The Enzyme Database

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EC 5.4.99.1     
Accepted name: methylaspartate mutase
Reaction: L-threo-3-methylaspartate = L-glutamate
Other name(s): glutamate mutase; glutamic mutase; glutamic isomerase; glutamic acid mutase; glutamic acid isomerase; methylaspartic acid mutase; β-methylaspartate-glutamate mutase; glutamate isomerase
Systematic name: L-threo-3-methylaspartate carboxy-aminomethylmutase
Comments: Requires a cobamide coenzyme.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9032-97-7
References:
1.  Barker, H.A., Rooze, V., Suzuki, F. and Iodice, A.A. The glutamate mutase system. Assays and properties. J. Biol. Chem. 239 (1964) 3260–3266. [PMID: 14245371]
2.  Weissbach, H., Toohey, J. and Barker, H.A. Isolation and properties of B12 coenzymes containing benzimidazole or dimethylbenzimidazole. Proc. Natl. Acad. Sci. USA 45 (1959) 521–528. [PMID: 16590408]
[EC 5.4.99.1 created 1961]
 
 
EC 5.4.99.2     
Accepted name: methylmalonyl-CoA mutase
Reaction: (R)-methylmalonyl-CoA = succinyl-CoA
For diagram of the 3-hydroxypropanoate cycle, click here
Other name(s): methylmalonyl-CoA CoA-carbonyl mutase; methylmalonyl coenzyme A mutase; methylmalonyl coenzyme A carbonylmutase; (S)-methylmalonyl-CoA mutase; (R)-2-methyl-3-oxopropanoyl-CoA CoA-carbonylmutase [incorrect]
Systematic name: (R)-methylmalonyl-CoA CoA-carbonylmutase
Comments: Requires a cobamide coenzyme.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 9023-90-9
References:
1.  Barker, H.A. Coenzyme B12-dependent mutases causing carbon chain rearrangements. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, Academic Press, New York, 1972, pp. 509–537.
[EC 5.4.99.2 created 1961, modified 1983]
 
 
EC 5.4.99.3     
Accepted name: 2-acetolactate mutase
Reaction: 2-acetolactate = 3-hydroxy-3-methyl-2-oxobutanoate
Other name(s): acetolactate mutase; acetohydroxy acid isomerase
Systematic name: 2-acetolactate methylmutase
Comments: Requires ascorbic acid; also converts 2-aceto-2-hydroxybutanoate to 3-hydroxy-3-methyl-2-oxopentanoate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37318-52-8
References:
1.  Allaudeen, H.S. and Ramakrishnan, T. Biosynthesis of isoleucine and valine in Mycobacterium tuberculosis H37 Rv. Arch. Biochem. Biophys. 125 (1968) 199–209. [PMID: 4384955]
[EC 5.4.99.3 created 1972]
 
 
EC 5.4.99.4     
Accepted name: 2-methyleneglutarate mutase
Reaction: 2-methyleneglutarate = 2-methylene-3-methylsuccinate
Other name(s): α-methyleneglutarate mutase
Systematic name: 2-methyleneglutarate carboxy-methylenemethylmutase
Comments: Requires a cobamide coenzyme.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9059-10-3
References:
1.  Kung, H.-F., Cederbaum, S., Tsai, L. and Stadtman, T.C. Nicotinic acid metabolism. V. A cobamide coenzyme-dependent conversion of α-methyleneglutaric acid to dimethylmaleic acid. Proc. Natl. Acad. Sci. USA 65 (1970) 978–984. [PMID: 5266166]
2.  Kung, H.-F. and Stadtman, T.C. Nicotinic acid metabolism. VI. Purification and properties of α-methyleneglutarate mutase (B12-dependent) and methylitaconate isomerase. J. Biol. Chem. 246 (1971) 3378–3388. [PMID: 5574401]
[EC 5.4.99.4 created 1972]
 
 
EC 5.4.99.5     
Accepted name: chorismate mutase
Reaction: chorismate = prephenate
For diagram of phenylalanine and tyrosine biosynthesis, click here and for mechanism of reaction, click here
Other name(s): hydroxyphenylpyruvate synthase
Systematic name: chorismate pyruvatemutase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9068-30-8
References:
1.  Cotton, R.G.H. and Gibson, F. The biosynthesis of phenylalanine and tyrosine; enzymes converting chorismic acid into prephenic acid and their relationships to prephenate dehydratase and prephenate dehydrogenase. Biochim. Biophys. Acta 100 (1965) 76–88. [PMID: 14323651]
2.  Lorence, J.H. and Nester, E.W. Multiple molecular forms of chorismate mutase in Bacillus subtillis. Biochemistry 6 (1967) 1541–1543. [PMID: 4962500]
3.  Sprössler, B. and Lingens, F. Chorismat-Mutase aus Claviceps. I. Eigenschaften der Chorismat-Mutase aus verschiedenen Claviceps-Stämmen. Hoppe-Seyler's Z. Physiol. Chem. 351 (1970) 448–458. [PMID: 5443801]
4.  Woodin, T.S. and Nishioka, L. Evidence for three isozymes of chorismate mutase in alfalfa. Biochim. Biophys. Acta 309 (1973) 211–223. [PMID: 4708674]
[EC 5.4.99.5 created 1972]
 
 
EC 5.4.99.6     
Transferred entry: isochorismate synthase. Now EC 5.4.4.2, isochorismate synthase
[EC 5.4.99.6 created 1972, deleted 2003]
 
 
EC 5.4.99.7     
Accepted name: lanosterol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = lanosterol
For diagram of lanosterol and cycloartenol biosynthesis, click here
Other name(s): 2,3-epoxysqualene lanosterol cyclase; squalene-2,3-oxide-lanosterol cyclase; lanosterol 2,3-oxidosqualene cyclase; squalene 2,3-epoxide:lanosterol cyclase; 2,3-oxidosqualene sterol cyclase; oxidosqualene cyclase; 2,3-oxidosqualene cyclase; 2,3-oxidosqualene-lanosterol cyclase; oxidosqualene-lanosterol cyclase; squalene epoxidase-cyclase; (S)-2,3-epoxysqualene mutase (cyclizing, lanosterol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, lanosterol-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9032-71-7
References:
1.  Dean, P.D.G., Oritz de Montellano, P.R., Bloch, K. and Corey, E.J. A soluble 2,3-oxidosqualene sterol cyclase. J. Biol. Chem. 242 (1967) 3014–3015. [PMID: 6027261]
[EC 5.4.99.7 created 1961 as EC 1.99.1.13, transferred 1965 to EC 1.14.1.3, part transferred 1972 to EC 5.4.99.7 rest to EC 1.14.99.7]
 
 
EC 5.4.99.8     
Accepted name: cycloartenol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = cycloartenol
For diagram of lanosterol and cycloartenol biosynthesis, click here
Other name(s): 2,3-epoxysqualene cycloartenol-cyclase; squalene-2,3-epoxide-cycloartenol cyclase; 2,3-epoxysqualene-cycloartenol cyclase; 2,3-oxidosqualene-cycloartenol cyclase; (S)-2,3-epoxysqualene mutase (cyclizing, cycloartenol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, cycloartenol-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9075-25-6
References:
1.  Rees, H.H., Goad, L.J. and Goodwin, T.W. 2,3-Oxidosqualene cycloartenol cyclase from Ochromonas malhamensis. Biochim. Biophys. Acta 176 (1969) 892–894. [PMID: 5797101]
[EC 5.4.99.8 created 1972]
 
 
EC 5.4.99.9     
Accepted name: UDP-galactopyranose mutase
Reaction: UDP-α-D-galactopyranose = UDP-α-D-galactofuranose
For diagram of UDP-glucose, UDP-galactose and UDP-glucuronate biosynthesis, click here
Other name(s): UGM; UDP-D-galactopyranose furanomutase
Systematic name: UDP-α-D-galactopyranose furanomutase
Comments: A flavoenzyme which generates UDP-α-D-glactofuranose required for cell wall formation in bacteria, fungi, and protozoa.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 174632-18-9
References:
1.  Trejo, A.G., Chittenden, G.J.F., Buchanan, J.G. and Baddiley, J. Uridine diphosphate α-D-galactofuranose, an intermediate in the biosynthesis of galactofuranosyl residues. Biochem. J. 117 (1970) 637–639. [PMID: 5419754]
2.  Karunan Partha, S., Bonderoff, S.A., van Straaten, K.E. and Sanders, D.A. Expression, purification and preliminary X-ray crystallographic analysis of UDP-galactopyranose mutase from Deinococcus radiodurans. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 843–845. [PMID: 19652355]
3.  Dhatwalia, R., Singh, H., Oppenheimer, M., Karr, D.B., Nix, J.C., Sobrado, P. and Tanner, J.J. Crystal structures and small-angle x-ray scattering analysis of UDP-galactopyranose mutase from the pathogenic fungus Aspergillus fumigatus. J. Biol. Chem. 287 (2012) 9041–9051. [PMID: 22294687]
4.  van Straaten, K.E., Routier, F.H. and Sanders, D.A. Towards the crystal structure elucidation of eukaryotic UDP-galactopyranose mutase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 (2012) 455–459. [PMID: 22505419]
[EC 5.4.99.9 created 1984, modified 2012]
 
 
EC 5.4.99.10     
Deleted entry: isomaltulose synthetase. Now included with EC 5.4.99.11, isomaltulose synthase
[EC 5.4.99.10 created 1984, deleted 1992]
 
 
EC 5.4.99.11     
Accepted name: isomaltulose synthase
Reaction: sucrose = 6-O-α-D-glucopyranosyl-D-fructofuranose
Other name(s): isomaltulose synthetase; sucrose α-glucosyltransferase; trehalulose synthase
Systematic name: sucrose glucosylmutase
Comments: The enzyme simultaneously produces isomaltulose (6-O-α-D-glucopyranosyl-D-fructose) and smaller amounts of trehalulose (1-O-α-D-glucopyranosyl-β-D-fructose) from sucrose.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 159940-49-5
References:
1.  Cheetham, P.S.J. The extraction and mechanism of a novel isomaltulose-synthesizing enzyme from Erwinia rhapontici. Biochem. J. 220 (1984) 213–220. [PMID: 6743261]
2.  Cheetham, P.S.J., Imber, C.E. and Isherwood, J. The formation of isomaltulose by immobilized Erwinia rhapontici. Nature 299 (1982) 628–631.
[EC 5.4.99.11 created 1989 (EC 5.4.99.10 created 1984, incorporated 1992)]
 
 
EC 5.4.99.12     
Accepted name: tRNA pseudouridine38-40 synthase
Reaction: tRNA uridine38-40 = tRNA pseudouridine38-40
Other name(s): TruA; tRNA pseudouridine synthase I; PSUI; hisT (gene name)
Systematic name: tRNA-uridine38-40 uracil mutase
Comments: The uridylate residues at positions 38, 39 and 40 of nearly all tRNAs are isomerized to pseudouridine. TruA specifically modifies uridines at positions 38, 39, and/or 40 in the anticodon stem loop of tRNAs with highly divergent sequences and structures [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 61506-89-6
References:
1.  Hur, S. and Stroud, R.M. How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA. Mol. Cell 26 (2007) 189–203. [PMID: 17466622]
2.  Huang, L., Pookanjanatavip, M., Gu, X. and Santi, D.V. A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst. Biochemistry 37 (1998) 344–351. [PMID: 9425056]
3.  Kammen, H.O., Marvel, C.C., Hardy, L. and Penhoet, E.E. Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. J. Biol. Chem. 263 (1988) 2255–2263. [PMID: 3276686]
4.  Turnbough, C.L., Jr., Neill, R.J., Landsberg, R. and Ames, B.N. Pseudouridylation of tRNAs and its role in regulation in Salmonella typhimurium. J. Biol. Chem. 254 (1979) 5111–5119. [PMID: 376505]
5.  Zhao, X. and Horne, D.A. The role of cysteine residues in the rearrangement of uridine to pseudouridine catalyzed by pseudouridine synthase I. J. Biol. Chem. 272 (1997) 1950–1955. [PMID: 8999885]
6.  Foster, P.G., Huang, L., Santi, D.V. and Stroud, R.M. The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I. Nat. Struct. Biol. 7 (2000) 23–27. [PMID: 10625422]
7.  Dong, X., Bessho, Y., Shibata, R., Nishimoto, M., Shirouzu, M., Kuramitsu, S. and Yokoyama, S. Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8. RNA Biol. 3 (2006) 115–122. [PMID: 17114947]
8.  Arena, F., Ciliberto, G., Ciampi, S. and Cortese, R. Purification of pseudouridylate synthetase I from Salmonella typhimurium. Nucleic Acids Res. 5 (1978) 4523–4536. [PMID: 370771]
[EC 5.4.99.12 created 1990, modified 2011]
 
 
EC 5.4.99.13     
Accepted name: isobutyryl-CoA mutase
Reaction: 2-methylpropanoyl-CoA = butanoyl-CoA
Glossary: pivalate = 2,2-dimethylpropanoate
Other name(s): isobutyryl coenzyme A mutase; butyryl-CoA:isobutyryl-CoA mutase; icmA (gene name); icmB (gene name); icmF (gene name)
Systematic name: 2-methylpropanoyl-CoA CoA-carbonylmutase
Comments: This bacterial enzyme utilizes 5′-deoxyadenosylcobalamin as a cofactor. Following substrate binding, the enzyme catalyses the homolytic cleavage of the cobalt-carbon bond of AdoCbl, yielding cob(II)alamin and a 5′-deoxyadenosyl radical, which initiates the the carbon skeleton rearrangement reaction by hydrogen atom abstraction from the substrate. At the end of each catalytic cycle the 5′-deoxyadenosyl radical and cob(II)alamin recombine, regenerating the resting form of the cofactor. The enzyme is prone to inactivation resulting from occassional loss of the 5′-deoxyadenosyl molecule. Inactivated enzymes are repaired by the action of EC 2.5.1.17, cob(I)yrinic acid a,c-diamide adenosyltransferase, and a G-protein chaperone, which restore cob(II)alamin (which is first reduced to cob(I)alamin by an unidentified reductase) to 5′-deoxyadenosylcobalamin and load it back on the mutase. Some mutases are fused with their G-protein chaperone. These enzyme can also catalyse the interconversion of isovaleryl-CoA with pivalyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 116405-23-3
References:
1.  Brendelberger, G., Rétey, J., Ashworth, D.M., Reynolds, K., Willenbrock, F. and Robinson, J.A. The enzymic interconversion of isobutyryl and N-butyrylcarba(dethia)-coenzyme-A - a coenzyme-B12-dependent carbon skeleton rearrangement. Angew. Chem. Int. Ed. Engl. 27 (1988) 1089–1091.
2.  Ratnatilleke, A., Vrijbloed, J.W. and Robinson, J.A. Cloning and sequencing of the coenzyme B12-binding domain of isobutyryl-CoA mutase from Streptomyces cinnamonensis, reconstitution of mutase activity, and characterization of the recombinant enzyme produced in Escherichia coli. J. Biol. Chem. 274 (1999) 31679–31685. [PMID: 10531377]
3.  Cracan, V., Padovani, D. and Banerjee, R. IcmF is a fusion between the radical B12 enzyme isobutyryl-CoA mutase and its G-protein chaperone. J. Biol. Chem. 285 (2010) 655–666. [PMID: 19864421]
4.  Cracan, V. and Banerjee, R. Novel coenzyme B12-dependent interconversion of isovaleryl-CoA and pivalyl-CoA. J. Biol. Chem. 287 (2012) 3723–3732. [PMID: 22167181]
5.  Jost, M., Born, D.A., Cracan, V., Banerjee, R. and Drennan, C.L. Structural basis for substrate specificity in adenosylcobalamin-dependent isobutyryl-CoA mutase and related acyl-CoA mutases. J. Biol. Chem. 290 (2015) 26882–26898. [PMID: 26318610]
6.  Li, Z., Kitanishi, K., Twahir, U.T., Cracan, V., Chapman, D., Warncke, K. and Banerjee, R. Cofactor editing by the G-protein metallochaperone domain regulates the radical B12 enzyme IcmF. J. Biol. Chem. 292 (2017) 3977–3987. [PMID: 28130442]
[EC 5.4.99.13 created 1992, revised 2017]
 
 
EC 5.4.99.14     
Accepted name: 4-carboxymethyl-4-methylbutenolide mutase
Reaction: 4-carboxymethyl-4-methylbut-2-en-1,4-olide = 4-carboxymethyl-3-methylbut-2-en-1,4-olide
Other name(s): 4-methyl-2-enelactone isomerase; 4-methylmuconolactone methylisomerase; 4-methyl-3-enelactone methyl isomerase
Systematic name: 4-carboxymethyl-4-methylbut-2-en-1,4-olide methylmutase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 115300-03-3
References:
1.  Bruce, N.C. and Cain, R.B. β-Methylmuconolactone, a key intermediate in the dissimilation of methylaromatic compounds by a modified 3-oxoadipate pathway evolved in nocardioform actinomycetes. FEMS Microbiol. Lett. 50 (1988) 233–239.
[EC 5.4.99.14 created 1992]
 
 
EC 5.4.99.15     
Accepted name: (1→4)-α-D-glucan 1-α-D-glucosylmutase
Reaction: 4-[(1→4)-α-D-glucosyl]n-1-D-glucose = 1-α-D-[(1→4)-α-D-glucosyl]n-1-α-D-glucopyranoside
Other name(s): malto-oligosyltrehalose synthase; maltodextrin α-D-glucosyltransferase
Systematic name: (1→4)-α-D-glucan 1-α-D-glucosylmutase
Comments: The enzyme from Arthrobacter sp., Sulfolobus acidocaldarius acts on (1→4)-α-D-glucans containing three or more (1→4)-α-linked D-glucose units. Not active towards maltose.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 170780-49-1
References:
1.  Maruta, K., Nakada, T., Kubota, M., Chaen, H., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Formation of trehalose from maltooligosaccharides by a novel enzymatic system. Biosci. Biotechnol. Biochem. 59 (1995) 1829–1834. [PMID: 8534970]
2.  Nakada, T., Maruta, K., Tsusaki, K., Kubota, M., Chaen, H., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Purification and properties of a novel enzyme, maltooligosyl trehalose synthase, from Arthrobacter sp. Q36. Biosci. Biotechnol. Biochem. 59 (1995) 2210–2214. [PMID: 8611744]
3.  Nakada, T., Ikegami, S., Chaen, H., Kubota, M., Fukuda, S., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Purification and characterization of thermostable maltooligosyl trehalose synthase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. Biosci. Biotechnol. Biochem. 60 (1996) 263–266. [PMID: 9063973]
[EC 5.4.99.15 created 1999]
 
 
EC 5.4.99.16     
Accepted name: maltose α-D-glucosyltransferase
Reaction: maltose = α,α-trehalose
Other name(s): trehalose synthase; maltose glucosylmutase
Systematic name: maltose α-D-glucosylmutase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 395644-91-4
References:
1.  Nishimoto, T., Nakano, M., Ikegami, S., Chaen, H., Fukuda, S., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Existence of a novel enzyme converting maltose to trehalose. Biosci. Biotechnol. Biochem. 59 (1995) 2189–2190.
2.  Nishimoto, T., Nakano, M., Nakada, T., Chaen, H., Fukuda, S., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Purification and properties of a novel enzyme, trehalose synthase, from Pimelobacter sp. R48. Biosci. Biotechnol. Biochem. 60 (1996) 640–644. [PMID: 8829531]
[EC 5.4.99.16 created 1999]
 
 
EC 5.4.99.17     
Accepted name: squalene—hopene cyclase
Reaction: squalene = hop-22(29)-ene
For diagram of hopene biosynthesis, 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, squalene—hopanol cyclase). Hopene and hopanol are formed at a constant ratio of 5:1.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, 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]
[EC 5.4.99.17 created 2002, modified 2011]
 
 
EC 5.4.99.18     
Accepted name: 5-(carboxyamino)imidazole ribonucleotide mutase
Reaction: 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
For diagram of the late stages of purine biosynthesis, click here
Other name(s): N5-CAIR mutase; PurE; N5-carboxyaminoimidazole ribonucleotide mutase; class I PurE
Systematic name: 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole carboxymutase
Comments: In eubacteria, fungi and plants, this enzyme, along with EC 6.3.4.18, 5-(carboxyamino)imidazole ribonucleotide synthase, is required to carry out the single reaction catalysed by EC 4.1.1.21, phosphoribosylaminoimidazole carboxylase, in vertebrates [6]. In the absence of EC 6.3.2.6, phosphoribosylaminoimidazolesuccinocarboxamide synthase, the reaction is reversible [3]. The substrate is readily converted into 5-amino-1-(5-phospho-D-ribosyl)imidazole by non-enzymic decarboxylation [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 255379-40-9
References:
1.  Meyer, E., Leonard, N.J., Bhat, B., Stubbe, J. and Smith, J.M. Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway. Biochemistry 31 (1992) 5022–5032. [PMID: 1534690]
2.  Mueller, E.J., Meyer, E., Rudolph, J., Davisson, V.J. and Stubbe, J. N5-Carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. Biochemistry 33 (1994) 2269–2278. [PMID: 8117684]
3.  Meyer, E., Kappock, T.J., Osuji, C. and Stubbe, J. Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase. Biochemistry 38 (1999) 3012–3018. [PMID: 10074353]
4.  Mathews, I.I., Kappock, T.J., Stubbe, J. and Ealick, S.E. Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway. Structure 7 (1999) 1395–1406. [PMID: 10574791]
5.  Firestine, S.M., Poon, S.W., Mueller, E.J., Stubbe, J. and Davisson, V.J. Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: a case for divergent catalytic mechanisms. Biochemistry 33 (1994) 11927–11934. [PMID: 7918411]
6.  Firestine, S.M., Misialek, S., Toffaletti, D.L., Klem, T.J., Perfect, J.R. and Davisson, V.J. Biochemical role of the Cryptococcus neoformans ADE2 protein in fungal de novo purine biosynthesis. Arch. Biochem. Biophys. 351 (1998) 123–134. [PMID: 9500840]
[EC 5.4.99.18 created 2006]
 
 
EC 5.4.99.19     
Accepted name: 16S rRNA pseudouridine516 synthase
Reaction: 16S rRNA uridine516 = 16S rRNA pseudouridine516
Other name(s): 16S RNA pseudouridine516 synthase; 16S PsiI516 synthase; 16S RNA Ψ516 synthase; RNA pseudouridine synthase RsuA; RsuA; 16S RNA pseudouridine 516 synthase
Systematic name: 16S rRNA-uridine516 uracil mutase
Comments: The enzyme is specific for uridine516 in 16S rRNA. In vitro, the enzyme does not modify free 16S rRNA. The preferred substrate is a 5′-terminal fragment of 16S rRNA complexed with 30S ribosomal proteins [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wrzesinski, J., Bakin, A., Nurse, K., Lane, B.G. and Ofengand, J. Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli. Biochemistry 34 (1995) 8904–8913. [PMID: 7612632]
2.  Conrad, J., Niu, L., Rudd, K., Lane, B.G. and Ofengand, J. 16S ribosomal RNA pseudouridine synthase RsuA of Escherichia coli: deletion, mutation of the conserved Asp102 residue, and sequence comparison among all other pseudouridine synthases. RNA 5 (1999) 751–763. [PMID: 10376875]
3.  Sivaraman, J., Sauve, V., Larocque, R., Stura, E.A., Schrag, J.D., Cygler, M. and Matte, A. Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Nat. Struct. Biol. 9 (2002) 353–358. [PMID: 11953756]
[EC 5.4.99.19 created 2011]
 
 
EC 5.4.99.20     
Accepted name: 23S rRNA pseudouridine2457 synthase
Reaction: 23S rRNA uridine2457 = 23S rRNA pseudouridine2457
Other name(s): RluE; YmfC
Systematic name: 23S rRNA-uridine2457 uracil mutase
Comments: The enzyme modifies uridine2457 in a stem of 23S RNA in Escherichia coli.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603–1615. [PMID: 11720289]
2.  Pan, H., Ho, J.D., Stroud, R.M. and Finer-Moore, J. The crystal structure of E. coli rRNA pseudouridine synthase RluE. J. Mol. Biol. 367 (2007) 1459–1470. [PMID: 17320904]
[EC 5.4.99.20 created 2011]
 
 
EC 5.4.99.21     
Accepted name: 23S rRNA pseudouridine2604 synthase
Reaction: 23S rRNA uridine2604 = 23S rRNA pseudouridine2604
Other name(s): RluF; YjbC
Systematic name: 23S rRNA-uridine2604 uracil mutase
Comments: The enzyme is not completely specific for uridine2604 and can, to a small extent, also react with uridine2605 [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603–1615. [PMID: 11720289]
2.  Alian, A., DeGiovanni, A., Griner, S.L., Finer-Moore, J.S. and Stroud, R.M. Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome. J. Mol. Biol. 388 (2009) 785–800. [PMID: 19298824]
3.  Sunita, S., Zhenxing, H., Swaathi, J., Cygler, M., Matte, A. and Sivaraman, J. Domain organization and crystal structure of the catalytic domain of E. coli RluF, a pseudouridine synthase that acts on 23S rRNA. J. Mol. Biol. 359 (2006) 998–1009. [PMID: 16712869]
[EC 5.4.99.21 created 2011]
 
 
EC 5.4.99.22     
Accepted name: 23S rRNA pseudouridine2605 synthase
Reaction: 23S rRNA uridine2605 = 23S rRNA pseudouridine2605
Other name(s): RluB; YciL
Systematic name: 23S rRNA-uridine2605 uracil mutase
Comments: Pseudouridine synthase RluB converts uridine2605 of 23S rRNA to pseudouridine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603–1615. [PMID: 11720289]
2.  Jiang, M., Sullivan, S.M., Walker, A.K., Strahler, J.R., Andrews, P.C. and Maddock, J.R. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J. Bacteriol. 189 (2007) 3434–3444. [PMID: 17337586]
[EC 5.4.99.22 created 2011]
 
 
EC 5.4.99.23     
Accepted name: 23S rRNA pseudouridine1911/1915/1917 synthase
Reaction: 23S rRNA uridine1911/uridine1915/uridine1917 = 23S rRNA pseudouridine1911/pseudouridine1915/pseudouridine1917
Other name(s): RluD; pseudouridine synthase RluD
Systematic name: 23S rRNA-uridine1911/1915/1917 uracil mutase
Comments: Pseudouridine synthase RluD converts uridines at positions 1911, 1915, and 1917 of 23S rRNA to pseudouridines. These nucleotides are located in the functionally important helix-loop 69 of 23S rRNA [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Leppik, M., Peil, L., Kipper, K., Liiv, A. and Remme, J. Substrate specificity of the pseudouridine synthase RluD in Escherichia coli. FEBS J. 274 (2007) 5759–5766. [PMID: 17937767]
2.  Ejby, M., Sorensen, M.A. and Pedersen, S. Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination. Proc. Natl. Acad. Sci. USA 104 (2007) 19410–19415. [PMID: 18032607]
3.  Sivaraman, J., Iannuzzi, P., Cygler, M. and Matte, A. Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. J. Mol. Biol. 335 (2004) 87–101. [PMID: 14659742]
4.  Wrzesinski, J., Bakin, A., Ofengand, J. and Lane, B.G. Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD). IUBMB Life 50 (2000) 33–37. [PMID: 11087118]
[EC 5.4.99.23 created 2011]
 
 
EC 5.4.99.24     
Accepted name: 23S rRNA pseudouridine955/2504/2580 synthase
Reaction: 23S rRNA uridine955/uridine2504/uridine2580 = 23S rRNA pseudouridine955/pseudouridine2504/pseudouridine2580
Other name(s): RluC; pseudouridine synthase RluC
Systematic name: 23S rRNA-uridine955/2504/2580 uracil mutase
Comments: The enzyme converts uridines at position 955, 2504 and 2580 of 23S rRNA to pseudouridines.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Jiang, M., Sullivan, S.M., Walker, A.K., Strahler, J.R., Andrews, P.C. and Maddock, J.R. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J. Bacteriol. 189 (2007) 3434–3444. [PMID: 17337586]
2.  Conrad, J., Sun, D., Englund, N. and Ofengand, J. The rluC gene of Escherichia coli codes for a pseudouridine synthase that is solely responsible for synthesis of pseudouridine at positions 955, 2504, and 2580 in 23 S ribosomal RNA. J. Biol. Chem. 273 (1998) 18562–18566. [PMID: 9660827]
3.  Corollo, D., Blair-Johnson, M., Conrad, J., Fiedler, T., Sun, D., Wang, L., Ofengand, J. and Fenna, R. Crystallization and characterization of a fragment of pseudouridine synthase RluC from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 302–304. [PMID: 10089432]
4.  Toh, S.M. and Mankin, A.S. An indigenous posttranscriptional modification in the ribosomal peptidyl transferase center confers resistance to an array of protein synthesis inhibitors. J. Mol. Biol. 380 (2008) 593–597. [PMID: 18554609]
[EC 5.4.99.24 created 2011]
 
 
EC 5.4.99.25     
Accepted name: tRNA pseudouridine55 synthase
Reaction: tRNA uridine55 = tRNA pseudouridine55
Other name(s): TruB; aCbf5; Pus4; YNL292w (gene name); Ψ55 tRNA pseudouridine synthase; tRNA:Ψ55-synthase; tRNA pseudouridine 55 synthase; tRNA:pseudouridine-55 synthase; Ψ55 synthase; tRNA Ψ55 synthase; tRNA:Ψ55 synthase; tRNA-uridine55 uracil mutase; Pus10; tRNA-uridine54/55 uracil mutase
Systematic name: tRNA-uridine55 uracil mutase
Comments: Pseudouridine synthase TruB from Escherichia coli specifically modifies uridine55 in tRNA molecules [1]. The bifunctional archaeal enzyme also catalyses the pseudouridylation of uridine54 [6]. It is not known whether the enzyme from Escherichia coli can also act on position 54 in vitro, since this position is occupied in Escherichia coli tRNAs by thymine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 430429-15-5
References:
1.  Nurse, K., Wrzesinski, J., Bakin, A., Lane, B.G. and Ofengand, J. Purification, cloning, and properties of the tRNA Ψ55 synthase from Escherichia coli. RNA 1 (1995) 102–112. [PMID: 7489483]
2.  Becker, H.F., Motorin, Y., Planta, R.J. and Grosjean, H. The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of Ψ55 in both mitochondrial and cytoplasmic tRNAs. Nucleic Acids Res. 25 (1997) 4493–4499. [PMID: 9358157]
3.  Pienkowska, J., Wrzesinski, J. and Szweykowska-Kulinska, Z. A cell-free yellow lupin extract containing activities of pseudouridine 35 and 55 synthases. Acta Biochim. Pol. 45 (1998) 745–754. [PMID: 9918501]
4.  Chaudhuri, B.N., Chan, S., Perry, L.J. and Yeates, T.O. Crystal structure of the apo forms of Ψ55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft. J. Biol. Chem. 279 (2004) 24585–24591. [PMID: 15028724]
5.  Hoang, C., Hamilton, C.S., Mueller, E.G. and Ferre-D'Amare, A.R. Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain. Protein Sci. 14 (2005) 2201–2206. [PMID: 15987897]
6.  Gurha, P. and Gupta, R. Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA. RNA 14 (2008) 2521–2527. [PMID: 18952823]
[EC 5.4.99.25 created 2011, modified 2011]
 
 
EC 5.4.99.26     
Accepted name: tRNA pseudouridine65 synthase
Reaction: tRNA uridine65 = tRNA pseudouridine65
Other name(s): TruC; YqcB
Systematic name: tRNA-uridine65 uracil mutase
Comments: TruC specifically modifies uridines at positions 65 in tRNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 430429-15-5
References:
1.  Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603–1615. [PMID: 11720289]
[EC 5.4.99.26 created 2011]
 
 
EC 5.4.99.27     
Accepted name: tRNA pseudouridine13 synthase
Reaction: tRNA uridine13 = tRNA pseudouridine13
Other name(s): TruD; YgbO; tRNA PSI13 synthase; RNA:PSI-synthase Pus7p; Pus7p; RNA:pseudouridine-synthase Pus7p; Pus7 protein
Systematic name: tRNA-uridine13 uracil mutase
Comments: Pseudouridine synthase TruD from Escherichia coli specifically acts on uridine13 in tRNA [2,3]. The Pus7 protein from Saccharomyces cerevisiae is a multisite-multisubstrate pseudouridine synthase that is able to modify uridine13 in several yeast tRNAs, uridine35 in the pre-tRNATyr, uridine35 in U2 small nuclear RNA, and uridine50 in 5S rRNA [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 430429-15-5
References:
1.  Ericsson, U.B., Nordlund, P. and Hallberg, B.M. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. FEBS Lett. 565 (2004) 59–64. [PMID: 15135053]
2.  Chan, C.M. and Huang, R.H. Enzymatic characterization and mutational studies of TruD—the fifth family of pseudouridine synthases. Arch. Biochem. Biophys. 489 (2009) 15–19. [PMID: 19664587]
3.  Kaya, Y. and Ofengand, J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA 9 (2003) 711–721. [PMID: 12756329]
4.  Behm-Ansmant, I., Urban, A., Ma, X., Yu, Y.T., Motorin, Y. and Branlant, C. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Ψ-synthase also acting on tRNAs. RNA 9 (2003) 1371–1382. [PMID: 14561887]
5.  Urban, A., Behm-Ansmant, I., Branlant, C. and Motorin, Y. RNA sequence and two-dimensional structure features required for efficient substrate modification by the Saccharomyces cerevisiae RNA:Ψ-synthase Pus7p. J. Biol. Chem. 284 (2009) 5845–5858. [PMID: 19114708]
[EC 5.4.99.27 created 2011]
 
 
EC 5.4.99.28     
Accepted name: tRNA pseudouridine32 synthase
Reaction: tRNA uridine32 = tRNA pseudouridine32
Other name(s): RluA (ambiguous); pseudouridine synthase RluA (ambiguous); Pus9p; Rib2/Pus8p
Systematic name: tRNA-uridine32 uracil mutase
Comments: The dual-specificity enzyme from Escherichia coli also catalyses the formation of pseudouridine746 in 23S rRNA [5]. cf. EC 5.4.99.29 (23S rRNA pseudouridine746 synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 430429-15-5
References:
1.  Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S., Mueller, E.G. and Ferre-D'Amare, A.R. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol. Cell 24 (2006) 535–545. [PMID: 17188032]
2.  Spedaliere, C.J., Hamilton, C.S. and Mueller, E.G. Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues. Biochemistry 39 (2000) 9459–9465. [PMID: 10924141]
3.  Raychaudhuri, S., Niu, L., Conrad, J., Lane, B.G. and Ofengand, J. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J. Biol. Chem. 274 (1999) 18880–18886. [PMID: 10383384]
4.  Ramamurthy, V., Swann, S.L., Spedaliere, C.J. and Mueller, E.G. Role of cysteine residues in pseudouridine synthases of different families. Biochemistry 38 (1999) 13106–13111. [PMID: 10529181]
5.  Wrzesinski, J., Nurse, K., Bakin, A., Lane, B.G. and Ofengand, J. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for Ψ746 in 23S RNA is also specific for Ψ32 in tRNAPhe. RNA 1 (1995) 437–448. [PMID: 7493321]
6.  Behm-Ansmant, I., Grosjean, H., Massenet, S., Motorin, Y. and Branlant, C. Pseudouridylation at position 32 of mitochondrial and cytoplasmic tRNAs requires two distinct enzymes in Saccharomyces cerevisiae. J. Biol. Chem. 279 (2004) 52998–53006. [PMID: 15466869]
[EC 5.4.99.28 created 2011, modified 2011]
 
 
EC 5.4.99.29     
Accepted name: 23S rRNA pseudouridine746 synthase
Reaction: 23S rRNA uridine746 = 23S rRNA pseudouridine746
Other name(s): RluA (ambiguous); 23S RNA PSI746 synthase; 23S rRNA pseudouridine synthase; pseudouridine synthase RluA (ambiguous)
Systematic name: 23S rRNA-uridine746 uracil mutase
Comments: RluA is the sole protein responsible for the in vivo formation of 23S RNA pseudouridine746 [2]. The dual-specificity enzyme also catalyses the formation of uridine32 in tRNA [3]. cf. EC 5.4.99.28 (tRNA pseudouridine32 synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S., Mueller, E.G. and Ferre-D'Amare, A.R. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol. Cell 24 (2006) 535–545. [PMID: 17188032]
2.  Raychaudhuri, S., Niu, L., Conrad, J., Lane, B.G. and Ofengand, J. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J. Biol. Chem. 274 (1999) 18880–18886. [PMID: 10383384]
3.  Wrzesinski, J., Nurse, K., Bakin, A., Lane, B.G. and Ofengand, J. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for Ψ746 in 23S RNA is also specific for Ψ32 in tRNAPhe. RNA 1 (1995) 437–448. [PMID: 7493321]
[EC 5.4.99.29 created 2011]
 
 
EC 5.4.99.30     
Accepted name: UDP-arabinopyranose mutase
Reaction: UDP-β-L-arabinofuranose = UDP-β-L-arabinopyranose
Other name(s): Os03g40270 protein; UAM1; UAM3; RGP1; RGP3; OsUAM1; OsUAM2; Os03g0599800 protein; Os07g41360 protein
Systematic name: UDP-arabinopyranose pyranomutase
Comments: The reaction is reversible and at thermodynamic equilibrium the pyranose form is favored over the furanose form (90:10) [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Konishi, T., Takeda, T., Miyazaki, Y., Ohnishi-Kameyama, M., Hayashi, T., O'Neill, M.A. and Ishii, T. A plant mutase that interconverts UDP-arabinofuranose and UDP-arabinopyranose. Glycobiology 17 (2007) 345–354. [PMID: 17182701]
2.  Konishi, T., Ohnishi-Kameyama, M., Funane, K., Miyazaki, Y., Konishi, T. and Ishii, T. An arginyl residue in rice UDP-arabinopyranose mutase is required for catalytic activity and autoglycosylation. Carbohydr. Res. 345 (2010) 787–791. [PMID: 20149347]
3.  Konishi, T., Miyazaki, Y., Yamakawa, S., Iwai, H., Satoh, S. and Ishii, T. Purification and biochemical characterization of recombinant rice UDP-arabinopyranose mutase generated in insect cells. Biosci. Biotechnol. Biochem. 74 (2010) 191–194. [PMID: 20057139]
[EC 5.4.99.30 created 2011]
 
 
EC 5.4.99.31     
Accepted name: thalianol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = thalianol
Other name(s): (S)-2,3-epoxysqualene mutase (cyclizing, thalianol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, thalianol-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Fazio, G.C., Xu, R. and Matsuda, S.P.T. Genome mining to identify new plant triterpenoids. J. Am. Chem. Soc. 126 (2004) 5678–5679. [PMID: 15125655]
[EC 5.4.99.31 created 2011]
 
 
EC 5.4.99.32     
Accepted name: protostadienol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = (17Z)-protosta-17(20),24-dien-3β-ol
For diagram of cucurbitadienol, cycloartenol, lanosterol and prostadienol biosynthesis, click here
Other name(s): PdsA; (S)-2,3-epoxysqualene mutase [cyclizing, (17Z)-protosta-17(20),24-dien-3β-ol-forming]
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase [cyclizing, (17Z)-protosta-17(20),24-dien-3β-ol-forming]
Comments: (17Z)-Protosta-17(20),24-dien-3β-ol is a precursor of the steroidal antibiotic helvolic acid.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lodeiro, S., Xiong, Q., Wilson, W.K., Ivanova, Y., Smith, M.L., May, G.S. and Matsuda, S.P. Protostadienol biosynthesis and metabolism in the pathogenic fungus Aspergillus fumigatus. Org. Lett. 11 (2009) 1241–1244. [PMID: 19216560]
[EC 5.4.99.32 created 2011]
 
 
EC 5.4.99.33     
Accepted name: cucurbitadienol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = cucurbitadienol
For diagram of cucurbitadienol, cycloartenol, lanosterol and prostadienol biosynthesis, click here
Other name(s): CPQ (gene name); (S)-2,3-epoxysqualene mutase (cyclizing, cucurbitadienol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, cucurbitadienol-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Shibuya, M., Adachi, S., and Ebizuka, Y. Cucurbitadienol synthase, the first committed enzyme for cucurbitacin biosynthesis, is a distinct enzyme from cycloartenol synthase for phytosterol biosynthesis. Tetrahedron 60 (2004) 6995–7003.
[EC 5.4.99.33 created 2011]
 
 
EC 5.4.99.34     
Accepted name: germanicol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = germanicol
For diagram of α-amyrin, α-seco-amyrin and germanicol biosynthesis, click here
Other name(s): RsM1; (S)-2,3-epoxysqualene mutase (cyclizing, germanicol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualenee mutase (cyclizing, germanicol-forming)
Comments: The enzyme produces germanicol, β-amyrin and lupeol in the ratio 63:33:4.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  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]
[EC 5.4.99.34 created 2011]
 
 
EC 5.4.99.35     
Accepted name: taraxerol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = taraxerol
For diagram of friedelin, glutinol, isomultiflorenol and taraxerol biosynthesis, click here
Other name(s): RsM2; (S)-2,3-epoxysqualene mutase (cyclizing, taraxerol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, taraxerol-forming)
Comments: The enzyme gives taraxerol, β-amyrin and lupeol in the ratio 70:17:13.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  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]
[EC 5.4.99.35 created 2011]
 
 
EC 5.4.99.36     
Accepted name: isomultiflorenol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = isomultiflorenol
For diagram of friedelin, glutinol, isomultiflorenol and taraxerol biosynthesis, click here
Other name(s): LcIMS1; (S)-2,3-epoxysqualene mutase (cyclizing, isomultiflorenol-forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualenee mutase (cyclizing, isomultiflorenol-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hayashi, H., Huang, P., Inoue, K., Hiraoka, N., Ikeshiro, Y., Yazaki, K., Tanaka, S., Kushiro, T., Shibuya, M. and Ebizuka, Y. Molecular cloning and characterization of isomultiflorenol synthase, a new triterpene synthase from Luffa cylindrica, involved in biosynthesis of bryonolic acid. Eur. J. Biochem. 268 (2001) 6311–6317. [PMID: 11733028]
[EC 5.4.99.36 created 2011]
 
 
EC 5.4.99.37     
Accepted name: dammaradiene synthase
Reaction: squalene = dammara-20,24-diene
For diagram of hopene biosynthesis, click here
Systematic name: squalene mutase (cyclizing, dammara-20,24-diene-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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]
[EC 5.4.99.37 created 2011]
 
 
EC 5.4.99.38     
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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]
[EC 5.4.99.38 created 2011]
 
 
EC 5.4.99.39     
Accepted name: β-amyrin synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = β-amyrin
For diagram of beta-amyrin and soysapogenol biosynthesis, click here
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].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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]
[EC 5.4.99.39 created 2011]
 
 
EC 5.4.99.40     
Accepted name: α-amyrin synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = α-amyrin
For diagram of α-amyrin, α-seco-amyrin and germanicol biosynthesis, click here
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).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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]
[EC 5.4.99.40 created 2011]
 
 
EC 5.4.99.41     
Accepted name: lupeol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = lupeol
For diagram of lupeol and lupan-3β,20-diol biosynthesis, click here
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).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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]
[EC 5.4.99.41 created 2011]
 
 
EC 5.4.99.42     
Accepted name: tRNA pseudouridine31 synthase
Reaction: tRNA uridine31 = tRNA pseudouridine31
Other name(s): Pus6p
Systematic name: tRNA-uridine31 uracil mutase
Comments: The enzyme specifically acts on uridine31 in tRNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ansmant, I., Motorin, Y., Massenet, S., Grosjean, H. and Branlant, C. Identification and characterization of the tRNA:Ψ31-synthase (Pus6p) of Saccharomyces cerevisiae. J. Biol. Chem. 276 (2001) 34934–34940. [PMID: 11406626]
[EC 5.4.99.42 created 2011]
 
 
EC 5.4.99.43     
Accepted name: 21S rRNA pseudouridine2819 synthase
Reaction: 21S rRNA uridine2819 = 21S rRNA pseudouridine2819
Other name(s): Pus5p
Systematic name: 21S rRNA-uridine2819 uracil mutase
Comments: The enzyme specifically acts on uridine2819 in 21S rRNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ansmant, I., Massenet, S., Grosjean, H., Motorin, Y. and Branlant, C. Identification of the Saccharomyces cerevisiae RNA:pseudouridine synthase responsible for formation of Ψ2819 in 21S mitochondrial ribosomal RNA. Nucleic Acids Res. 28 (2000) 1941–1946. [PMID: 10756195]
[EC 5.4.99.43 created 2011]
 
 
EC 5.4.99.44     
Accepted name: mitochondrial tRNA pseudouridine27/28 synthase
Reaction: mitochondrial tRNA uridine27/28 = mitochondrial tRNA pseudouridine27/28
Other name(s): Pus2; Pus2p; RNA:pseudouridine synthases 2
Systematic name: mitochondrial tRNA-uridine27/28 uracil mutase
Comments: The mitochondrial enzyme Pus2p is specific for position 27 or 28 in mitochondrial tRNA [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Behm-Ansmant, I., Branlant, C. and Motorin, Y. The Saccharomyces cerevisiae Pus2 protein encoded by YGL063w ORF is a mitochondrial tRNA:Ψ27/28-synthase. RNA 13 (2007) 1641–1647. [PMID: 17684231]
[EC 5.4.99.44 created 2011]
 
 
EC 5.4.99.45     
Accepted name: tRNA pseudouridine38/39 synthase
Reaction: tRNA uridine38/39 = tRNA pseudouridine38/39
Other name(s): Deg1; Pus3p; pseudouridine synthase 3
Systematic name: tRNA-uridine38/39 uracil mutase
Comments: The enzyme from Saccharomyces cerevisiae is active only towards uridine38 and uridine39, and shows no activity with uridine40 (cf. EC 5.4.99.12, tRNA pseudouridine38-40 synthase) [1]. In vitro the enzyme from mouse is active on uridine39 and very slightly on uridine38 (human tRNALeu) [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lecointe, F., Simos, G., Sauer, A., Hurt, E.C., Motorin, Y. and Grosjean, H. Characterization of yeast protein Deg1 as pseudouridine synthase (Pus3) catalyzing the formation of Ψ38 and Ψ39 in tRNA anticodon loop. J. Biol. Chem. 273 (1998) 1316–1323. [PMID: 9430663]
2.  Chen, J. and Patton, J.R. Pseudouridine synthase 3 from mouse modifies the anticodon loop of tRNA. Biochemistry 39 (2000) 12723–12730. [PMID: 11027153]
[EC 5.4.99.45 created 2011]
 
 
EC 5.4.99.46     
Accepted name: shionone synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = shionone
For diagram of baccharis oxide, baruol and shionone biosynthesis, click here
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, shionone-forming)
Comments: The enzyme gives traces of four other triterpenoids
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sawai, S., Uchiyama, H., Mizuno, S., Aoki, T., Akashi, T., Ayabe, S. and Takahashi, T. Molecular characterization of an oxidosqualene cyclase that yields shionone, a unique tetracyclic triterpene ketone of Aster tataricus. FEBS Lett. 585 (2011) 1031–1036. [PMID: 21377465]
[EC 5.4.99.46 created 2011]
 
 
EC 5.4.99.47     
Accepted name: parkeol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = parkeol
For diagram of cucurbitadienol, cycloartenol, lanosterol and prostadienol biosynthesis, click here
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, parkeol-forming)
Comments: The enzyme from rice (Oryza sativa) produces parkeol as a single product [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ito, R., Mori, K., Hashimoto, I., Nakano, C., Sato, T. and Hoshino, T. Triterpene cyclases from Oryza sativa L.: cycloartenol, parkeol and achilleol B synthases. Org. Lett. 13 (2011) 2678–2681. [PMID: 21526825]
[EC 5.4.99.47 created 2011]
 
 
EC 5.4.99.48     
Accepted name: achilleol B synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = achilleol B
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, achilleol-B-forming)
Comments: Achilleol B is probably formed by cleavage of the 8-14 and 9-10 bonds of (3S)-2,3-epoxy-2,3-dihydrosqualene as part of the cyclization reaction, after formation of the oleanane skeleton.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ito, R., Mori, K., Hashimoto, I., Nakano, C., Sato, T. and Hoshino, T. Triterpene cyclases from Oryza sativa L.: cycloartenol, parkeol and achilleol B synthases. Org. Lett. 13 (2011) 2678–2681. [PMID: 21526825]
[EC 5.4.99.48 created 2011]
 
 
EC 5.4.99.49     
Accepted name: glutinol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = glutinol
For diagram of friedelin, glutinol, isomultiflorenol and taraxerol biosynthesis, click here
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, glutinol-forming)
Comments: The enzyme from Kalanchoe daigremontiana also gives traces of other triterpenoids.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wang, Z., Yeats, T., Han, H. and Jetter, R. Cloning and characterization of oxidosqualene cyclases from Kalanchoe daigremontiana: enzymes catalyzing up to 10 rearrangement steps yielding friedelin and other triterpenoids. J. Biol. Chem. 285 (2010) 29703–29712. [PMID: 20610397]
[EC 5.4.99.49 created 2011]
 
 
EC 5.4.99.50     
Accepted name: friedelin synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = friedelin
For diagram of friedelin, glutinol, isomultiflorenol and taraxerol biosynthesis, click here
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, friedelin-forming)
Comments: The enzyme from Kalanchoe daigremontiana also gives traces of other triterpenoids.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wang, Z., Yeats, T., Han, H. and Jetter, R. Cloning and characterization of oxidosqualene cyclases from Kalanchoe daigremontiana: enzymes catalyzing up to 10 rearrangement steps yielding friedelin and other triterpenoids. J. Biol. Chem. 285 (2010) 29703–29712. [PMID: 20610397]
[EC 5.4.99.50 created 2011]
 
 


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