α-D-glucopyranosyl)-D-glycerate via the two-step pathway in which glucosyl-3-phosphoglycerate synthase catalyses the conversion of GDP-glucose and 3-phospho-D-glycerate into 2-O-(α-D-glucopyranosyl)-3-phospho-D-glycerate, which is then converted to 2-O-(α-D-glucopyranosyl)-D-glycerate by EC 3.1.3.85 glucosyl-3-phosphoglycerate phosphatase. The activity is dependent on divalent cations (Mn2+, Co2+, or Mg2+). The enzyme from Persephonella marina shows moderate flexibility on the sugar donor concerning the nucleotide moiety (UDP-glucose, ADP-glucose, GDP-glucose) but is strictly specific for glucose. The enzyme is also strictly specific for 3-phospho-D-glycerate as acceptor [1]. The enzyme from Methanococcoides burtonii is strictly specific for GDP-glucose and 3-phospho-D-glycerate [2]. This enzyme catalyses the first glucosylation step in methylglucose lipopolysaccharide biosynthesis in mycobacteria [4,5].
References:
1. Costa, J., Empadinhas, N. and da Costa, M.S. Glucosylglycerate biosynthesis in the deepest lineage of the bacteria: characterization of the thermophilic proteins GpgS and GpgP from Persephonella marina. J. Bacteriol. 189 (2007) 1648-1654. [PMID: 17189358]
2. Costa, J., Empadinhas, N., Goncalves, L., Lamosa, P., Santos, H. and da Costa, M.S. Characterization of the biosynthetic pathway of glucosylglycerate in the archaeon Methanococcoides burtonii. J. Bacteriol. 188 (2006) 1022-1030. [PMID: 16428406]
3. Empadinhas, N., Albuquerque, L., Mendes, V., Macedo-Ribeiro, S. and da Costa, M.S. Identification of the mycobacterial glucosyl-3-phosphoglycerate synthase. FEMS Microbiol. Lett. 280 (2008) 195-202. [PMID: 18221489]
4. Pereira, P.J., Empadinhas, N., Albuquerque, L., Sa-Moura, B., da Costa, M.S. and Macedo-Ribeiro, S. Mycobacterium tuberculosis glucosyl-3-phosphoglycerate synthase: structure of a key enzyme in methylglucose lipopolysaccharide biosynthesis. PLoS One 3 (2008) e3748. [PMID: 19015727]
5. Gest, P., Kaur, D., Pham, H.T., van der Woerd, M., Hansen, E., Brennan, P.J., Jackson, M. and Guerin, M.E. Preliminary crystallographic analysis of GpgS, a key glucosyltransferase involved in methylglucose lipopolysaccharide biosynthesis in Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 1121-1124. [PMID: 19052364]
6. Kaur, D., Pham, H., Larrouy-Maumus, G., Riviere, M., Vissa, V., Guerin, M.E., Puzo, G., Brennan, P.J. and Jackson, M. Initiation of methylglucose lipopolysaccharide biosynthesis in mycobacteria. PLoS One 4 (2009) e544. [PMID: 19421329]
Accepted name: Dol-P-Glc:Man9GlcNAc2-PP-Dol α-1,3-glucosyltransferase
Reaction: dolichyl β-D-glucosyl phosphate + D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate
For diagram of reaction click here.
Other name(s): ALG6
Systematic name: dolichyl β-D-glucosyl phosphate:D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,3-glucosyltransferase
Comments: The successive addition of three glucose residues by EC 2.4.1.267, EC 2.4.1.265 (Dol-P-Glc:Glc1Man9GlcNAc2-PP-Dol -1,3-glucosyltransferase) and EC 2.4.1.256 (Dol-P-Glc:Glc2Man9GlcNAc2-PP-Dol 1,2-glucosyltransferase) represents the final stage of the lipid-linked oligosaccharide assembly.
References:
1. Reiss, G., te Heesen, S., Zimmerman, J., Robbins, P.W. and Aebi, M. Isolation of the ALG6 locus of Saccharomyces cerevisiae required for glucosylation in the N-linked glycosylation pathway. Glycobiology 6 (1996) 493-498. [PMID: 8877369]
2. Runge, K.W., Huffaker, T.C. and Robbins, P.W. Two yeast mutations in glucosylation steps of the asparagine glycosylation pathway. J. Biol. Chem. 259 (1984) 412-417. [PMID: 6423630]
3. Westphal, V., Xiao, M., Kwok, P.Y. and Freeze, H.H. Identification of a frequent variant in ALG6, the cause of congenital disorder of glycosylation-Ic. Hum. Mutat. 22 (2003) 420-421. [PMID: 14517965]
Accepted name: glucosylglycerate synthase
Reaction: ADP-glucose + D-glycerate = 2-O-(α-D-glucopyranosyl)-D-glycerate + ADP
Other name(s): Ggs (gene name)
Systematic name: ADP-glucose:D-glycerate 2-α-D-glucosyltransferase
Comments: Persephonella marina possesses two enzymatic systems for the synthesis of glucosylglycerate. The first one is a single-step pathway in which glucosylglycerate synthase catalyses the synthesis of 2-O-(α-D-glucopyranosyl)-D-glycerate in one-step from ADP-glucose and D-glycerate. The second system is a two-step pathway in which EC 2.4.1.266 (glucosyl-3-phosphoglycerate synthase) catalyses the conversion of NDP-glucose and 3-phospho-D-glycerate into 2-O-(α-D-glucopyranosyl)-3-phospho-D-glycerate, which is then converted to 2-O-(α-D-glucopyranosyl)-D-glycerate by EC 3.1.3.85 (glucosyl-3-phosphoglycerate phosphatase).
References:
1. Fernandes, C., Empadinhas, N. and da Costa, M.S. Single-step pathway for synthesis of glucosylglycerate in Persephonella marina. J. Bacteriol. 189 (2007) 4014-4019. [PMID: 17369297]
2. Fernandes, C., Mendes, V., Costa, J., Empadinhas, N., Jorge, C., Lamosa, P., Santos, H. and da Costa, M.S. Two alternative pathways for the synthesis of the rare compatible solute mannosylglucosylglycerate in Petrotoga mobilis. J. Bacteriol. 192 (2010) 1624-1633. [PMID: 20061481]
Accepted name: mannosylglycerate synthase
Reaction: GDP-mannose + D-glycerate = GDP + 2-O-(α-D-mannopyranosyl)-D-glycerate
Systematic name: GDP-mannose:D-glycerate 2-α-D-mannosyltransferase
Comments: Rhodothermus marinus can also form mannosylglycerate via a two-step pathway catalysed by EC 2.4.1.217 (mannosyl-3-phosphoglycerate synthase) and EC 3.1.3.70 (mannosyl-3-phosphoglycerate phosphatase) [1]. Depending on experimental conditions mannosylglycerate synthase is more or less specific for the GDP-mannose and D-glycerate [1,2].
References:
1. Martins, L.O., Empadinhas, N., Marugg, J.D., Miguel, C., Ferreira, C., da Costa, M.S. and Santos, H. Biosynthesis of mannosylglycerate in the thermophilic bacterium Rhodothermus marinus. Biochemical and genetic characterization of a mannosylglycerate synthase. J. Biol. Chem. 274 (1999) 35407-35414. [PMID: 10585410]
2. Flint, J., Taylor, E., Yang, M., Bolam, D.N., Tailford, L.E., Martinez-Fleites, C., Dodson, E.J., Davis, B.G., Gilbert, H.J. and Davies, G.J. Structural dissection and high-throughput screening of mannosylglycerate synthase. Nat. Struct. Mol. Biol. 12 (2005) 608-614. [PMID: 15951819]
Accepted name: mannosylglucosyl-3-phosphoglycerate synthase
Reaction: GDP-mannose + 2-O-(α-D-glucopyranosyl)-3-phospho-D-glycerate = GDP + 2-O-[2-O-(α-D-mannopyranosyl)-α-D-glucopyranosyl]-3-phospho-D-glycerate
Other name(s): MggA
Systematic name: GDP-mannose:2-O-(α-D-glucosyl)-3-phospho-D-glycerate 2-O-α-D-mannosyltransferase
Comments: The enzyme is involved in synthesis of 2-[2-O-(α-D-mannopranosyl)-α-D-glucopyranosyl]-D-glycerate. Petrotoga miotherma and Petrotoga mobilis accumulate this compound in response to water stress imposed by salt.
References:
1. Fernandes, C., Mendes, V., Costa, J., Empadinhas, N., Jorge, C., Lamosa, P., Santos, H. and da Costa, M.S. Two alternative pathways for the synthesis of the rare compatible solute mannosylglucosylglycerate in Petrotoga mobilis. J. Bacteriol. 192 (2010) 1624-1633. [PMID: 20061481]
Accepted name: lipid IVA 4-amino-4-deoxy-L-arabinosyltransferase
Reaction: (1) 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + α-Kdo-(2→4)-α-Kdo-(2→6)-lipid A = -Kdo-(24)--Kdo-(26)-[4'-P-L-Ara4N]-lipid A + ditrans,octacis-undecaprenyl phosphate
(2) 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + lipid IVA = lipid IIA + ditrans,octacis-undecaprenyl phosphate
(3) 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = 4'-α-L-Ara4N-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + ditrans,octacis-undecaprenyl phosphate
Glossary: lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phospho-α-D-glucopyranose
lipid IIA = 4-amino-4-deoxy-β-L-arabinopyranosyl 2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-α-D-glucopyranosyl phosphate
α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
4'-α-L-Ara4N-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = 4-amino-4-deoxy-α-L-arabinopyranosyl 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-phospho-β-D-glucopyranosy-(1→6)-2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-α-D-glucopyranosyl phosphate
lipid A = lipid A of Escherichia coli = 2-deoxy-2-{[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino}-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phospho-α-D-glucopyranose
α-Kdo-(2→4)-α-Kdo-(2→6)-lipid A = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino}-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phospho-α-D-glucopyranose
α-Kdo-(2→4)-α-Kdo-(2→6)-[4'-P-α-L-Ara4N]-lipid A = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino}-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-(4-amino-4-deoxy-α-L-arabinopyranosyl)phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phospho-α-D-glucopyranose
Other name(s): undecaprenyl phosphate-α-L-Ara4N transferase; 4-amino-4-deoxy-L-arabinose lipid A transferase; polymyxin resistance protein PmrK, arnT (gene name)
Systematic name: 4-amino-4-deoxy-α-L-2-aminoarabinopyranosyl ditrans,octacis-undecaprenyl phosphate:lipid IVA L-2-aminoarabinopyranosyltransferase
Comments: Integral membrane protein present in the inner membrane of certain Gram negative endobacteria. In strains that do not produce 3-deoxy-D-manno-octulosonic acid (Kdo), the enzyme adds a single arabinose unit to the 1-phosphate moiety of the tetra-acylated lipid A precursor, lipid IVA. In the presence of a Kdo disaccharide, the enzyme primarily adds an arabinose unit to the 4-phosphate of lipid A molecules. The Salmonella typhimurium enzyme can add arabinose units to both positions.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:
References:
1. Trent, M.S., Ribeiro, A.A., Lin, S., Cotter, R.J. and Raetz, C.R. An inner membrane enzyme in Salmonella and Escherichia coli that transfers 4-amino-4-deoxy-L-arabinose to lipid A: induction on polymyxin-resistant mutants and role of a novel lipid-linked donor. J. Biol. Chem. 276 (2001) 43122-43131. [PMID: 11535604]
2. Trent, M.S., Ribeiro, A.A., Doerrler, W.T., Lin, S., Cotter, R.J. and Raetz, C.R. Accumulation of a polyisoprene-linked amino sugar in polymyxin-resistant Salmonella typhimurium and Escherichia coli: structural characterization and transfer to lipid A in the periplasm. J. Biol. Chem. 276 (2001) 43132-43144. [PMID: 11535605]
3. Zhou, Z., Ribeiro, A.A., Lin, S., Cotter, R.J., Miller, S.I. and Raetz, C.R. Lipid A modifications in polymyxin-resistant Salmonella typhimurium: PMRA-dependent 4-amino-4-deoxy-L-arabinose, and phosphoethanolamine incorporation. J. Biol. Chem. 276 (2001) 43111-43121. [PMID: 11535603]
4. Bretscher, L.E., Morrell, M.T., Funk, A.L. and Klug, C.S. Purification and characterization of the L-Ara4N transferase protein ArnT from Salmonella typhimurium. Protein Expr. Purif. 46 (2006) 33-39. [PMID: 16226890]
5. Impellitteri, N.A., Merten, J.A., Bretscher, L.E. and Klug, C.S. Identification of a functionally important loop in Salmonella typhimurium ArnT. Biochemistry 49 (2010) 29-35. [PMID: 19947657]
Accepted name: S-methyl-5'-thioinosine phosphorylase
Reaction: S-methyl-5'-thioinosine + phosphate = hypoxanthine + S-methyl-5-thio-α-D-ribose 1-phosphate
Other name(s): MTIP; MTI phosphorylase; methylthioinosine phosphorylase
Systematic name: S-methyl-5'-thioinosine:phosphate S-methyl-5-thio-α-D-ribosyl-transferase
Comments: No activity with S-methyl-5'-thioadenosine. The catabolism of of 5'-methylthioadenosine in Pseudomonas aeruginosa involves deamination to S-methyl-5'-thioinosine (EC 3.5.4.31, S-methyl-5'-thioadenosine deaminase) and phosphorolysis to hypoxanthine [1].
References:
1. Guan, R., Ho, M.C., Almo, S.C. and Schramm, V.L. Methylthioinosine phosphorylase from Pseudomonas aeruginosa. Structure and annotation of a novel enzyme in quorum sensing. Biochemistry 50 (2011) 1247-1254. [PMID: 21197954]
Accepted name: protein-fructosamine 3-kinase
Reaction: ATP + [protein]-N6-D-fructosyl-L-lysine = ADP + [protein]-N6-(3-O-phospho-D-fructosyl)-L-lysine
Other name(s): FN3K; fructosamine 3-kinase
Systematic name: ATP:[protein]-N6-D-fructosyl-L-lysine 3-phosphotransferase
Comments: Nonenzymatic glycation is an important factor in the pathogenesis of diabetic complications. Key early intermediates in this process are fructosamines, such as [protein]-N6-D-fructosyl-L-lysine. Fructosamine-3-kinase is part of an ATP-dependent system for removing carbohydrates from nonenzymatically glycated proteins. The phosphorylation destablilizes the [protein]-N6-D-fructosyl-L-lysine adduct and leads to its spontaneous decomposition. cf. EC 2.7.1.172, protein-ribulosamine 3-kinase.
References:
1. Szwergold, B.S., Howell, S. and Beisswenger, P.J. Human fructosamine-3-kinase: purification, sequencing, substrate specificity, and evidence of activity in vivo. Diabetes 50 (2001) 2139-2147. [PMID: 11522682]
2. Delpierre, G., Rider, M.H., Collard, F., Stroobant, V., Vanstapel, F., Santos, H. and Van Schaftingen, E. Identification, cloning, and heterologous expression of a mammalian fructosamine-3-kinase. Diabetes 49 (2000) 1627-1634. [PMID: 11016445]
Accepted name: protein-ribulosamine 3-kinase
Reaction: ATP + [protein]-N6-D-ribulosyl-L-lysine = ADP + [protein]-N6-(3-O-phospho-D-ribulosyl)-L-lysine
Other name(s): Fn3KRP; FN3K-related protein; FN3K-RP; ketosamine 3-kinase 2; fructosamine-3-kinase-related protein; ribulosamine/erythrulosamine 3-kinase; ribulosamine 3-kinase
Systematic name: ATP:[protein]-N6-D-ribulosyl-L-lysine 3-phosphotransferase
Comments: This enzyme plays a role in freeing proteins from ribulosamines or psicosamines, which might arise from the reaction of amines with glucose and/or glycolytic intermediates. This role is shared by EC 2.7.1.171 (protein-fructosamine 3-kinase), which has, in addition, the unique capacity to phosphorylate fructosamines [1]. The plant enzyme also phosphorylates [protein]-N6-D-erythrulosyl-L-lysine [2]. No activity with [protein]-N6-D-fructosyl-L-lysine [1,2].
References:
1. Collard, F., Delpierre, G., Stroobant, V., Matthijs, G. and Van Schaftingen, E. A mammalian protein homologous to fructosamine-3-kinase is a ketosamine-3-kinase acting on psicosamines and ribulosamines but not on fructosamines. Diabetes 52 (2003) 2888-2895. [PMID: 14633848]
2. Fortpied, J., Gemayel, R., Stroobant, V. and van Schaftingen, E. Plant ribulosamine/erythrulosamine 3-kinase, a putative protein-repair enzyme. Biochem. J. 388 (2005) 795-802. [PMID: 15705060]
3. Payne, L.S., Brown, P.M., Middleditch, M., Baker, E., Cooper, G.J. and Loomes, K.M. Mapping of the ATP-binding domain of human fructosamine 3-kinase-related protein by affinity labelling with 5'-[p-(fluorosulfonyl)benzoyl]adenosine. Biochem. J. 416 (2008) 281-288. [PMID: 18637789]
Accepted name: 1L-myo-inositol 1-phosphate cytidylyltransferase
Reaction: CTP + 1L-myo-inositol 1-phosphate = diphosphate + CDP-1L-myo-inositol
For diagram of reaction click here.
Glossary: 1L-myo-inositol 1-phosphate = 1D-myo-inositol 3-phosphate
Other name(s): CTP:inositol-1-phosphate cytidylyltransferase (bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase (IPCT/DIPPS)); IPCT (bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase (IPCT/DIPPS)); L-myo-inositol-1-phosphate cytidylyltransferase
Systematic name: CTP:1L-myo-inositol 1-phosphate cytidylyltransferase
Comments: In many organisms this activity is catalysed by a bifunctional enzyme. The cytidylyltransferase domain of the bifunctional EC 2.7.7.74/EC 2.7.8.34 (CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase) is absolutely specific for CTP and 1L-myo-inositol 1-phosphate. The enzyme is involved in biosynthesis of bis(1L-myo-inositol) 1,3'-phosphate, a widespread organic solute in microorganisms adapted to hot environments.
References:
1. Rodrigues, M.V., Borges, N., Henriques, M., Lamosa, P., Ventura, R., Fernandes, C., Empadinhas, N., Maycock, C., da Costa, M.S. and Santos, H. Bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase, the key enzyme for di-myo-inositol-phosphate synthesis in several (hyper)thermophiles. J. Bacteriol. 189 (2007) 5405-5412. [PMID: 17526717]
Accepted name: molybdopterin adenylyltransferase
Reaction: ATP + molybdopterin = diphosphate + adenylyl-molybdopterin
Glossary: molybdopterin = H2Dtpp-mP = ((5aR,8R,9aR)-2-amino-6,7-dimercapto-4-oxo-4,5,5a,8,9a,10-hexahydro-1H-pyrano[3,2-g]pteridin-8-yl)methyl dihydrogen phosphate = [(5aR,8R,9aR)-2-amino-4-oxo-6,7-disulfanyl-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogen phosphate
Other name(s): MogA; Cnx1 (ambiguous)
Systematic name: ATP:molybdopterin adenylyltransferase
Comments: Catalyses the activation of molybdopterin for molybdenum insertion. In eukaryotes, this reaction is catalysed by the C-terminal domain of a fusion protein that also includes molybdopterin molybdotransferase (EC 2.10.1.1). The reaction requires a divalent cation such as Mg2+ or Mn2+.
References:
1. Nichols, J.D. and Rajagopalan, K.V. In vitro molybdenum ligation to molybdopterin using purified components. J. Biol. Chem. 280 (2005) 7817-7822. [PMID: 15632135]
2. Kuper, J., Palmer, T., Mendel, R.R. and Schwarz, G. Mutations in the molybdenum cofactor biosynthetic protein Cnx1G from Arabidopsis thaliana define functions for molybdopterin binding, molybdenum insertion, and molybdenum cofactor stabilization. Proc. Natl. Acad. Sci. USA 97 (2000) 6475-6480. [PMID: 10823911]
3. Llamas, A., Mendel, R.R. and Schwarz, G. Synthesis of adenylated molybdopterin: an essential step for molybdenum insertion. J. Biol. Chem. 279 (2004) 55241-55246. [PMID: 15504727]
Accepted name: molybdenum cofactor cytidylyltransferase
Reaction: CTP + molybdenum cofactor = diphosphate + cytidylyl molybdenum cofactor
Glossary: molybdenum cofactor = MoCo = MoO2(OH)Dtpp-mP = {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kS)-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)molybdate
Other name(s): MocA, CTP:molybdopterin cytidylyltransferase, MoCo cytidylyltransferase, Mo-MPT cytidyltransferase
Systematic name: CTP:molybdenum cofactor cytidylyltransferase
Comments: Catalyses the cytidylation of the molybdenum cofactor. This modification occurs only in prokaryotes. Divalent cations such as Mg2+ or Mn2+ are required for activity. ATP or GTP cannot replace CTP.
References:
1. Neumann, M., Mittelstadt, G., Seduk, F., Iobbi-Nivol, C. and Leimkuhler, S. MocA is a specific cytidylyltransferase involved in molybdopterin cytosine dinucleotide biosynthesis in Escherichia coli. J. Biol. Chem. 284 (2009) 21891-21898. [PMID: 19542235]
2. Neumann, M., Seduk, F., Iobbi-Nivol, C. and Leimkuhler, S. Molybdopterin dinucleotide biosynthesis in Escherichia coli: Identification of amino acid residues of molybdopterin dinucleotide transferases that determine specificity for binding of guanine or cytosine nucleotides. J. Biol. Chem. 286 (2011) 1400-1408. [PMID: 21081498]
Accepted name: CDP-L-myo-inositol myo-inositolphosphotransferase
Reaction: CDP-1L-myo-inositol + 1L-myo-inositol 1-phosphate = CMP + bis(1L-myo-inositol) 3,1'-phosphate 1-phosphate
For diagram of reaction click here.
Glossary: 1L-myo-inositol 1-phosphate = 1D-myo-inositol 3-phosphate
Other name(s): CDP-inositol:inositol-1-phosphate transferase (bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase (IPCT/DIPPS)); DIPPS (bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase (IPCT/DIPPS))
Systematic name: CDP-1L-myo-inositol:1L-myo-inositol 1-phosphate myo-inositolphosphotransferase
Comments: In many organisms this activity is catalysed by a bifunctional enzyme. The di-myo-inositol-1,3'-phosphate-1'-phosphate synthase domain of the bifunctional EC 2.7.7.74/EC 2.7.8.34 (CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase) uses only 1L-myo-inositol 1-phosphate as an alcohol acceptor, but CDP-glycerol, as well as CDP-1L-myo-inositol and CDP-D-myo-inositol, are recognized as alcohol donors. The enzyme is involved in biosynthesis of bis(1L-myo-inositol) 1,3-phosphate, a widespread organic solute in microorganisms adapted to hot environments.
References:
1. Rodrigues, M.V., Borges, N., Henriques, M., Lamosa, P., Ventura, R., Fernandes, C., Empadinhas, N., Maycock, C., da Costa, M.S. and Santos, H. Bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase, the key enzyme for di-myo-inositol-phosphate synthesis in several (hyper)thermophiles. J. Bacteriol. 189 (2007) 5405-5412. [PMID: 17526717]
EC 2.10 Transferring molybdenum- or tungsten-containing groups
EC 2.10.1 Molybdenumtransferases or tungstentransferases with sulfide groups as acceptors.
Accepted name: molybdopterin molybdotransferase
Reaction: adenylyl-molybdopterin + molybdate = molybdenum cofactor + AMP
Glossary: molybdopterin = H2Dtpp-mP = ((5aR,8R,9aR)-2-amino-6,7-dimercapto-4-oxo-4,5,5a,8,9a,10-hexahydro-1H-pyrano[3,2-g]pteridin-8-yl)methyl dihydrogen phosphate = [(5aR,8R,9aR)-2-amino-4-oxo-6,7-disulfanyl-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogen phosphate
Other name(s): MoeA; Cnx1 (ambiguous)
Systematic name: adenylyl-molybdopterin:molybdate molybdate transferase (AMP-forming)
Comments: Catalyses the insertion of molybdenum into the ene-dithiol group of molybdopterin. In eukaryotes this reaction is catalysed by the N-terminal domain of a fusion protein whose C-terminal domain catalyses EC 2.7.7.75, molybdopterin adenylyltransferase. Requires divalent cations such as Mg2+ or Zn2+ for activity.
References:
1. Nichols, J.D. and Rajagopalan, K.V. In vitro molybdenum ligation to molybdopterin using purified components. J. Biol. Chem. 280 (2005) 7817-7822. [PMID: 15632135]
2. Nichols, J.D., Xiang, S., Schindelin, H. and Rajagopalan, K.V. Mutational analysis of Escherichia coli MoeA: two functional activities map to the active site cleft. Biochemistry 46 (2007) 78-86. [PMID: 17198377]
3. Llamas, A., Otte, T., Multhaup, G., Mendel, R.R. and Schwarz, G. The Mechanism of nucleotide-assisted molybdenum insertion into molybdopterin. A novel route toward metal cofactor assembly. J. Biol. Chem. 281 (2006) 18343-18350. [PMID: 16636046]
Accepted name: fumonisin B1 esterase
Reaction: fumonisin B1 + 2 H2O = aminopentol + 2 propane-1,2,3-tricarboxylate
Glossary: fumonisin B1 = (2R,2'R)-2,2'-{[(5R,6R,7S,9S,11R,16R,18S,19S)-19-amino-11,16,18-trihydroxy-5,9-dimethylicosane-6,7-diyl]bis[oxy(2-oxoethane-2,1-diyl)]}dibutanedioic acid
Other name(s): fumD (gene name)
Systematic name: fumonisin B1 acylhydrolase
Comments: The enzyme is involved in degradation of fumonisin B1 [1].
References:
1. Heinl, S., Hartinger, D., Thamhesl, M., Vekiru, E., Krska, R., Schatzmayr, G., Moll, W.D. and Grabherr, R. Degradation of fumonisin B1 by the consecutive action of two bacterial enzymes. J. Biotechnol. 145 (2010) 120-129. [PMID: 19922747]
Accepted name: pyrethroid hydrolase
Reaction: trans-permethrin + H2O = (3-phenoxyphenyl)methanol + (1S,3R)-3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropanecarboxylate
Other name(s): pyrethroid-hydrolyzing carboxylesterase; pyrethroid-hydrolysing esterase; pyrethroid-hydrolyzing esterase; pyrethroid-selective esterase; pyrethroid-cleaving enzyme; permethrinase; PytH; EstP
Systematic name: pyrethroid-ester hydrolase
Comments: The enzyme is involved in degradation of pyrethroid pesticides. The enzymes from Sphingobium sp., Klebsiella sp. and Aspergillus niger hydrolyse cis-permethrin at approximately equal rate to trans-permethrin [1-3]. The enzyme from mouse hydrolyses trans-permethrin at a rate about 22-fold higher than cis-permethrin [4].
References:
1. Wang, B.Z., Guo, P., Hang, B.J., Li, L., He, J. and Li, S.P. Cloning of a novel pyrethroid-hydrolyzing carboxylesterase gene from Sphingobium sp. strain JZ-1 and characterization of the gene product. Appl. Environ. Microbiol. 75 (2009) 5496-5500. [PMID: 19581484]
2. Wu, P.C., Liu, Y.H., Wang, Z.Y., Zhang, X.Y., Li, H., Liang, W.Q., Luo, N., Hu, J.M., Lu, J.Q., Luan, T.G. and Cao, L.X. Molecular cloning, purification, and biochemical characterization of a novel pyrethroid-hydrolyzing esterase from Klebsiella sp. strain ZD112. J. Agric. Food Chem. 54 (2006) 836-842. [PMID: 16448191]
3. Liang, W.Q., Wang, Z.Y., Li, H., Wu, P.C., Hu, J.M., Luo, N., Cao, L.X. and Liu, Y.H. Purification and characterization of a novel pyrethroid hydrolase from Aspergillus niger ZD11. J. Agric. Food Chem. 53 (2005) 7415-7420. [PMID: 16159167]
4. Stok, J.E., Huang, H., Jones, P.D., Wheelock, C.E., Morisseau, C. and Hammock, B.D. Identification, expression, and purification of a pyrethroid-hydrolyzing carboxylesterase from mouse liver microsomes. J. Biol. Chem. 279 (2004) 29863-29869. [PMID: 15123619]
5. Maloney, S.E., Maule, A. and Smith, A.R. Purification and preliminary characterization of permethrinase from a pyrethroid-transforming strain of Bacillus cereus. Appl. Environ. Microbiol. 59 (1993) 2007-2013. [PMID: 8357241]
6. Guo, P., Wang, B., Hang, B., Li, L., Ali, W., He, J.and Li, S. Pyrethroid-degrading Sphingobium sp. JZ-2 and the purification and characterization of a novel pyrethroid hydrolase. Int. Biodeter. Biodegrad. 63 (2009) 1107-1112.
Accepted name: glucosyl-3-phosphoglycerate phosphatase
Reaction: 2-O-(α-D-glucopyranosyl)-3-phospho-D-glycerate + H2O = 2-O-(α-D-glucopyranosyl)-D-glycerate + phosphate
Other name(s): GpgP protein
Systematic name: α-D-glucosyl-3-phospho-D-glycerate phosphohydrolase
Comments: The enzyme is involved in biosynthesis of 2-O-(α-D-glucopyranosyl)-D-glycerate via the two-step pathway in which EC 2.4.1.266 (glucosyl-3-phosphoglycerate synthase) catalyses the conversion of GDP-glucose and 3-phospho-D-glycerate into 2-O-(α-D-glucopyranosyl)-3-phospho-D-glycerate, which is then converted to 2-O-(α-D-glucopyranosyl)-D-glycerate by glucosyl-3-phosphoglycerate phosphatase. In vivo the enzyme catalyses the dephosphorylation of 2-O-(α-D-mannopyranosyl)-3-phospho-D-glycerate with lower efficiency [1,2]. Divalent metal ions (Mg2+, Mn2+ or Co2+) stimulate activity [1,2].
References:
1. Costa, J., Empadinhas, N. and da Costa, M.S. Glucosylglycerate biosynthesis in the deepest lineage of the bacteria: characterization of the thermophilic proteins GpgS and GpgP from Persephonella marina. J. Bacteriol. 189 (2007) 1648-1654. [PMID: 17189358]
2. Costa, J., Empadinhas, N., Goncalves, L., Lamosa, P., Santos, H. and da Costa, M.S. Characterization of the biosynthetic pathway of glucosylglycerate in the archaeon Methanococcoides burtonii. J. Bacteriol. 188 (2006) 1022-1030. [PMID: 16428406]
Accepted name: α-N-acetylgalactosaminidase
Reaction: Cleavage of nonreducing α-(1→3)-N-acetylgalactosamine residues from human blood group A and AB mucin glycoproteins, Forssman hapten and blood group A lacto series glycolipids
Other name(s): α-acetylgalactosaminidase; N-acetyl-α-D-galactosaminidase; N-acetyl-α-galactosaminidase; α-NAGAL; α-NAGA; α-GalNAcase
Systematic name: α-N-acetyl-D-galactosaminide N-acetylgalactosaminohydrolase
Comments: The human lysosomal enzyme is involved in the degradation of blood type A epitope.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 9075-63-2
References:
1. Asfaw, B., Schindler, D., Ledvinova, J., Cerny, B., Smid, F. and Conzelmann, E. Degradation of blood group A glycolipid A-6-2 by normal and mutant human skin fibroblasts. J. Lipid Res. 39 (1998) 1768-1780. [PMID: 9741689]
2. Zhu, A., Monahan, C., Wang, Z.K. and Goldstein, J. Expression, purification, and characterization of recombinant α-N-acetylgalactosaminidase produced in the yeast Pichia pastoris. Protein Expr. Purif. 8 (1996) 456-462. [PMID: 8954893]
3. Clark, N.E. and Garman, S.C. The 1.9 Å structure of human α-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases. J. Mol. Biol. 393 (2009) 435-447. [PMID: 19683538]
4. Hoskins, L.C., Boulding, E.T. and Larson, G. Purification and characterization of blood group A-degrading isoforms of α-N-acetylgalactosaminidase from Ruminococcus torques strain IX-70. J. Biol. Chem. 272 (1997) 7932-7939. [PMID: 9065462]
5. Harun-Or-Rashid, M., Matsuzawa, T., Satoh, Y., Shiraishi, T., Ando, M., Sadik, G. and Uda, Y. Purification and characterization of α-N-acetylgalactosaminidases I and II from the starfish Asterina amurensis. Biosci. Biotechnol. Biochem. 74 (2010) 256-261. [PMID: 20139603]
6. Weignerova, L., Filipi, T., Manglova, D. and Kren, V. Induction, purification and characterization of α-N-acetylgalactosaminidase from Aspergillus niger. Appl. Microbiol. Biotechnol. 79 (2008) 769-774. [PMID: 18443780]
7. Ashida, H., Tamaki, H., Fujimoto, T., Yamamoto, K. and Kumagai, H. Molecular cloning of cDNA encoding α-N-acetylgalactosaminidase from Acremonium sp. and its expression in yeast. Arch. Biochem. Biophys. 384 (2000) 305-310. [PMID: 11368317]
Accepted name: endo-α-N-acetylgalactosaminidase
Reaction: 3-O-β-D-galactosyl-N-acetyl-α-D-galactosaminyl-L-serine-[protein] + H2O = 3-O-β-D-galactosyl-N-acetyl-α-D-galactosamine + L-serine-[protein]
Other name(s): endo-α-acetylgalactosaminidase; endo-α-N-acetyl-D-galactosaminidase; mucinaminylserine mucinaminidase; D-galactosyl-3-(N-acetyl-α-D-galactosaminyl)-L-serine mucinaminohydrolase; endo-α-GalNAc-ase; glycopeptide α-N-acetylgalactosaminidase; D-galactosyl-N-acetyl-α-D-galactosamine D-galactosyl-N-acetyl-galactosaminohydrolase
Systematic name: glycopeptide-D-galactosyl-N-acetyl-α-D-galactosamine D-galactosyl-N-acetyl-galactosaminohydrolase
Comments: The enzyme catalyses the liberation of Gal-(1→3)-β-GalNAc α-linked to serine or threonine residues of mucin-type glycoproteins. EngBF from Bifidobacterium longum specifically acts on core 1-type O-glycan to release the disaccharide Gal-(1→3)-β-GalNAc. The enzymes from Clostridium perfringens, Enterococcus faecalis, Propionibacterium acnes and Alcaligenes faecalis show broader specificity (e.g. release of the core 2 trisaccharide Gal-(1→3)-β-(GlcNAc-(1→6)-β)-GalNAc or the core 3 disaccharide GlcNAc-(1→3)-β-GalNAc) [1,2]. The enzyme may play an important role in the degradation and utilization of mucins having core 1 O-glycan.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 59793-96-3
References:
1. Ashida, H., Maki, R., Ozawa, H., Tani, Y., Kiyohara, M., Fujita, M., Imamura, A., Ishida, H., Kiso, M. and Yamamoto, K. Characterization of two different endo-α-N-acetylgalactosaminidases from probiotic and pathogenic enterobacteria, Bifidobacterium longum and Clostridium perfringens. Glycobiology 18 (2008) 727-734. [PMID: 18559962]
2. Koutsioulis, D., Landry, D. and Guthrie, E.P. Novel endo-α-N-acetylgalactosaminidases with broader substrate specificity. Glycobiology 18 (2008) 799-805. [PMID: 18635885]
3. Fujita, K., Oura, F., Nagamine, N., Katayama, T., Hiratake, J., Sakata, K., Kumagai, H. and Yamamoto, K. Identification and molecular cloning of a novel glycoside hydrolase family of core 1 type O-glycan-specific endo-α-N-acetylgalactosaminidase from Bifidobacterium longum. J. Biol. Chem. 280 (2005) 37415-37422. [PMID: 16141207]
4. Suzuki, R., Katayama, T., Kitaoka, M., Kumagai, H., Wakagi, T., Shoun, H., Ashida, H., Yamamoto, K. and Fushinobu, S. Crystallographic and mutational analyses of substrate recognition of endo-α-N-acetylgalactosaminidase from Bifidobacterium longum. J. Biochem. 146 (2009) 389-398. [PMID: 19502354]
5. Gregg, K.J. and Boraston, A.B. Cloning, recombinant production, crystallization and preliminary X-ray diffraction analysis of a family 101 glycoside hydrolase from Streptococcus pneumoniae. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 133-135. [PMID: 19194003]
6. Ashida, H., Yamamoto, K., Murata, T., Usui, T. and Kumagai, H. Characterization of endo-α-N-acetylgalactosaminidase from Bacillus sp. and syntheses of neo-oligosaccharides using its transglycosylation activity. Arch. Biochem. Biophys. 373 (2000) 394-400. [PMID: 10620364]
7. Goda, H.M., Ushigusa, K., Ito, H., Okino, N., Narimatsu, H. and Ito, M. Molecular cloning, expression, and characterization of a novel endo-α-N-acetylgalactosaminidase from Enterococcus faecalis. Biochem. Biophys. Res. Commun. 375 (2008) 441-446. [PMID: 18725192]
Accepted name: rhamnogalacturonan hydrolase
Reaction: Endohydrolysis of α-D-GalA-(1→2)-α-L-Rha glycosidic bond in the rhamnogalacturonan I backbone with initial inversion of anomeric configuration releasing oligosaccharides with β-D-GalA at the reducing end.
For diagram of reaction click here.
Other name(s): rhamnogalacturonase A; RGase A; RG-hydrolase
Systematic name: rhamnogalacturonan α-D-GalA-(1→2)-α-L-Rha hydrolase
Comments: The enzyme is part of the degradation system for rhamnogalacturonan I in Aspergillus aculeatus.
References:
1. Petersen, T.N., Kauppinen, S. and Larsen, S. The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel β helix. Structure 5 (1997) 533-544. [PMID: 9115442]
2. Kofod, L.V., Kauppinen, S., Christgau, S., Andersen, L.N., Heldt-Hansen, H.P., Dorreich, K. and Dalboge, H. Cloning and characterization of two structurally and functionally divergent rhamnogalacturonases from Aspergillus aculeatus. J. Biol. Chem. 269 (1994) 29182-29189. [PMID: 7961884]
3. Azadi, P., O'Neill, M.A., Bergmann, C., Darvill, A.G. and Albersheim, P. The backbone of the pectic polysaccharide rhamnogalacturonan I is cleaved by an endohydrolase and an endolyase. Glycobiology 5 (1995) 783-789. [PMID: 8720076]
4. Petersen, T.N., Christgau, S., Kofod, L.V., Kauppinen, S., Johnson, A.H. and Larsen, S. Crystallization and preliminary X-ray studies of rhamnogalacturonase A from Aspergillus aculeatus. Acta Crystallogr. D Biol. Crystallogr. 53 (1997) 105-107. [PMID: 15299976]
5. Pitson, S.M., Mutter, M., van den Broek, L.A., Voragen, A.G. and Beldman, G. Stereochemical course of hydrolysis catalysed by α-L-rhamnosyl and α-D-galacturonosyl hydrolases from Aspergillus aculeatus. Biochem. Biophys. Res. Commun. 242 (1998) 552-559. [PMID: 9464254]
Accepted name: unsaturated rhamnogalacturonyl hydrolase
Reaction: 2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose + H2O = 4-deoxy-β-L-threo-hex-4-enopyranuronose + L-rhamnopyranose
For diagram of reaction click here.
Glossary: 6-deoxy-2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-mannopyranose =
Other name(s): YteR; YesR
Systematic name: 2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose hydrolase
Comments: The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168.
References:
1. Itoh, T., Ochiai, A., Mikami, B., Hashimoto, W. and Murata, K. A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide. J. Mol. Biol. 360 (2006) 573-585. [PMID: 16781735]
2. Zhang, R., Minh, T., Lezondra, L., Korolev, S., Moy, S.F., Collart, F. and Joachimiak, A. 1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Proteins 60 (2005) 561-565. [PMID: 15906318]
3. Itoh, T., Ochiai, A., Mikami, B., Hashimoto, W. and Murata, K. Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate. Biochem. Biophys. Res. Commun. 347 (2006) 1021-1029. [PMID: 16870154]
Accepted name: rhamnogalacturonan galacturonohydrolase
Reaction: Exohydrolysis of the α-D-GalA-(1→2)-α-L-Rha bond in rhamnogalacturonan oligosaccharides with initial inversion of configuration releasing D-galacturonic acid from the non-reducing end of rhamnogalacturonan oligosaccharides.
For diagram of reaction click here.
Other name(s): RG-galacturonohydrolase
Systematic name: rhamnogalacturonan oligosaccharide α-D-GalA-(1→2)-α-L-Rha galacturonohydrolase
Comments: The enzyme is part of the degradation system for rhamnogalacturonan I in Aspergillus aculeatus.
References:
1. Mutter, M., Beldman, G., Pitson, S.M., Schols, H.A. and Voragen, A.G. Rhamnogalacturonan α-D-galactopyranosyluronohydrolase. An enzyme that specifically removes the terminal nonreducing galacturonosyl residue in rhamnogalacturonan regions of pecti. Plant Physiol. 117 (1998) 153-163. [PMID: 9576784]
Accepted name: rhamnogalacturonan rhamnohydrolase
Reaction: Exohydrolysis of the α-L-Rha-(1→4)-α-D-GalA bond in rhamnogalacturonan oligosaccharides with initial inversion of configuration releasing β-L-rhamnose from the non-reducing end of rhamnogalacturonan oligosaccharides.
For diagram of reaction click here.
Other name(s): RG-rhamnohydrolase; RG α-L-rhamnopyranohydrolase
Systematic name: rhamnogalacturonan oligosaccharide α-L-Rha-(1→4)-α-D-GalA rhamnohydrolase
Comments: The enzyme is part of the degradation system for rhamnogalacturonan I in Aspergillus aculeatus.
References:
1. Pitson, S.M., Mutter, M., van den Broek, L.A., Voragen, A.G. and Beldman, G. Stereochemical course of hydrolysis catalysed by α-L-rhamnosyl and α-D-galacturonosyl hydrolases from Aspergillus aculeatus. Biochem. Biophys. Res. Commun. 242 (1998) 552-559. [PMID: 9464254]
2. Mutter, M., Beldman, G., Schols, H.A. and Voragen, A.G. Rhamnogalacturonan α-L-rhamnopyranohydrolase. A novel enzyme specific for the terminal nonreducing rhamnosyl unit in rhamnogalacturonan regions of pectin. Plant Physiol. 106 (1994) 241-250. [PMID: 7972516]
Accepted name: β-D-glucopyranosyl abscisate β-glucosidase
Reaction: β-D-glucopyranosyl abscisate + H2O = β-D-glucose + abscisate
For diagram of reaction click here.
Other name(s): AtBG1; ABA-β-D-glucosidase; ABA-specific β-glucosidase; ABA-GE hydrolase; β-D-glucopyranosyl abscisate hydrolase
Systematic name: β-D-glucopyranosyl abscisate glucohydrolase
Comments: The enzyme hydrolzes the biologically inactive β-D-glucopyranosyl ester of abscisic acid to produce active abscisate. Abscisate is a phytohormone critical for plant growth, development and adaption to various stress conditions. The enzyme does not hydrolyse β-D-glucopyranosyl zeatin [1].
References:
1. Lee, K.H., Piao, H.L., Kim, H.Y., Choi, S.M., Jiang, F., Hartung, W., Hwang, I., Kwak, J.M., Lee, I.J. and Hwang, I. Activation of glucosidase via stress-induced polymerization rapidly increases active pools of abscisic acid. Cell 126 (2006) 1109-1120. [PMID: 16990135]
2. Kato-Noguchi, H. and Tanaka, Y. Effect of ABA-β-D-glucopyranosyl ester and activity of ABA-β-D-glucosidase in Arabidopsis thaliana. J. Plant Physiol. 165 (2008) 788-790. [PMID: 17923167]
3. Dietz, K.J., Sauter, A., Wichert, K., Messdaghi, D. and Hartung, W. Extracellular β-glucosidase activity in barley involved in the hydrolysis of ABA glucose conjugate in leaves. J. Exp. Bot. 51 (2000) 937-944. [PMID: 10948220]
Accepted name: β-peptidyl aminopeptidase
Reaction: Cleaves N-terminal β-homoamino acids from peptides composed of 2 to 6 amino acids
Other name(s): BapA (ambiguous)
Comments: Sphingosinicella xenopeptidilytica strain 3-2W4 is able to utilize the β-peptides β-homoVal-β-homoAla-β-homoLeu and β-homoAla-β-homoLeu as sole carbon and energy sources [2].
References:
1. Heck, T., Limbach, M., Geueke, B., Zacharias, M., Gardiner, J., Kohler, H.P. and Seebach, D. Enzymatic degradation of β- and mixed α,β-oligopeptides. Chem. Biodivers. 3 (2006) 1325-1348. [PMID: 17193247]
2. Geueke, B., Namoto, K., Seebach, D. and Kohler, H.P. A novel β-peptidyl aminopeptidase (BapA) from strain 3-2W4 cleaves peptide bonds of synthetic β-tri- and β-dipeptides. J. Bacteriol. 187 (2005) 5910-5917. [PMID: 16109932]
3. Geueke, B., Heck, T., Limbach, M., Nesatyy, V., Seebach, D. and Kohler, H.P. Bacterial β-peptidyl aminopeptidases with unique substrate specificities for β-oligopeptides and mixed β,α-oligopeptides. FEBS J. 273 (2006) 5261-5272. [PMID: 17064315]
4. Heck, T., Kohler, H.P., Limbach, M., Flšgel, O., Seebach, D. and Geueke, B. Enzyme-catalyzed formation of β-peptides: β-peptidyl aminopeptidases BapA and DmpA acting as β-peptide-synthesizing enzymes. Chem. Biodivers. 4 (2007) 2016. [PMID: 17886858]
[EC 3.4.13.3 Deleted entry: Xaa-His dipeptidase. The activity is covered by EC 3.4.13.18, cytosol nonspecific dipeptidase and EC 3.4.13.20, β-Ala-His dipeptidase. (EC 3.4.13.3 created 1961 as EC 3.4.3.3, transferred 1972 to EC 3.4.13.3, modified 1989 (EC 3.4.13.13 created 1981, incorporated 1992), deleted 2011)]
Accepted name: S-methyl-5'-thioadenosine deaminase
Reaction: S-methyl-5'-thioadenosine + H2O = 5'-S-methyl-5'-thioinosine + NH3
Other name(s): MTA deaminase; 5-methylthioadenosine deaminase
Systematic name: S-methyl-5'-thioadenosine amidohydrolase
Comments: The enzyme from Thermotoga maritima also functions as S-adenosylhomocysteine deaminase (EC 3.5.4.28) and has some activity against adenosine. Adenosine-5-monophosphate (AMP) and S-adenosyl-L-methionine (SAM) are not substrates.
References:
1. Hermann, J.C., Marti-Arbona, R., Fedorov, A.A., Fedorov, E., Almo, S.C., Shoichet, B.K. and Raushel, F.M. Structure-based activity prediction for an enzyme of unknown function. Nature 448 (2007) 775-779. [PMID: 17603473]
Accepted name: salicylate decarboxylase
Reaction: salicylate = phenol + CO2
Other name(s): salicylic acid decarboxylase; Scd
Systematic name: salicylate carboxy-lyase
Comments: In the reverse direction the enzyme catalyses the regioselective carboxylation of phenol into stoichiometric amounts of salicylate. The enzyme also catalyses the reversible decarboxylation of 2,4-dihydroxybenzoate, 2,6-dihydroxybenzoate, 2,3-dihydroxybenzoate and 4-aminosalicylate [1].
References:
1. Kirimura, K., Gunji, H., Wakayama, R., Hattori, T. and Ishii, Y. Enzymatic Kolbe-Schmitt reaction to form salicylic acid from phenol: enzymatic characterization and gene identification of a novel enzyme, Trichosporon moniliiforme salicylic acid decarboxylase. Biochem. Biophys. Res. Commun. 394 (2010) 279-284. [PMID: 20188702]
Accepted name: indole-3-carboxylate decarboxylase
Reaction: indole-3-carboxylate = indole + CO2
Systematic name: indole-3-carboxylate carboxy-lyase
Comments: Activated by Zn2+, Mn2+ or Mg2+.
References:
1. Yoshida, T., Fujita, K. and Nagasawa, T. Novel reversible indole-3-carboxylate decarboxylase catalyzing nonoxidative decarboxylation. Biosci. Biotechnol. Biochem. 66 (2002) 2388-2394. [PMID: 12506977]
Accepted name: linalool dehydratase
Reaction: linalool = myrcene + H2O
Systematic name: linalool hydro-lyase (myrcene-forming)
Comments: In absence of oxygen the bifunctional linalool dehydratase-isomerase can catalyse in vitro two reactions, the dehydration of linalool to myrcene and the isomerization of geraniol to linalool (the latter activity is classified as EC 5.4.4.4, geraniol isomerase).
References:
1. Brodkorb, D., Gottschall, M., Marmulla, R., Luddeke, F. and Harder, J. Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes. J. Biol. Chem. 285 (2010) 30436-30442. [PMID: 20663876]
Accepted name: lupan-3β,20-diol synthase
Reaction: lupan-3β,20-diol = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
Other name(s): LUP1 (gene name); (S)-squalene-2,3-epoxide hydro-lyase (lupan-3β,20-diol forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (lupan-3β,20-diol forming)
Comments: The reaction occurs in the reverse direction. The recombinant enzyme from Arabidopsis thaliana gives a 1:1 mixture of lupeol and lupan-3β,20-diol with small amounts of β-amyrin, germanicol, taraxasterol and ψ-taraxasterol. See EC 5.4.99.41 (lupeol synthase).
References:
1. Segura, M.J., Meyer, M.M. and Matsuda, S.P. Arabidopsis thaliana LUP1 converts oxidosqualene to multiple triterpene alcohols and a triterpene diol. Org. Lett. 2 (2000) 2257-2259. [PMID: 10930257]
2. Kushiro, T., Hoshino, M., Tsutsumi, T., Kawai, K., Shiro, M., Shibuya, M. and Ebizuka, Y. Stereochemical course in water addition during LUP1-catalyzed triterpene cyclization. Org. Lett. 8 (2006) 5589-5592. [PMID: 17107079]
Accepted name: squalene—hopanol cyclase
Reaction: hopan-22-ol = squalene + H2O
For diagram of reaction click here.
Other name(s): squalene—hopene cyclase (ambiguos)
Systematic name: hopan-22-ol hydro-lyase
Comments: The enzyme produces the cyclization products hopene (cf. EC 5.4.99.17) and hopanol from squalene at a constant ratio of 5:1.
References:
1. Hoshino, T., Nakano, S., Kondo, T., Sato, T. and Miyoshi, A. Squalene-hopene cyclase: final deprotonation reaction, conformational analysis for the cyclization of (3R,S)-2,3-oxidosqualene and further evidence for the requirement of an isopropylidene moiety both for initiation of the polycyclization cascade and for the formation of the 5-membered E-ring. Org Biomol Chem 2 (2004) 1456-1470. [PMID: 15136801]
2. Sato, T., Kouda, M. and Hoshino, T. Site-directed mutagenesis experiments on the putative deprotonation site of squalene-hopene cyclase from Alicyclobacillus acidocaldarius. Biosci. Biotechnol. Biochem. 68 (2004) 728-738. [PMID: 15056909]
Accepted name: rhamnogalacturonan endolyase
Reaction: Endotype eliminative cleavage of L-α-rhamnopyranosyl-(1→4)-α-D-galactopyranosyluronic acid bonds of rhamnogalacturonan I domains in ramified hairy regions of pectin leaving L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the nonreducing end.
For diagram of reaction click here.
Other name(s): rhamnogalacturonase B; α-L-rhamnopyranosyl-(1→4)-α-D-galactopyranosyluronide lyase; Rgase B; rhamnogalacturonan α-L-rhamnopyranosyl-(1,4)-α-D-galactopyranosyluronide lyase; RG-lyase; YesW; RGL4; Rgl11A; Rgl11Y; RhiE
Systematic name: α-L-rhamnopyranosyl-(1→4)-α-D-galactopyranosyluronate endolyase
Comments: The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168 and Aspergillus aculeatus.
References:
1. Mutter, M., Colquhoun, I.J., Schols, H.A., Beldman, G. and Voragen, A.G. Rhamnogalacturonase B from Aspergillus aculeatus is a rhamnogalacturonan α-L-rhamnopyranosyl-(1→4)-α-D-galactopyranosyluronide lyase. Plant Physiol. 110 (1996) 73-77. [PMID: 8587995]
2. Azadi, P., O'Neill, M.A., Bergmann, C., Darvill, A.G. and Albersheim, P. The backbone of the pectic polysaccharide rhamnogalacturonan I is cleaved by an endohydrolase and an endolyase. Glycobiology 5 (1995) 783-789. [PMID: 8720076]
3. Mutter, M., Colquhoun, I.J., Beldman, G., Schols, H.A., Bakx, E.J. and Voragen, A.G. Characterization of recombinant rhamnogalacturonan α-L-rhamnopyranosyl-(1,4)-α-D-galactopyranosyluronide lyase from Aspergillus aculeatus. An enzyme that fragments rhamnogalacturonan I regions of pectin. Plant Physiol. 117 (1998) 141-152. [PMID: 9576783]
4. Kadirvelraj, R., Harris, P., Poulsen, J.C., Kauppinen, S. and Larsen, S. A stepwise optimization of crystals of rhamnogalacturonan lyase from Aspergillus aculeatus. Acta Crystallogr. D Biol. Crystallogr. 58 (2002) 1346-1349. [PMID: 12136151]
5. Laatu, M. and Condemine, G. Rhamnogalacturonate lyase RhiE is secreted by the out system in Erwinia chrysanthemi. J. Bacteriol. 185 (2003) 1642-1649. [PMID: 12591882]
6. Pages, S., Valette, O., Abdou, L., Belaich, A. and Belaich, J.P. A rhamnogalacturonan lyase in the Clostridium cellulolyticum cellulosome. J. Bacteriol. 185 (2003) 4727-4733. [PMID: 12896991]
7. Ochiai, A., Yamasaki, M., Itoh, T., Mikami, B., Hashimoto, W. and Murata, K. Crystallization and preliminary X-ray analysis of the rhamnogalacturonan lyase YesW from Bacillus subtilis strain 168, a member of polysaccharide lyase family 11. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (2006) 438-440. [PMID: 16682770]
8. Jensen, M.H., Otten, H., Christensen, U., Borchert, T.V., Christensen, L.L., Larsen, S. and Leggio, L.L. Structural and biochemical studies elucidate the mechanism of rhamnogalacturonan lyase from Aspergillus aculeatus. J. Mol. Biol. 404 (2010) 100-111. [PMID: 20851126]
Accepted name: rhamnogalacturonan exolyase
Reaction: Exotype eliminative cleavage of α-L-rhamnopyranosyl-(1→4)-α-D-galactopyranosyluronic acid bonds of rhamnogalacturonan I oligosacharides containing α-L-rhamnopyranose at the reducing end and 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the nonreducing end. The products are the disaccharide 2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose and the shortened rhamnogalacturonan oligosaccharide containing one 4-deoxy-4,5-unsaturated D-galactopyranosyluronic acid at the non-reducing end.
For diagram of reaction click here.
Glossary: 6-deoxy-2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-mannopyranose =
Other name(s): YesX
Systematic name: α-L-rhamnopyranosyl-(1→4)-α-D-galactopyranosyluronate exolyase
Comments: The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168.
References:
1. Ochiai, A., Itoh, T., Mikami, B., Hashimoto, W. and Murata, K. Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. J. Biol. Chem. 284 (2009) 10181-10189. [PMID: 19193638]
2. Ochiai, A., Itoh, T., Kawamata, A., Hashimoto, W. and Murata, K. Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization. Appl. Environ. Microbiol. 73 (2007) 3803-3813. [PMID: 17449691]
Accepted name: germacradienol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
For diagram of reaction click here.
Other name(s): germacradienol/germacrene-D synthase; 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase [(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol-forming]
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol-forming]
Comments: Requires Mg2+ for activity. H-1si of farnesyl diphosphate is lost in the formation of (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol. Formation of (–)-germacrene D involves a stereospecific 1,3-hydride shift of H-1si of farnesyl diphosphate. Both products are formed from a common intermediate [2]. Other enzymes produce germacrene D as the sole product using a different mechanism. The enzyme mediates a key step in the biosynthesis of geosmin (see EC 4.1.99.16 geosmin synthase), a widely occurring metabolite of many streptomycetes, bacteria and fungi [2]. Also catalyses the reaction of EC 4.2.3.75, (–)-germacrene D synthase.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 211049-88-6
References:
1. Cane, D.E. and Watt, R.M. Expression and mechanistic analysis of a germacradienol synthase from Streptomyces coelicolor implicated in geosmin biosynthesis. Proc. Natl. Acad. Sci. USA 100 (2003) 1547-1551. [PMID: 12556563]
2. He, X. and Cane, D.E. Mechanism and stereochemistry of the germacradienol/germacrene D synthase of Streptomyces coelicolor A3(2). J. Am. Chem. Soc. 126 (2004) 2678-2679. [PMID: 14995166]
3. Gust, B., Challis, G.L., Fowler, K., Kieser, T. and Chater, K.F. PCR-targeted Streptomyces gene replacement identifies a protein domain
needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc. Natl. Acad. Sci. USA 100 (2003) 1541-1546. [PMID: 12563033]
Accepted name: (2R)-sulfolactate sulfo-lyase
Reaction: (2R)-3-sulfolactate = pyruvate + bisulfite
Other name(s): Suy; SuyAB; 3-sulfolactate bisulfite-lyase; sulfolactate sulfo-lyase (ambigious)
Systematic name: (2R)-3-sulfolactate bisulfite-lyase (pyruvate-forming)
Comments: Requires iron(II). This inducible enzyme participates in cysteate degradation in Paracoccus pantotrophus NKNCYSA and in 3-sulfolactate degradation in Chromohalobacter salexigens. The enzyme is specific for the (R) isomer.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 1256650-35-7
References:
1. Graham, D.E. and White, R.H. Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat. Prod. Rep. 19 (2002) 133-147. [PMID: 12013276]
2. Rein, U., Gueta, R., Denger, K., Ruff, J., Hollemeyer, K. and Cook, A.M. Dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in Paracoccus pantotrophus NKNCYSA. Microbiology 151 (2005) 737-747. [PMID: 15758220]
3. Denger, K. and Cook, A.M. Racemase activity effected by two dehydrogenases in sulfolactate degradation by Chromohalobacter salexigens: purification of (S)-sulfolactate dehydrogenase. Microbiology 156 (2010) 967-974. [PMID: 20007648]
Accepted name: ζ-carotene isomerase
Reaction: 9,15,9'-tricis-ζ-carotene = 9,9'-dicis-ζ-carotene
For diagram of reaction click here.
Other name(s): Z-ISO; 15-cis-ζ-carotene isomerase
Systematic name: 9,15,9'-tricis-ζ-carotene cis-trans-isomerase
Comments: Involved in carotenoid biosynthesis.
References:
1. Chen, Y., Li, F. and Wurtzel, E.T. Isolation and characterization of the Z-ISO gene encoding a missing component of carotenoid biosynthesis in plants. Plant Physiol. 153 (2010) 66-79. [PMID: 20335404]
2. Li, F., Murillo, C. and Wurtzel, E.T. Maize Y9 encodes a product essential for 15-cis-ζ-carotene isomerization. Plant Physiol. 144 (2007) 1181-1189. [PMID: 17434985]
Accepted name: prolycopene isomerase
Reaction: 7,9,7',9'-tetracis-lycopene = all-trans-lycopene
For diagram of reaction click here.
Glossary: prolycopene = 7,9,7',9'-tetracis-lycopene
Other name(s): CRTISO; carotene cis-trans isomerase; ZEBRA2 (gene name); carotene isomerase; carotenoid isomerase
Systematic name: 7,9,7',9'-tetracis-lycopene cis-trans-isomerase
Comments: Requires FADH2 [1]. The enzyme is involved in carotenoid biosynthesis.
References:
1. Yu, Q., Ghisla, S., Hirschberg, J., Mann, V. and Beyer, P. Plant carotene cis-trans isomerase CRTISO: a new member of the FADred-dependent flavoproteins catalyzing non-redox reactions. J. Biol. Chem. 286 (2011) 8666-8676. [PMID: 21209101]
2. Li, Q., Farre, G., Naqvi, S., Breitenbach, J., Sanahuja, G., Bai, C., Sandmann, G., Capell, T., Christou, P. and Zhu, C. Cloning and functional characterization of the maize carotenoid isomerase and β-carotene hydroxylase genes and their regulation during endosperm maturation. Transgenic Res. 19 (2010) 1053-1068. [PMID: 20221689]
3. Isaacson, T., Ronen, G., Zamir, D. and Hirschberg, J. Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of β-carotene and xanthophylls in plants. Plant Cell 14 (2002) 333-342. [PMID: 11884678]
4. Chai, C., Fang, J., Liu, Y., Tong, H., Gong, Y., Wang, Y., Liu, M., Wang, Y., Qian, Q., Cheng, Z. and Chu, C. ZEBRA2, encoding a carotenoid isomerase, is involved in photoprotection in rice. Plant Mol. Biol. 75 (2011) 211-221. [PMID: 21161331]
Accepted name: trans-2,3-dihydro-3-hydroxyanthranilate isomerase
Reaction: (5S,6S)-6-amino-5-hydroxycyclohexane-1,3-diene-1-carboxyate = (1R,6S)-6-amino-5-oxocyclohex-2-ene-1-carboxylate
Glossary: (5S,6S)-6-amino-5-hydroxycyclohexane-1,3-diene-1-carboxylate = trans-2,3-dihydro-3-hydroxyanthranilate
Other name(s): phzF (gene name)
Systematic name: (5S,6S)-6-amino-5-hydroxycyclohexane-1,3-diene-1-carboxyate isomerase
Comments: The enzyme is involved in phenazine biosynthesis.
References:
1. Parsons, J.F., Song, F., Parsons, L., Calabrese, K., Eisenstein, E. and Ladner, J.E. Structure and function of the phenazine biosynthesis protein PhzF from Pseudomonas fluorescens 2-79. Biochemistry 43 (2004) 12427-12435. [PMID: 15449932]
2. Blankenfeldt, W., Kuzin, A.P., Skarina, T., Korniyenko, Y., Tong, L., Bayer, P., Janning, P., Thomashow, L.S. and Mavrodi, D.V. Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens. Proc. Natl. Acad. Sci. USA 101 (2004) 16431-16436. [PMID: 15545603]
3. Parsons, J.F., Calabrese, K., Eisenstein, E. and Ladner, J.E. Structure of the phenazine biosynthesis enzyme PhzG. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 2110-2113. [PMID: 15502343]
4. Mavrodi, D.V., Bleimling, N., Thomashow, L.S. and Blankenfeldt, W. The purification, crystallization and preliminary structural characterization of PhzF, a key enzyme in the phenazine-biosynthesis pathway from Pseudomonas fluorescens 2-79. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 184-186. [PMID: 14684924]
5. Ahuja, E.G., Janning, P., Mentel, M., Graebsch, A., Breinbauer, R., Hiller, W., Costisella, B., Thomashow, L.S., Mavrodi, D.V. and Blankenfeldt, W. PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis. J. Am. Chem. Soc. 130 (2008) 17053-17061. [PMID: 19053436]
Accepted name: geraniol isomerase
Reaction: geraniol = linalool
Systematic name: geraniol hydroxymutase
Comments: In absence of oxygen the bifunctional linalool dehydratase-isomerase can catalyse in vitro two reactions, the isomerization of geraniol to linalool and the dehydration of linalool to myrcene, the latter activity being classified as EC 4.2.1.127, linalool dehydratase.
References:
1. Brodkorb, D., Gottschall, M., Marmulla, R., Luddeke, F. and Harder, J. Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes. J. Biol. Chem. 285 (2010) 30436-30442. [PMID: 20663876]
Accepted name: squalene—hopene cyclase
Reaction: squalene = hop-22(29)-ene
For diagram of reaction click here
Systematic name: squalene mutase (cyclizing, hop-22(29)-ene-forming)
Comments: The enzyme also produces the cyclization product hopan-22-ol by addition of water (cf. EC 4.2.1.129, squaleneÑhopanol cyclase). Hopene and hopanol are formed at a constant ratio of 5:1.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 76600-69-6
References:
1. Hoshino, T. and Sato, T. Squalene-hopene cyclase: catalytic mechanism and substrate recognition. Chem. Commun. (2002) 291-301. [PMID: 12120044]
2. Hoshino, T., Nakano, S., Kondo, T., Sato, T. and Miyoshi, A. Squalene-hopene cyclase: final deprotonation reaction, conformational analysis for the cyclization of (3R,S)-2,3-oxidosqualene and further evidence for the requirement of an isopropylidene moiety both for initiation of the polycyclization cascade and for the formation of the 5-membered E-ring. Org Biomol Chem 2 (2004) 1456-1470. [PMID: 15136801]
3. Sato, T., Kouda, M. and Hoshino, T. Site-directed mutagenesis experiments on the putative deprotonation site of squalene-hopene cyclase from Alicyclobacillus acidocaldarius. Biosci. Biotechnol. Biochem. 68 (2004) 728-738. [PMID: 15056909]
4. Reinert, D.J., Balliano, G. and Schulz, G.E. Conversion of squalene to the pentacarbocyclic hopene. Chem. Biol. 11 (2004) 121-126. [PMID: 15113001]
Accepted name: dammaradiene synthase
Reaction: squalene = dammara-20,24-diene
For diagram of reaction click here.
Systematic name: squalene mutase (cyclizing, dammara-20,24-diene-forming)
References:
1. Shinozaki, J., Shibuya, M., Masuda, K. and Ebizuka, Y. Dammaradiene synthase, a squalene cyclase, from Dryopteris crassirhizoma Nakai. Phytochemistry 69 (2008) 2559-2564. [PMID: 18790509]
Accepted name: camelliol C synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = camelliol C
Other name(s): CAMS1; LUP3 (gene name)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, camelliol-C-forming)
Comments: The product is 97% camelliol, 2% achilleol A and 0.2% β-amyrin. Achilleol is an isomer of camelliol C with a 4-methylenecyclohexanol ring system. This enzyme probably evolved from EC 5.4.99.39, β-amyrin synthase.
References:
1. Kolesnikova, M.D., Wilson, W.K., Lynch, D.A., Obermeyer, A.C. and Matsuda, S.P. Arabidopsis camelliol C synthase evolved from enzymes that make pentacycles. Org. Lett. 9 (2007) 5223-5226. [PMID: 17985917]
Accepted name: β-amyrin synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = β-amyrin
Other name(s): 2,3-oxidosqualene β-amyrin cyclase; AsbAS1; BPY; EtAS; GgbAS1; LjAMY1; MtAMY1; PNY; BgbAS
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, β-amyrin-forming)
Comments: Some organism possess a monofunctional β-amyrin synthase [3,4,6-11], other have a multifunctional enzyme that also catalyses the synthesis of α amyrin (EC 5.4.99.40) [5] or lupeol (EC 5.4.99.41) [6].
References:
1. Abe, I, Ebizuka, Y., Seo, S. and Sankawa, U. Purification of squalene-2,3-epoxide cyclases from cell suspension cultures of Rabdosia japonica Hara. FEBS Lett. 249 (1989) 100-104.
2. Abe, I., Sankawa, U. and Ebizuka, Y. Purification of 2,3-oxdosqualene:β-amyrin cyclase from pea seedlings. Chem. Pharm. Bull. 37 (1989) 536.
3. Kushiro, T., Shibuya, M. and Ebizuka, Y. β-Amyrin synthase-cloning of oxidosqualene cyclase that catalyzes the formation of the most popular triterpene among higher plants. Eur. J. Biochem. 256 (1998) 238-244. [PMID: 9746369]
4. Hayashi, H., Huang, P., Kirakosyan, A., Inoue, K., Hiraoka, N., Ikeshiro, Y., Kushiro, T., Shibuya, M. and Ebizuka, Y. Cloning and characterization of a cDNA encoding β-amyrin synthase involved in glycyrrhizin and soyasaponin biosyntheses in licorice. Biol. Pharm. Bull. 24 (2001) 912-916. [PMID: 11510484]
5. Husselstein-Muller, T., Schaller, H. and Benveniste, P. Molecular cloning and expression in yeast of 2,3-oxidosqualene-triterpenoid cyclases from Arabidopsis thaliana. Plant Mol. Biol. 45 (2001) 75-92. [PMID: 11247608]
6. Iturbe-Ormaetxe, I., Haralampidis, K., Papadopoulou, K. and Osbourn, A.E. Molecular cloning and characterization of triterpene synthases from Medicago truncatula and Lotus japonicus. Plant Mol. Biol. 51 (2003) 731-743. [PMID: 12683345]
7. Zhang, H., Shibuya, M., Yokota, S. and Ebizuka, Y. Oxidosqualene cyclases from cell suspension cultures of Betula platyphylla var. japonica: molecular evolution of oxidosqualene cyclases in higher plants. Biol. Pharm. Bull. 26 (2003) 642-650. [PMID: 12736505]
8. Hayashi, H., Huang, P., Takada, S., Obinata, M., Inoue, K., Shibuya, M. and Ebizuka, Y. Differential expression of three oxidosqualene cyclase mRNAs in Glycyrrhiza glabra. Biol. Pharm. Bull. 27 (2004) 1086-1092. [PMID: 15256745]
9. Kajikawa, M., Yamato, K.T., Fukuzawa, H., Sakai, Y., Uchida, H. and Ohyama, K. Cloning and characterization of a cDNA encoding β-amyrin synthase from petroleum plant Euphorbia tirucalli L. Phytochemistry 66 (2005) 1759-1766. [PMID: 16005035]
10. Basyuni, M., Oku, H., Tsujimoto, E., Kinjo, K., Baba, S. and Takara, K. Triterpene synthases from the Okinawan mangrove tribe, Rhizophoraceae. FEBS J. 274 (2007) 5028-5042. [PMID: 17803686]
11. Liu, Y., Cai, Y., Zhao, Z., Wang, J., Li, J., Xin, W., Xia, G. and Xiang, F. Cloning and functional analysis of a β-amyrin synthase gene associated with oleanolic acid biosynthesis in Gentiana straminea MAXIM. Biol. Pharm. Bull. 32 (2009) 818-824. [PMID: 19420748]
Accepted name: α-amyrin synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = α-amyrin
Other name(s): 2,3-oxidosqualene α-amyrin cyclase; mixed amyrin synthase
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, α-amyrin-forming)
Comments: A multifunctional enzyme which produces both α- and β-amyrin. (see EC 5.4.99.39, β-amyrin synthase)
References:
1. Morita, M., Shibuya, M., Kushiro, T., Masuda, K. and Ebizuka, Y. Molecular cloning and functional expression of triterpene synthases from pea (Pisum sativum) new α-amyrin-producing enzyme is a multifunctional triterpene synthase. Eur. J. Biochem. 267 (2000) 3453-3460. [PMID: 10848960]
Accepted name: lupeol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = lupeol
Other name(s): LUPI; BPW; RcLUS
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, lupeol-forming)
Comments: Also forms some β-amyrin. The recombinant enzyme from Arabidopsis thaliana [3] gives a 1:1 mixture of lupeol and lupan-3β,20-diol with small amounts of β-amyrin, germanicol, taraxasterol and ψ-taraxasterol. See EC 4.2.1.128 (lupan-3β,20-diol synthase).
References:
1. Herrera, J.B., Bartel, B., Wilson, W.K. and Matsuda, S.P. Cloning and characterization of the Arabidopsis thaliana lupeol synthase gene. Phytochemistry 49 (1998) 1905-1911. [PMID: 9883589]
2. Shibuya, M., Zhang, H., Endo, A., Shishikura, K., Kushiro, T. and Ebizuka, Y. Two branches of the lupeol synthase gene in the molecular evolution of plant oxidosqualene cyclases. Eur. J. Biochem. 266 (1999) 302-307. [PMID: 10542078]
3. Segura, M.J., Meyer, M.M. and Matsuda, S.P. Arabidopsis thaliana LUP1 converts oxidosqualene to multiple triterpene alcohols and a triterpene diol. Org. Lett. 2 (2000) 2257-2259. [PMID: 10930257]
4. Zhang, H., Shibuya, M., Yokota, S. and Ebizuka, Y. Oxidosqualene cyclases from cell suspension cultures of Betula platyphylla var. japonica: molecular evolution of oxidosqualene cyclases in higher plants. Biol. Pharm. Bull. 26 (2003) 642-650. [PMID: 12736505]
5. Hayashi, H., Huang, P., Takada, S., Obinata, M., Inoue, K., Shibuya, M. and Ebizuka, Y. Differential expression of three oxidosqualene cyclase mRNAs in Glycyrrhiza glabra. Biol. Pharm. Bull. 27 (2004) 1086-1092. [PMID: 15256745]
6. Guhling, O., Hobl, B., Yeats, T. and Jetter, R. Cloning and characterization of a lupeol synthase involved in the synthesis of epicuticular wax crystals on stem and hypocotyl surfaces of Ricinus communis. Arch. Biochem. Biophys. 448 (2006) 60-72. [PMID: 16445885]
7. Basyuni, M., Oku, H., Tsujimoto, E., Kinjo, K., Baba, S. and Takara, K. Triterpene synthases from the Okinawan mangrove tribe, Rhizophoraceae. FEBS J. 274 (2007) 5028-5042. [PMID: 17803686]
Accepted name: 3-hydroxybenzoate—CoA ligase
Reaction: ATP + 3-hydroxybenzoate + CoA = AMP + diphosphate + 3-hydroxybenzoyl-CoA
Other name(s): 3-hydroxybenzoyl-CoA synthetase; 3-hydroxybenzoate—coenzyme A ligase (AMP-forming); 3-hydroxybenzoyl coenzyme A synthetase; 3-hydroxybenzoyl-CoA ligase
Systematic name: 3-hydroxybenzoate:CoA ligase (AMP-forming)
Comments: The enzyme works equally well with 4-hydroxybenzoate but shows low activity towards benzoate, 4-aminobenzoate, 3-aminobenzoate, 3-fluorobenzoate, 4-fluorobenzoate, 3-chlorobenzoate, and 4-chlorobenzoate. There is no activity with 3,4-dihydroxybenzoate, 2,3-dihydroxybenzoate, and 2-hydroxybenzoate as substrates.
References:
1. Laempe, D., Jahn, M., Breese, K., Schägger, H. and Fuchs, G. Anaerobic metabolism of 3-hydroxybenzoate by the denitrifying bacterium Thauera aromatica. J. Bacteriol. 183 (2001) 968-979. [PMID: 11208796]
Accepted name: tRNAIle-lysidine synthetase
Reaction: [tRNAIle2]-cytidine34 + L-lysine + ATP = [tRNAIle2]-lysidine34 + AMP + diphosphate + H2O
Glossary: lysidine = N6-(4-amino-1-β-D-ribofuranosylpyrimidin-2-ylidene)-L-lysine
Other name(s): TilS; mesJ (gene name); yacA (gene name); isoleucine-specific transfer ribonucleate lysidine synthetase
Systematic name: L-lysine:[tRNAIle2]-cytidine34 ligase (AMP-forming)
Comments: The bacterial enzyme modifies the wobble base of the CAU anticodon of tRNAIle at the oxo group in position 2 of cytidine34. This modification determines both codon and amino acid specificities of tRNAIle.
References:
1. Ikeuchi, Y., Soma, A., Ote, T., Kato, J., Sekine, Y. and Suzuki, T. molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol. Cell 19 (2005) 235-246. [PMID: 16039592]
2. Salowe, S.P., Wiltsie, J., Hawkins, J.C. and Sonatore, L.M. The catalytic flexibility of tRNAIle-lysidine synthetase can generate alternative tRNA substrates for isoleucyl-tRNA synthetase. J. Biol. Chem. 284 (2009) 9656-9662. [PMID: 19233850]
3. Nakanishi, K., Fukai, S., Ikeuchi, Y., Soma, A., Sekine, Y., Suzuki, T. and Nureki, O. Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain. Proc. Natl. Acad. Sci. USA 102 (2005) 7487-7492. [PMID: 15894617]
4. Soma, A., Ikeuchi, Y., Kanemasa, S., Kobayashi, K., Ogasawara, N., Ote, T., Kato, J., Watanabe, K., Sekine, Y. and Suzuki, T. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell 12 (2003) 689-698. [PMID: 14527414]
5. Nakanishi, K., Bonnefond, L., Kimura, S., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature 461 (2009) 1144-1148. [PMID: 19847269]
MoO2(OH)Dtpp-mP = molybdenum cofactor = MoCo = {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kappaS)-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)molybdate
aminopentol = (2S,3S,5R,10S,12R,14R,15S,16S)-2-amino-12,16-dimethylicosane-3,5,10,14,15-pentol
2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose
2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose
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