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An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: quinate dehydrogenase (quinone)
Reaction: quinate + quinone = 3-dehydroquinate + quinol
For diagram of reaction, click here
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram). The use of the term “5-dehydroquinate” for this compound is based on an earlier system of numbering.
Other name(s): NAD(P)+-independent quinate dehydrogenase; quinate:pyrroloquinoline-quinone 5-oxidoreductase
Systematic name: quinate:quinol 3-oxidoreductase
Comments: The enzyme is membrane-bound. Does not use NAD(P)+ as acceptor. Contains pyrroloquinoline-quinone.
Links to other databases: CAS registry number: 115299-99-5
References:
1. van Kleef, M.A.G. and Duine, J.A. Bacterial NAD(P)-independent quinate dehydrogenase is a quinoprotein. Arch. Microbiol. 150 (1988) 32-36. [PMID: 3044290]
2. Adachi, O., Tanasupawat, S., Yoshihara, N., Toyama, H. and Matsushita, K. 3-Dehydroquinate production by oxidative fermentation and further conversion of 3-dehydroquinate to the intermediates in the shikimate pathway. Biosci. Biotechnol. Biochem. 67 (2003) 2124-2131. [PMID: 14586099]
3. Vangnai, A.S., Toyama, H., De-Eknamkul, W., Yoshihara, N., Adachi, O. and Matsushita, K. Quinate oxidation in Gluconobacter oxydans IFO3244: purification and characterization of quinoprotein quinate dehydrogenase. FEMS Microbiol. Lett. 241 (2004) 157-162. [PMID: 15598527]
[EC 1.1.99.25 Transferred entry: quinate dehydrogenase (pyrroloquinoline-quinone). Now EC 1.1.5.8, quinate dehydrogenase (quinone) (EC 1.1.99.25 created 1992, modified 2004, deleted 2010)]
Accepted name: succinate-semialdehyde dehydrogenase (NAD+)
Reaction: succinate semialdehyde + NAD+ + H2O = succinate + NADH + 2 H+
Other name(s): succinate semialdehyde dehydrogenase (NAD+); succinic semialdehyde dehydrogenase (NAD+); succinyl semialdehyde dehydrogenase (NAD+); succinate semialdehyde:NAD+ oxidoreductase
Systematic name: succinate-semialdehyde:NAD+ oxidoreductase
Comments: This enzyme participates in the degradation of glutamate and 4-aminobutyrate. It is similar to EC 1.2.1.79 [succinate-semialdehyde dehydrogenase (NADP+)], and EC 1.2.1.16 [succinate-semialdehyde dehydrogenase (NAD(P)+)], but is specific for NAD+.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9028-95-9
References:
1. Albers, R.W. and Koval, G.J. Succinic semialdehyde dehydrogenase : purification and properties of the enzyme from monkey brain. Biochim. Biophys. Acta 52 (1961) 29-35. [PMID: 13860092]
2. Ryzlak, M.T. and Pietruszko, R. Human brain "high Km" aldehyde dehydrogenase: purification, characterization, and identification as NAD+-dependent succinic semialdehyde dehydrogenase. Arch. Biochem. Biophys. 266 (1988) 386-396. [PMID: 3190233]
3. Busch, K.B. and Fromm, H. Plant succinic semialdehyde dehydrogenase. Cloning, purification, localization in mitochondria, and regulation by adenine nucleotides. Plant Physiol. 121 (1999) 589-597. [PMID: 10517851]
Accepted name: succinate-semialdehyde dehydrogenase (NADP+)
Reaction: succinate semialdehyde + NADP+ + H2O = succinate + NADPH + 2 H+
Other name(s): succinic semialdehyde dehydrogenase (NADP+); succinyl semialdehyde dehydrogenase (NADP+); succinate semialdehyde:NADP+ oxidoreductase; NADP-dependent succinate-semialdehyde dehydrogenase; GabD
Systematic name: succinate-semialdehyde:NADP+ oxidoreductase
Comments: This enzyme participates in the degradation of glutamate and 4-aminobutyrate. It is similar to EC 1.2.1.24 [succinate-semialdehyde dehydrogenase (NAD+)], and EC 1.2.1.16 [succinate-semialdehyde dehydrogenase (NAD(P)+)], but is specific for NADP+. The enzyme from Escherichia coli is 20-fold more active with NADP+ than NAD+ [2].
References:
1. Bartsch, K., von Johnn-Marteville, A. and Schulz, A. Molecular analysis of two genes of the Escherichia coli gab cluster: nucleotide sequence of the glutamate:succinic semialdehyde transaminase gene (gabT) and characterization of the succinic semialdehyde dehydrogenase gene (gabD). J. Bacteriol. 172 (1990) 7035-7042. [PMID: 2254272]
2. Jaeger, M., Rothacker, B. and Ilg, T. Saturation transfer difference NMR studies on substrates and inhibitors of succinic semialdehyde dehydrogenases. Biochem. Biophys. Res. Commun. 372 (2008) 400-406. [PMID: 18474219]
[EC 1.2.2.2 Deleted entry: pyruvate dehydrogenase (cytochrome). Now covered by EC 1.2.5.1, pyruvate dehydrogenase (quinone) (EC 1.2.2.2 created 1961, deleted 2010)]
Accepted name: fumarate reductase (menaquinone)
Reaction: succinate + a menaquinone = fumarate + a menaquinol
Other name(s): FRD; menaquinol-fumarate oxidoreductase; succinate dehydrogenase (menaquinone)
Systematic name: succinate:menaquinone oxidoreductase
Comments: The reaction is catalysed in the opposite direction. The enzyme is part of the anaerobic electron transfer chain of certain bacteria. It allows fumarate to serve as a terminal electron acceptor. The enzyme from Escherichia coli contains a catalytic domain and an anchor domain, each consisting of two subunits. One of the subunits of the catalytic domain contains a covalently-bound FAD cofactor and the fumarate binding site, and the other contains 3 iron-sulfur clusters. The anchor domain interacts with the menaquinone. The enzyme is closely related to EC 1.3.5.1 [succinate dehydrogenase (ubiquinone)].
References:
1. Iverson, T.M., Luna-Chavez, C., Cecchini, G. and Rees, D.C. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284 (1999) 1961-1966. [PMID: 10373108]
2. Cecchini, G., Schroder, I., Gunsalus, R.P. and Maklashina, E. Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim. Biophys. Acta 1553 (2002) 140-157. [PMID: 11803023]
3. Iverson, T.M., Luna-Chavez, C., Croal, L.R., Cecchini, G. and Rees, D.C. Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. J. Biol. Chem. 277 (2002) 16124-16130. [PMID: 11850430]
Accepted name: biphenyl-2,3-diol 1,2-dioxygenase
Reaction: biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H2O
Other name(s): 2,3-dihydroxybiphenyl dioxygenase; biphenyl-2,3-diol dioxygenase; BphC (gene name)
Systematic name: biphenyl-2,3-diol:oxygen 1,2-oxidoreductase (decyclizing)
Comments: Contains Fe2+ or Mn2+ [3]. This enzyme participates in the degradation pathway of biphenyl and PCB (poly chlorinated biphenyls), and catalyses the first ring cleavage step by incorporating two atomic oxygens to the catechol ring formed by EC 1.3.1.56, cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase. The enzyme from the bacterium Burkholderia xenovorans LB400 can also process catechol, 3-methylcatechol, and 4-methylcatechol, but less efficiently [1]. The enzyme from the bacterium Ralstonia sp. SBUG 290 could also accept 1,2-dihydroxydibenzofuran and 1,2-dihydroxynaphthalene [4]. The enzyme is strongly inhibited by the substrate [1]. Not identical with EC 1.13.11.2 catechol 2,3-dioxygenase.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, UM-BBD, CAS registry number: 103679-58-9
References:
1. Eltis, L.D., Hofmann, B., Hecht, H.J., Lunsdorf, H. and Timmis, K.N. Purification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase. J. Biol. Chem. 268 (1993) 2727-2732. [PMID: 8428946]
2. Uragami, Y., Senda, T., Sugimoto, K., Sato, N., Nagarajan, V., Masai, E., Fukuda, M. and Mitsu, Y. Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase. J. Inorg. Biochem. 83 (2001) 269-279. [PMID: 11293547]
3. Hatta, T., Mukerjee-Dhar, G., Damborsky, J., Kiyohara, H. and Kimbara, K. Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8. J. Biol. Chem. 278 (2003) 21483-21492. [PMID: 12672826]
4. Wesche, J., Hammer, E., Becher, D., Burchhardt, G. and Schauer, F. The bphC gene-encoded 2,3-dihydroxybiphenyl-1,2-dioxygenase is involved in complete degradation of dibenzofuran by the biphenyl-degrading bacterium Ralstonia sp. SBUG 290. J Appl Microbiol 98 (2005) 635-645. [PMID: 15715866]
Accepted name: carbazole 1,9a-dioxygenase
Reaction: 9H-carbazole + NAD(P)H + H+ + O2 = 2'-aminobiphenyl-2,3-diol + NAD(P)+
Other name(s): CARDO
Systematic name: 9H-carbazole,NAD(P)H:oxygen oxidoreductase (2,3-hydroxylating)
Comments: This enzyme catalyses the first reaction in the pathway of carbazole degradation. The enzyme attacks at the 1 and 9a positions of carbazle, resulting in the formation of a highly unstable hemiaminal intermediate that undergoes a spontaneous cleavage and rearomatization, resulting in 2'-aminobiphenyl-2,3-diol. In most bacteria the enzyme is a complex composed of a terminal oxygenase, a ferredoxin, and a ferredoxin reductase. The terminal oxygenase component contains a nonheme iron centre and a Rieske [2Fe-2S] iron-sulfur cluster.
References:
1. Nam, J.W., Nojiri, H., Noguchi, H., Uchimura, H., Yoshida, T., Habe, H., Yamane, H. and Omori, T. Purification and characterization of carbazole 1,9a-dioxygenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10. Appl. Environ. Microbiol. 68 (2002) 5882-5890. [PMID: 12450807]
2. Gai, Z., Wang, X., Liu, X., Tai, C., Tang, H., He, X., Wu, G., Deng, Z. and Xu, P. The genes coding for the conversion of carbazole to catechol are flanked by IS6100 elements in Sphingomonas sp. strain XLDN2-5. PLoS One 5 (2010) e10018. [PMID: 20368802]
Accepted name: geranylhydroquinone 3"-hydroxylase
Reaction: geranylhydroquinone + NADPH + H+ + O2 = 3"-hydroxygeranylhydroquinone + NADP+ + H2O
Glossary: 3"-hydroxygeranylhydroquinone = 2-[(2Z)-3-(hydroxymethyl)-7-methylocta-2,6-dien-1-yl]benzene-1,4-diol
Other name(s): GHQ 3"-hydroxylase
Systematic name: geranylhydroquinone,NADPH:oxygen oxidoreductase (3"-hydroxylating)
Comments: Contains cytochrome P450.
References:
1. Yamamoto, H., Inoue, K., Li, S.M. and Heide, L. Geranylhydroquinone 3"-hydroxylase, a cytochrome P-450 monooxygenase from Lithospermum erythrorhizon cell suspension cultures. Planta 210 (2000) 312-317. [PMID: 10664138]
Accepted name: isoleucine N-monooxygenase
Reaction: L-isoleucine + 2 O2 + 2 NADPH + 2 H+ = (E)-2-methylbutanal oxime + 2 NADP+ + CO2 + 3 H2O
(1a) L-isoleucine + O2 + NADPH + H+ = N-hydroxy-L-isoleucine + NADP+ + H2O
(1b) N-hydroxy-L-isoleucine + O2 + NADPH + H+ = N,N-dihydroxy-L-isoleucine + NADP+ + H2O
(1c) N,N-dihydroxy-L-isoleucine = (E)-2-methylbutanal oxime + CO2 + H2O (spontaneous)
Other name(s): CYP79D3; CYP79D4
Systematic name: L-isoleucine,NADPH:oxygen oxidoreductase (N-hydroxylating)
Comments: A heme-thiolate protein (P-450). This enzyme catalyses two successive N-hydroxylations of L-isoleucine, the first committed steps in the biosynthesis of the cyanogenic glucoside lotaustralin in the plant Lotus japonicus. The product of the two hydroxylations, N,N-dihydroxy-L-isoleucine, is extremely labile and dehydrates spontaneously. The dehydrated product is then subject to a decarboxylation that produces the oxime. It is still not known whether the decarboxylation is spontaneous or catalysed by the enzyme. The product, (E)-2-methylbutanal oxime, undergoes a spontaneous isomerization to the (Z) form. The enzyme can also accept L-valine as substrate, with a lower activity. It is different from EC 1.14.13.118 (valine N-monooxygenase), which prefers L-valine.
References:
1. Andersen, M.D., Busk, P.K., Svendsen, I. and Moller, B.L. Cytochromes P-450 from cassava (Manihot esculenta Crantz) catalyzing the first steps in the biosynthesis of the cyanogenic glucosides linamarin and lotaustralin. Cloning, functional expression in Pichia pastoris, and substrate specificity of the isolated recombinant enzymes. J. Biol. Chem. 275 (2000) 1966-1975. [PMID: 10636899]
2. Forslund, K., Morant, M., Jorgensen, B., Olsen, C.E., Asamizu, E., Sato, S., Tabata, S. and Bak, S. Biosynthesis of the nitrile glucosides rhodiocyanoside A and D and the cyanogenic glucosides lotaustralin and linamarin in Lotus japonicus. Plant Physiol. 135 (2004) 71-84. [PMID: 15122013]
Accepted name: valine N-monooxygenase
Reaction: L-valine + 2 O2 + 2 NADPH + 2 H+ = (E)-2-methylpropanal oxime + 2 NADP+ + CO2 + 3 H2O
(1a) L-valine + O2 + NADPH + H+ = N-hydroxy-L-valine + NADP+ + H2O
(1b) N-hydroxy-L-valine + O2 + NADPH + H+ = N,N-dihydroxy-L-valine + NADP+ + H2O
(1c) N,N-dihydroxy-L-valine = (E)-2-methylpropanal oxime + CO2 + H2O (spontaneous)
Other name(s): CYP79D1; CYP79D2
Systematic name: L-valine,NADPH:oxygen oxidoreductase (N-hydroxylating)
Comments: A heme-thiolate protein (P-450). This enzyme catalyses two successive N-hydroxylations of L-valine, the first committed steps in the biosynthesis of the cyanogenic glucoside linamarin in Manihot esculenta (cassava). The product of the two hydroxylations, N,N-dihydroxy-L-valine, is extremely labile and dehydrates spontaneously. The dehydrated product is then subject to a decarboxylation that produces the oxime. It is still not known whether the decarboxylation is spontaneous or catalysed by the enzyme. The product, (E)-2-methylpropanal-oxime, undergoes a spontaneous isomerization to the (Z) form. The enzyme can also accept L-isoleucine as substrate, with a lower activity. It is different from EC 1.14.13.117 (isoleucine N-monooxygenase), which prefers L-isoleucine.
References:
1. Andersen, M.D., Busk, P.K., Svendsen, I. and Moller, B.L. Cytochromes P-450 from cassava (Manihot esculenta Crantz) catalyzing the first steps in the biosynthesis of the cyanogenic glucosides linamarin and lotaustralin. Cloning, functional expression in Pichia pastoris, and substrate specificity of the isolated recombinant enzymes. J. Biol. Chem. 275 (2000) 1966-1975. [PMID: 10636899]
2. Forslund, K., Morant, M., Jorgensen, B., Olsen, C.E., Asamizu, E., Sato, S., Tabata, S. and Bak, S. Biosynthesis of the nitrile glucosides rhodiocyanoside A and D and the cyanogenic glucosides lotaustralin and linamarin in Lotus japonicus. Plant Physiol. 135 (2004) 71-84. [PMID: 15122013]
Accepted name: all-trans-8'-apo-β-carotenal 15,15'-oxygenase
Reaction: all-trans-8'-apo-β-carotenal + O2 = all-trans-retinal + (2E,4E,6E)-2,6-dimethylocta-2,4,6-trienedial
Other name(s): Diox1; ACO; 8'-apo-β-carotenal 15,15'-oxygenase
Systematic name: all-trans-8'-apo-β-carotenal:oxygen 15,15'-oxidoreductase (bond-cleaving)
Comments: Contains an Fe2+-4His arrangement. The enzyme is involved in retinal biosynthesis in bacteria [2].
References:
1. Ruch, S., Beyer, P., Ernst, H. and Al-Babili, S. Retinal biosynthesis in Eubacteria: in vitro characterization of a novel carotenoid oxygenase from Synechocystis sp. PCC 6803. Mol. Microbiol. 55 (2005) 1015-1024. [PMID: 15686550]
2. Kloer, D.P., Ruch, S., Al-Babili, S., Beyer, P. and Schulz, G.E. The structure of a retinal-forming carotenoid oxygenase. Science 308 (2005) 267-269. [PMID: 15821095]
Accepted name: caffeine dehydrogenase
Reaction: caffeine + ubiquinone + H2O = 1,3,7-trimethylurate + ubiquinol
Glossary: caffeine = 1,3,7-trimethylxanthine
Systematic name: caffeine:ubiquinone oxidoreductase
Comments: This enzyme, characterized from the soil bacterium Pseudomonas sp. CBB1, catalyses the incorporation of an oxygen atom originating from a water molecule into position C-8 of caffeine. The enzyme utilizes short-tail ubiquinones as the preferred electron acceptor.
References:
1. Yu, C.L., Kale, Y., Gopishetty, S., Louie, T.M. and Subramanian, M. A novel caffeine dehydrogenase in Pseudomonas sp. strain CBB1 oxidizes caffeine to trimethyluric acid. J. Bacteriol. 190 (2008) 772-776. [PMID: 17981969]
[EC 2.1.1.51 Transferred entry: rRNA (guanine-N1-)-methyltransferase. Now covered by EC 2.1.1.187 [23S rRNA (guanine745-N1)-methyltransferase] and EC 2.1.1.188 [23S rRNA (guanine748-N1)-methyltransferase]. (EC 2.1.1.51 created 1976, deleted 2010)]
Accepted name: thymidylate synthase (FAD)
Reaction: 5,10-methylenetetrahydrofolate + dUMP + NADPH + H+ = dTMP + tetrahydrofolate + NADP+
Other name(s): Thy1; ThyX
Systematic name: 5,10-methylenetetrahydrofolate,FADH2:dUMP C-methyltransferase
Comments: Contains FAD. All thymidylate synthases catalyse a reductive methylation involving the transfer of the methylene group of 5,10-methylenetetrahydrofolate to the C5-position of dUMP and a two electron reduction of the methylene group to a methyl group. Unlike the classical thymidylate synthase, ThyA (EC 2.1.1.45), which uses folate as both a 1-carbon donor and a source of reducing equivalents, this enzyme uses a flavin coenzyme as a source of reducing equivalents, which are derived from NADPH.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 850167-13-4
References:
1. Myllykallio, H., Lipowski, G., Leduc, D., Filee, J., Forterre, P. and Liebl, U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science 297 (2002) 105-107. [PMID: 12029065]
2. Griffin, J., Roshick, C., Iliffe-Lee, E. and McClarty, G. Catalytic mechanism of Chlamydia trachomatis flavin-dependent thymidylate synthase. J. Biol. Chem. 280 (2005) 5456-5467. [PMID: 15591067]
3. Graziani, S., Bernauer, J., Skouloubris, S., Graille, M., Zhou, C.Z., Marchand, C., Decottignies, P., van Tilbeurgh, H., Myllykallio, H. and Liebl, U. Catalytic mechanism and structure of viral flavin-dependent thymidylate synthase ThyX. J. Biol. Chem. 281 (2006) 24048-24057. [PMID: 16707489]
4. Koehn, E.M., Fleischmann, T., Conrad, J.A., Palfey, B.A., Lesley, S.A., Mathews, I.I. and Kohen, A. An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene. Nature 458 (2009) 919-923. [PMID: 19370033]
5. Koehn, E.M. and Kohen, A. Flavin-dependent thymidylate synthase: a novel pathway towards thymine. Arch. Biochem. Biophys. 493 (2010) 96-102. [PMID: 19643076]
Accepted name: 23S rRNA (guanine745-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine745 in 23S rRNA = S-adenosyl-L-homocysteine + N1-methylguanine745 in 23S rRNA
Other name(s): Rlma(I); Rlma1; 23S rRNA m1G745 methyltransferase; YebH; RlmAI methyltransferase; ribosomal RNA(m1G)-methylase (ambiguous); rRNA(m1G)methylase (ambiguous); RrmA (ambiguous); 23S rRNA:m1G745 methyltransferase
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine745-N1)-methyltransferase
Comments: The enzyme specifically methylates guanine745 at N1 in 23S rRNA.
References:
1. Liu, M., Novotny, G.W. and Douthwaite, S. Methylation of 23S rRNA nucleotide G745 is a secondary function of the RlmAI methyltransferase. RNA 10 (2004) 1713-1720. [PMID: 15388872]
2. Gustafsson, C. and Persson, B.C. Identification of the rrmA gene encoding the 23S rRNA m1G745 methyltransferase in Escherichia coli and characterization of an m1G745-deficient mutant. J. Bacteriol. 180 (1998) 359-365. [PMID: 9440525]
3. Das, K., Acton, T., Chiang, Y., Shih, L., Arnold, E. and Montelione, G.T. Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc. Natl. Acad. Sci. USA 101 (2004) 4041-4046. [PMID: 14999102]
4. Hansen, L.H., Kirpekar, F. and Douthwaite, S. Recognition of nucleotide G745 in 23 S ribosomal RNA by the rrmA methyltransferase. J. Mol. Biol. 310 (2001) 1001-1010. [PMID: 11501991]
5. Liu, M. and Douthwaite, S. Methylation at nucleotide G745 or G748 in 23S rRNA distinguishes Gram-negative from Gram-positive bacteria. Mol. Microbiol. 44 (2002) 195-204. [PMID: 11967079]
Accepted name: 23S rRNA (guanine748-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine748 in 23S rRNA = S-adenosyl-L-homocysteine + N1-methylguanine748 in 23S rRNA
Other name(s): Rlma(II); Rlma2; 23S rRNA m1G748 methyltransferase; RlmaII; Rlma II; tylosin-resistance methyltransferase RlmA(II); TlrB; rRNA large subunit methyltransferase II
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine748-N1)-methyltransferase
Comments: The enzyme specifically methylates guanine748 at N1 in 23S rRNA. The methyltransferase RlmAII confers resistance to the macrolide antibiotic tylosin in the drug-producing strain Streptomyces fradiae [1].
References:
1. Douthwaite, S., Crain, P.F., Liu, M. and Poehlsgaard, J. The tylosin-resistance methyltransferase RlmAII (TlrB) modifies the N-1 position of 23S rRNA nucleotide G748. J. Mol. Biol. 337 (2004) 1073-1077. [PMID: 15046978]
2. Liu, M., Kirpekar, F., Van Wezel, G.P. and Douthwaite, S. The tylosin resistance gene tlrB of Streptomyces fradiae encodes a methyltransferase that targets G748 in 23S rRNA. Mol. Microbiol. 37 (2000) 811-820. [PMID: 10972803]
3. Lebars, I., Yoshizawa, S., Stenholm, A.R., Guittet, E., Douthwaite, S. and Fourmy, D. Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII. EMBO J. 22 (2003) 183-192. [PMID: 12514124]
4. Lebars, I., Husson, C., Yoshizawa, S., Douthwaite, S. and Fourmy, D. Recognition elements in rRNA for the tylosin resistance methyltransferase RlmAII. J. Mol. Biol. 372 (2007) 525-534. [PMID: 17673230]
5. Douthwaite, S., Jakobsen, L., Yoshizawa, S. and Fourmy, D. Interaction of the tylosin-resistance methyltransferase RlmAII at its rRNA target differs from the orthologue RlmAI. J. Mol. Biol. 378 (2008) 969-975. [PMID: 18406425]
6. Liu, M. and Douthwaite, S. Methylation at nucleotide G745 or G748 in 23S rRNA distinguishes Gram-negative from Gram-positive bacteria. Mol. Microbiol. 44 (2002) 195-204. [PMID: 11967079]
Accepted name: 23S rRNA (uracil747-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + uracil747 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Other name(s): YbjF; RumB; RNA uridine methyltransferase B
Systematic name: S-adenosyl-L-methionine:23S rRNA (uracil747-C5)-methyltransferase
Comments: The enzyme specifically methylates uracil747 at C5 in 23S rRNA.
References:
1. Madsen, C.T., Mengel-Jorgensen, J., Kirpekar, F. and Douthwaite, S. Identifying the methyltransferases for m5U747 and m5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 31 (2003) 4738-4746. [PMID: 12907714]
Accepted name: 23S rRNA (uracil1939-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + uracil1939 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
Other name(s): RumA; RNA uridine methyltransferase A; YgcA
Systematic name: S-adenosyl-L-methionine:23S rRNA (uracil1939-C5)-methyltransferase
Comments: The enzyme specifically methylates uracil1939 at C5 in 23S rRNA [1]. The enzyme contains an [4Fe-4S] cluster coordinated by four conserved cysteine residues [2].
References:
1. Agarwalla, S., Kealey, J.T., Santi, D.V. and Stroud, R.M. Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli. J. Biol. Chem. 277 (2002) 8835-8840. [PMID: 11779873]
2. Lee, T.T., Agarwalla, S. and Stroud, R.M. Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase. Structure 12 (2004) 397-407. [PMID: 15016356]
3. Madsen, C.T., Mengel-Jorgensen, J., Kirpekar, F. and Douthwaite, S. Identifying the methyltransferases for m5U747 and m5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 31 (2003) 4738-4746. [PMID: 12907714]
4. Persaud, C., Lu, Y., Vila-Sanjurjo, A., Campbell, J.L., Finley, J. and O'Connor, M. Mutagenesis of the modified bases, m5U1939 and Ψ2504, in Escherichia coli 23S rRNA. Biochem. Biophys. Res. Commun. 392 (2010) 223-227. [PMID: 20067766]
5. Agarwalla, S., Stroud, R.M. and Gaffney, B.J. Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. J. Biol. Chem. 279 (2004) 34123-34129. [PMID: 15181002]
6. Lee, T.T., Agarwalla, S. and Stroud, R.M. A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 120 (2005) 599-611. [PMID: 15766524]
Accepted name: 23S rRNA (cytosine1962-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytosine1962 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine1962 in 23S rRNA
Other name(s): RlmI; rRNA large subunit methyltransferase I; YccW
Systematic name: S-adenosyl-L-methionine:23S rRNA (cytosine1962-C5)-methyltransferase
Comments: The enzyme specifically methylates cytosine1962 at C5 in 23S rRNA.
References:
1. Purta, E., O'Connor, M., Bujnicki, J.M. and Douthwaite, S. YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. J. Mol. Biol. 383 (2008) 641-651. [PMID: 18786544]
2. Sunita, S., Tkaczuk, K.L., Purta, E., Kasprzak, J.M., Douthwaite, S., Bujnicki, J.M. and Sivaraman, J. Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J. Mol. Biol. 383 (2008) 652-666. [PMID: 18789337]
Accepted name: 23S rRNA (adenine2503-C2)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine2503 in 23S rRNA = S-adenosyl-L-homocysteine + 2-methyladenine2503 in 23S rRNA
Other name(s): RlmN; YgfB; RlmN/YgfB; methyltransferase YfgB/RlmN
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine2503-C2)-methyltransferase
Comments: Contains an [4Fe-4S] cluster [2]. RlmN is an endogenous enzyme used by the cell to refine functions of the ribosome in protein synthesis [2]. cf. EC 2.1.1.194 [23S rRNA (adenine2503-C2,C8)-dimethyltransferase].
References:
1. Toh, S.M., Xiong, L., Bae, T. and Mankin, A.S. The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA 14 (2008) 98-106. [PMID: 18025251]
2. Yan, F., LaMarre, J.M., Röhrich, R., Wiesner, J., Jomaa, H., Mankin, A.S., Fujimori, D.G. RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA. J. Am. Chem. Soc. 132 (2010) 3953-3964. [PMID: 20184321]
Accepted name: 16S rRNA (uracil1498-N3)-methyltransferase
Reaction: S-adenosyl-L-methionine + uracil1498 in 16S rRNA = S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
Other name(s): DUF558 protein; YggJ; RsmE; m3U1498 specific methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (uracil1498-N3)-methyltransferase
Comments: The enzyme specifically methylates uracil1498 at N3 in 16S rRNA.
References:
1. Basturea, G.N., Rudd, K.E. and Deutscher, M.P. Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family. RNA 12 (2006) 426-434. [PMID: 16431987]
2. Basturea, G.N. and Deutscher, M.P. Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE. RNA 13 (2007) 1969-1976. [PMID: 17872509]
Accepted name: 23S rRNA (adenine2503-C2,C8)-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA = 2 S-adenosyl-L-homocysteine + 2,8-dimethyladenine2503 in 23S rRNA
Other name(s): Cfr; Cfr methyltransferase; Cfr rRNA methyltransferase
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine2503-C2,C8)-dimethyltransferase
Comments: Contains an [4Fe-S] cluster [1]. Cfr is an plasmid-acquired methyltransferase that protects cells from the action of antibiotics [1]. Cfr methylates position 2 of A2503 after the primary methylation at position 8 is complete [2]. cf. 23S rRNA (adenine2503-C2)-methyltransferase (EC 2.1.1.192).
References:
1. Yan, F., LaMarre, J.M., Röhrich, R., Wiesner, J., Jomaa, H., Mankin, A.S., Fujimori, D.G. RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA. J. Am. Chem. Soc. 132 (2010) 3953-3964. [PMID: 20184321]
2. Giessing, A.M., Jensen, S.S., Rasmussen, A., Hansen, L.H., Gondela, A., Long, K., Vester, B. and Kirpekar, F. Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria. RNA 15 (2009) 327-336. [PMID: 19144912]
3. Kaminska, K.H., Purta, E., Hansen, L.H., Bujnicki, J.M., Vester, B. and Long, K.S. Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria. Nucleic Acids Res. 38 (2010) 1652-1663. [PMID: 20007606]
Accepted name: cobalt-precorrin-5B (C1)-methyltransferase
Reaction: cobalt-precorrin-5B + S-adenosyl-L-methionine = cobalt-precorrin-6A + S-adenosyl-L-homocysteine
Glossary: cobalt-precorrin-6A = cobalt-precorrin-6x
Other name(s): cobalt-precorrin-6A synthase; CbiD (gene name)
Systematic name: S-adenosyl-L-methionine:cobalt-precorrin-5B (C1)-methyltransferase
Comments: This enzyme catalyses the C-1 methylation of cobalt-precorrin-5B in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis.
References:
1. Roper, J.M., Raux, E., Brindley, A.A., Schubert, H.L., Gharbia, S.E., Shah, H.N. and Warren, M.J. The enigma of cobalamin (Vitamin B12) biosynthesis in Porphyromonas gingivalis. Identification and characterization of a functional corrin pathway. J. Biol. Chem. 275 (2000) 40316-40323. [PMID: 11007789]
2. Roessner, C.A., Williams, H.J. and Scott, A.I. Genetically engineered production of 1-desmethylcobyrinic acid, 1-desmethylcobyrinic acid a,c-diamide, and cobyrinic acid a,c-diamide in Escherichia coli implies a role for CbiD in C-1 methylation in the anaerobic pathway to cobalamin. J. Biol. Chem. 280 (2005) 16748-16753. [PMID: 15741157]
Accepted name: cobalt-precorrin-7 (C15)-methyltransferase [decarboxylating]
Reaction: cobalt-precorrin-7 + S-adenosyl-L-methionine = cobalt-precorrin-8x + S-adenosyl-L-homocysteine + CO2
Glossary: cobalt-precorrin-7 = cobalt-precorrin-6Y
Other name(s): cobalt-precorrin-6Y (C15)-methyltransferase [decarboxylating]; CbiT (gene name)
Comments: This enzyme catalyses both methylation at C-15 and decarboxylation of the C-12 acetate side chain of cobalt-precorrin-7, a step in the anaerobic (early cobalt insertion) adenosylcobalamin biosynthesis pathway.
References:
1. Keller, J.P., Smith, P.M., Benach, J., Christendat, D., deTitta, G.T. and Hunt, J.F. The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase. Structure 10 (2002) 1475-1487. [PMID: 12429089]
2. Santander, P.J., Kajiwara, Y., Williams, H.J. and Scott, A.I. Structural characterization of novel cobalt corrinoids synthesized by enzymes of the vitamin B12 anaerobic pathway. Bioorg. Med. Chem. 14 (2006) 724-731. [PMID: 16198574]
Accepted name: malonyl-CoA O-methyltransferase
Reaction: S-adenosyl-L-methionine + malonyl-CoA = S-adenosyl-L-homocysteine + malonyl-CoA methyl ester
Other name(s): BioC
Systematic name: S-adenosyl-L-methionine:malonyl-CoA N-methyltransferase
Comments: Involved in an early step of biotin biosynthesis in Gram-negative bacteria. This enzyme catalyses the transfer of a methyl group to the ω-carboxyl group of malonyl-CoA forming a methyl ester. The methyl ester is recognized by the fatty acid synthetic enzymes, which process it via the fatty acid elongation cycle to give pimelyl-[acyl-carrier-protein] methyl ester [5].
References:
1. Del Campillo-Campbell, A., Kayajanian, G., Campbell, A. and Adhya, S. Biotin-requiring mutants of Escherichia coli K-12. J. Bacteriol. 94 (1967) 2065-2066. [PMID: 4864413]
2. Rolfe, B. and Eisenberg, M.A. Genetic and biochemical analysis of the biotin loci of Escherichia coli K-12. J. Bacteriol. 96 (1968) 515-524. [PMID: 4877129]
3. Otsuka, A.J., Buoncristiani, M.R., Howard, P.K., Flamm, J., Johnson, C., Yamamoto, R., Uchida, K., Cook, C., Ruppert, J. and Matsuzaki, J. The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon. J. Biol. Chem. 263 (1988) 19577-19585. [PMID: 3058702]
4. Cleary, P.P. and Campbell, A. Deletion and complementation analysis of biotin gene cluster of Escherichia coli. J. Bacteriol. 112 (1972) 830-839. [PMID: 4563978]
5. Lin, S., Hanson, R.E. and Cronan, J.E. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat. Chem. Biol. (2010) . [PMID: 20693992]
Accepted name: 16S rRNA (cytidine1402-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytidine1402 in 16S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine1402 in 16S rRNA
Other name(s): RsmI; YraL
Systematic name: S-adenosyl-L-methionine:16S rRNA (cytidine1402-2'-O)-methyltransferase
Comments: RsmI catalyses the 2'-O-methylation of cytidine1402 and RsmH (EC 2.1.1.199) catalyses the N4-methylation of cytidine1402 in 16S rRNA. Both methylations are necessary for efficient translation initiation at the UUG and GUG codons.
References:
1. Kimura, S. and Suzuki, T. Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res. 38 (2010) 1341-1352. [PMID: 19965768]
Accepted name: 16S rRNA (cytidine1402-N4)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytidine1402 in 16S rRNA = S-adenosyl-L-homocysteine + N4-methylcytidine1402 in 16S rRNA
Other name(s): RsmH; MraW
Systematic name: S-adenosyl-L-methionine:16S rRNA (cytidine1402-N4)-methyltransferase
Comments: RsmH catalyses the N4-methylation of cytidine1402 and RsmI (EC 2.1.1.198) catalyses the 2'-O-methylation of cytidine1402 in 16S rRNA. Both methylations are necessary for efficient translation initiation at the UUG and GUG codons.
References:
1. Kimura, S. and Suzuki, T. Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res. 38 (2010) 1341-1352. [PMID: 19965768]
Accepted name: glycine N-phenylacetyltransferase
Reaction: phenylacetyl-CoA + glycine = phenylacetylglycine + CoA
Other name(s): arylacetyl-CoA N-acyltransferase; arylacetyltransferase; GAT (gene name)
Systematic name: phenylacetyl-CoA:glycine N-phenylacetyltransferase
Comments: Not identical with EC 2.3.1.13 (glycine N-acyltransferase). This enzyme was purified from bovine liver mitochondria. L-asparagine, L-glutamine and L-arginine are alternative substrates to glycine, but have higher Km values.
References:
1. Nandi, D.L., Lucas, S.V. and Webster, L.T. Benzoyl-coenzyme A:glycine N-acyltransferase and phenylacetyl-coenzyme A:glycine N-acyltransferase from bovine liver mitochondria. Purification and characterization. J. Biol. Chem. 254 (1979) 7230-7237. [PMID: 457678]
2. Kelley, M. and Vessey, D.A. The effects of ions on the conjugation of xenobiotics by the aralkyl-CoA and arylacetyl-CoA N-acyltransferases from bovine liver mitochondria. J. Biochem. Toxicol. 5 (1990) 125-135. [PMID: 2283662]
3. Vessey, D.A. and Lau, E. Determination of the sequence of the arylacetyl acyl-CoA:amino acid N-acyltransferase from bovine liver mitochondria and its homology to the aralkyl acyl-CoA:amino acid N-acyltransferase. J Biochem Mol Toxicol 12 (1998) 275-279. [PMID: 9664233]
Accepted name: (2E,6E)-farnesyl diphosphate synthase
Reaction: geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): farnesyl-diphosphate synthase; geranyl transferase I; prenyltransferase; farnesyl pyrophosphate synthetase; farnesylpyrophosphate synthetase; geranyltranstransferase
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate geranyltranstransferase
Comments: Some forms of this enzyme will also use dimethylallyl diphosphate as a substrate. The enzyme will not accept larger prenyl diphosphates as efficient donors.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 37277-79-5
References:
1. Lynen, F., Agranoff, B.W., Eggerer, H., Henning, V. and Möslein, E.M. Zur Biosynthese der Terpene. VI. γ,γ-Dimethyl-allyl-pyrophosphat und Geranyl-pyrophosphat, biologische Vorstufen des Squalens. Angew. Chem. 71 (1959) 657-663.
2. Ogura, K., Nishino, T. and Seto, S. The purification of prenyltransferase and isopentenyl pyrophosphate isomerase of pumpkin fruit and their some properties. J. Biochem. (Tokyo) 64 (1968) 197-203. [PMID: 4303505]
3. Reed, B.C. and Rilling, H. Crystallization and partial characterization of prenyltransferase from avian liver. Biochemistry 14 (1975) 50-54. [PMID: 1109590]
4. Takahashi, I. and Ogura, K. Farnesyl pyrophosphate synthetase from Bacillus subtilis. J. Biochem. (Tokyo) 89 (1981) 1581-1587. [PMID: 6792191]
5. Takahashi, I. and Ogura, K. Prenyltransferases of Bacillus subtilis: undecaprenyl pyrophosphate synthetase and geranylgeranyl pyrophosphate synthetase. J. Biochem. (Tokyo) 92 (1982) 1527-1537. [PMID: 6818223]
Accepted name: heptaprenyl diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): all-trans-heptaprenyl-diphosphate synthase; heptaprenyl pyrophosphate synthase; heptaprenyl pyrophosphate synthetase; HepPP synthase; HepPS; heptaprenylpyrophosphate synthetase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 4 isopentenyl units)
Comments: This enzyme catalyses the condensation reactions resulting in the formation of all-trans-heptaprenyl diphosphate, the isoprenoid side chain of ubiquinone-7 and menaquinone-7. The enzyme adds four isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 74506-59-5
References:
1. Takahashi, I., Ogura, K. and Seto, S. Heptaprenyl pyrophosphate synthetase from Bacillus subtilis. J. Biol. Chem. 255 (1980) 4539-4543. [PMID: 6768722]
2. Zhang, Y.W., Koyama, T., Marecak, D.M., Prestwich, G.D., Maki, Y. and Ogura, K. Two subunits of heptaprenyl diphosphate synthase of Bacillus subtilis form a catalytically active complex. Biochemistry 37 (1998) 13411-13420. [PMID: 9748348]
3. Zhang, Y.W., Li, X.Y., Sugawara, H. and Koyama, T. Site-directed mutagenesis of the conserved residues in component I of Bacillus subtilis heptaprenyl diphosphate synthase. Biochemistry 38 (1999) 14638-14643. [PMID: 10545188]
4. Suzuki, T., Zhang, Y.W., Koyama, T., Sasaki, D.Y. and Kurihara, K. Direct observation of substrate-enzyme complexation by surface forces measurement. J. Am. Chem. Soc. 128 (2006) 15209-15214. [PMID: 17117872]
Accepted name: (2Z,6E)-farnesyl diphosphate synthase
Reaction: geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2Z,6E)-farnesyl diphosphate
For diagram of reaction, click here
Other name(s): (Z)-farnesyl diphosphate synthase; Z-farnesyl diphosphate synthase
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate geranylcistransferase
Comments: Requires Mg2+ or Mn2+ for activity. The product of this reaction is an intermediate in the synthesis of decaprenyl phosphate, which plays a central role in the biosynthesis of most features of the mycobacterial cell wall, including peptidoglycan, linker unit galactan and arabinan. Neryl diphosphate can also act as substrate.
Links to other databases: BRENDA, EXPASY, KEGG CAS registry number:
References:
1. Schulbach, M.C., Mahapatra, S., Macchia, M., Barontini, S., Papi, C., Minutolo, F., Bertini, S., Brennan, P.J. and Crick, D.C. Purification, enzymatic characterization, and inhibition of the Z-farnesyl diphosphate synthase from Mycobacterium tuberculosis. J. Biol. Chem. 276 (2001) 11624-11630. [PMID: 11152452]
Accepted name: all-trans-octaprenyl-diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-octaprenyl diphosphate
Glossary: all-trans-octaprenyl diphosphate = OPP
Other name(s): octaprenyl-diphosphate synthase; octaprenyl pyrophosphate synthetase; polyprenylpyrophosphate synthetase; terpenoidallyltransferase; terpenyl pyrophosphate synthetase; trans-heptaprenyltranstransferase; trans-prenyltransferase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 5 isopentenyl units)
Comments: This enzyme catalyses the condensation reactions resulting in the formation of all-trans-octaprenyl diphosphate, the isoprenoid side chain of ubiquinone-8 and menaquinone-8. The enzyme adds five isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry
References:
1. Fujisaki, S., Nishino, T. and Katsuki, H. Isoprenoid synthesis in Escherichia coli. Separation and partial purification of four enzymes involved in the synthesis. J. Biochem. 99 (1986) 1327-1337. [PMID: 3519603]
2. Asai, K., Fujisaki, S., Nishimura, Y., Nishino, T., Okada, K., Nakagawa, T., Kawamukai, M. and Matsuda, H. The identification of Escherichia coli ispB (cel) gene encoding the octaprenyl diphosphate synthase. Biochem. Biophys. Res. Commun. 202 (1994) 340-345. [PMID: 8037730]
Accepted name: all-trans-decaprenyl-diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-decaprenyl diphosphate
Other name(s): decaprenyl-diphosphate synthase; decaprenyl pyrophosphate synthetase; polyprenylpyrophosphate synthetase; terpenoidallyltransferase; terpenyl pyrophosphate synthetase; trans-prenyltransferase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 7 isopentenyl units)
Comments: This enzyme catalyses the condensation reactions resulting in the formation of all-trans-decaprenyl diphosphate, the isoprenoid side chain of ubiquinone-10 and menaquinone-10. The enzyme adds seven isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry.
References:
1. Saiki, R., Nagata, A., Kainou, T., Matsuda, H. and Kawamukai, M. Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans. FEBS J. 272 (2005) 5606-5622. [PMID: 16262699]
Accepted name: (2Z,6Z)-farnesyl diphosphate synthase
Reaction: dimethylallyl diphosphate + 2 isopentenyl diphosphate = 2 diphosphate + (2Z,6Z)-farnesyl diphosphate
Other name(s): cis,cis-farnesyl diphosphate synthase; Z,Z-FPP synthase; zFPS; Z,Z-farnesyl pyrophosphate synthase
Systematic name: dimethylallyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 2 isopentenyl units)
Comments: This enzyme, originally characterized from wild tomato, specifically forms (2Z,6Z)-farnesyl diphosphate from geranyl diphosphate and isopentenyl diphosphate. In wild tomato it is involved in the biosynthesis of several sesquiterpenes. cf. EC 2.5.1.68 [(2Z,6E)-farnesyl diphosphate synthase] and EC 2.5.1.10 [(2E,6E)-farnesyl diphosphate synthase].
References:
1. Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301-317. [PMID: 19155349]
Accepted name: 4-hydroxybenzoate geranyltransferase
Reaction: geranyl diphosphate + 4-hydroxybenzoate = 3-geranyl-4-hydroxybenzoate + diphosphate
Other name(s): PGT1; PGT2; 4HB geranyltransferase; 4HB:geranyltransferase; p-hydroxybenzoate geranyltransferase; PHB geranyltransferase; geranyl diphosphate:4-hydroxybenzoate geranyltransferase; p-hydroxybenzoate geranyltransferase
Systematic name: geranyl-diphosphate:4-hydroxybenzoate 3-geranyltransferase
Comments: The enzyme is involved in shikonin biosynthesis. It has a strict substrate specificity for geranyl diphosphate and an absolute requirement for Mg2+ [2].
References:
1. Ohara, K., Muroya, A., Fukushima, N. and Yazaki, K. Functional characterization of LePGT1, a membrane-bound prenyltransferase involved in the geranylation of p-hydroxybenzoic acid. Biochem. J. 421 (2009) 231-241. [PMID: 19392660]
2. Muhlenweg, A., Melzer, M., Li, S.M. and Heide, L. 4-Hydroxybenzoate 3-geranyltransferase from Lithospermum erythrorhizon: purification of a plant membrane-bound prenyltransferase. Planta 205 (1998) 407-413. [PMID: 9640665]
3. Yazaki, K., Kunihisa, M., Fujisaki, T. and Sato, F. Geranyl diphosphate:4-hydroxybenzoate geranyltransferase from Lithospermum erythrorhizon. Cloning and characterization of a key enzyme in shikonin biosynthesis. J. Biol. Chem. 277 (2002) 6240-6246. [PMID: 11744717]
[EC 2.7.7.21 Transferred entry: tRNA cytidylyltransferase. Now EC 2.7.7.72, CCA tRNA nucleotidyltransferase (EC 2.7.7.21 created 1965, deleted 2010)]
[EC 2.7.7.25 Transferred entry: tRNA adenylyltransferase. Now EC 2.7.7.72, CCA tRNA nucleotidyltransferase (EC 2.7.7.25 created 1965, deleted 2010)]
Accepted name: CCA tRNA nucleotidyltransferase
Reaction: (1) a tRNA precursor + 2 CTP + ATP = a tRNA with a 3' CCA end + 3 diphosphate (overall reaction)
(1a) a tRNA precursor + CTP = a tRNA with a 3' cytidine end + diphosphate
(1b) a tRNA with a 3' cytidine + CTP = a tRNA with a 3' CC end + diphosphate
(1c) a tRNA with a 3' CC end + ATP = a tRNA with a 3' CCA end + diphosphate
Other name(s): CCA-adding enzyme, tRNA adenylyltransferase, tRNA cytidylyltransferase, tRNA CCA-pyrophosphorylase; tRNA-nucleotidyltransferase; transfer-RNA nucleotidyltransferase; transfer ribonucleic acid nucleotidyl transferase; CTP(ATP):tRNA nucleotidyltransferase; transfer ribonucleate adenylyltransferase; transfer ribonucleate adenyltransferase; transfer RNA adenylyltransferase; transfer ribonucleate nucleotidyltransferase; ATP (CTP):tRNA nucleotidyltransferase; ribonucleic cytidylic cytidylic adenylic pyrophosphorylase; transfer ribonucleic adenylyl (cytidylyl) transferase; transfer ribonucleic-terminal trinucleotide nucleotidyltransferase; transfer ribonucleate cytidylyltransferase; ribonucleic cytidylyltransferase; -C-C-A pyrophosphorylase; tRNA cytidylyltransferase; ATP(CTP)-tRNA nucleotidyltransferase; tRNA adenylyl(cytidylyl)transferase; CTP:tRNA cytidylyltransferase
Systematic name: CTP,CTP,ATP:tRNA cytidylyl,cytidylyl,adenylyltransferase
Comments: The acylation of all tRNAs with an amino acid occurs at the terminal ribose of a 3' CCA sequence. The CCA sequence is added to the tRNA precursor by stepwise nucleotide addition performed by a single enzyme that is ubiquitous in all living organisms. Although the enzyme has the option of releasing the product after each addition, it prefers to stay bound to the product and proceed with the next addition [5].
References:
1. Schofield, P. and Williams, K.R. Purification and some properties of Escherichia coli tRNA nucleotidyltransferase. J. Biol. Chem. 252 (1977) 5584-5588. [PMID: 328503]
2. Shi, P.Y., Maizels, N. and Weiner, A.M. CCA addition by tRNA nucleotidyltransferase: polymerization without translocation. EMBO J. 17 (1998) 3197-3206. [PMID: 9606201]
3. Augustin, M.A., Reichert, A.S., Betat, H., Huber, R., Morl, M. and Steegborn, C. Crystal structure of the human CCA-adding enzyme: insights into template-independent polymerization. J. Mol. Biol. 328 (2003) 985-994. [PMID: 12729736]
4. Yakunin, A.F., Proudfoot, M., Kuznetsova, E., Savchenko, A., Brown, G., Arrowsmith, C.H. and Edwards, A.M. The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2',3'-cyclic phosphodiesterase, 2'-nucleotidase, and phosphatase activities. J. Biol. Chem. 279 (2004) 36819-36827. [PMID: 15210699]
5. Hou, Y.M. CCA addition to tRNA: implications for tRNA quality control. IUBMB Life 62 (2010) 251-260. [PMID: 20101632]
Accepted name: N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase
Reaction: (1) 3-phospho-5-adenylyl sulfate + [dermatan]-4-O-sulfo-N-acetyl-D-galactosamine = adenosine 3',5'-bisphosphate + [dermatan]-4,6-di-O-sulfo-N-acetyl-D-galactosamine
(2) 3-phospho-5-adenylyl sulfate + [chondroitin]-4-O-sulfo-N-acetyl-D-galactosamine = adenosine 3',5'-bisphosphate + [chondroitin]-4,6-di-O-sulfo-N-acetyl-D-galactosamine
Other name(s): GalNAc4S-6ST; CHST15 (gene name)
Systematic name: 3'-phosphoadenylyl-sulfate:[dermatan]-4-O-sulfo-N-acetyl-D-galactosamine
Comments: The enzyme is activated by divalent cations and reduced glutathione. The enzyme from human transfers sulfate to position 6 of both internal residues and nonreducing terminal GalNAc 4-sulfate residues of chondroitin sulfate and dermatan sulfate. Oligosaccharides derived from chondroitin sulfate also serve as acceptors but chondroitin sulfate E, keratan sulfate and heparan sulfate do not. Differs from EC 2.8.2.17, chondroitin 6-sulfotransferase, in being able to use both chondroitin and dermatan as effective substrates
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 242469-38-1
References:
1. Ito, Y. and Habuchi, O. Purification and characterization of N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase from the squid cartilage. J. Biol. Chem. 275 (2000) 34728-34736. [PMID: 10871629]
2. Ohtake, S., Ito, Y., Fukuta, M. and Habuchi, O. Human N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase cDNA is related to human B cell recombination activating gene-associated gene. J. Biol. Chem. 276 (2001) 43894-43900. [PMID: 11572857]
Accepted name: dermatan 4-sulfotransferase
Reaction: 3'-phospho-5'-adenylyl sulfate + [dermatan]-N-acetyl-D-galactosamine = adenosine 3',5'-bisphosphate + [dermatan]-4-O-sulfo-N-acetyl-D-galactosamine
Other name(s): dermatan-specific N-acetylgalactosamine 4-O-sulfotransferase; dermatan-4-sulfotransferase-1; dermatan-4-sulfotransferase 1; D4ST-1; dermatan N-acetylgalactosamine 4-O-sulfotransferase; CHST14 protein; CHST14
Systematic name: 3'-phospho-5'-adenylyl sulfate:[dermatan]-N-acetyl-D-galactosamine 4-sulfotransferase
Comments: The sulfation takes place at the 4-position of N-acetylgalactosamine residues of dermatan. D4ST-1 shows a strong preference in vitro for sulfate transfer to IdoUAα(1,3)GalNAcβ(1,4) that is flanked by GlcUAβ(1,3)GalNAcβ(1,4) as compared with IdoUAα(1,3)GalNAcβ(1,4) flanked by IdoUAα(1,3)GalNAcβ(1,4) [1].
References:
1. Evers, M.R., Xia, G., Kang, H.G., Schachner, M. and Baenziger, J.U. Molecular cloning and characterization of a dermatan-specific N-acetylgalactosamine 4-O-sulfotransferase. J. Biol. Chem. 276 (2001) 36344-36353. [PMID: 11470797]
2. Mikami, T., Mizumoto, S., Kago, N., Kitagawa, H. and Sugahara, K. Specificities of three distinct human chondroitin/dermatan N-acetylgalactosamine 4-O-sulfotransferases demonstrated using partially desulfated dermatan sulfate as an acceptor: implication of differential roles in dermatan sulfate biosynthesis. J. Biol. Chem. 278 (2003) 36115-36127. [PMID: 12847091]
3. Pacheco, B., Maccarana, M. and Malmstrom, A. Dermatan 4-O-sulfotransferase 1 is pivotal in the formation of iduronic acid blocks in dermatan sulfate. Glycobiology 19 (2009) 1197-1203. [PMID: 19661164]
4. Mitsunaga, C., Mikami, T., Mizumoto, S., Fukuda, J. and Sugahara, K. Chondroitin sulfate/dermatan sulfate hybrid chains in the development of cerebellum. Spatiotemporal regulation of the expression of critical disulfated disaccharides by specific sulfotransferases. J. Biol. Chem. 281 (2006) 18942-18952. [PMID: 16702220]
Accepted name: 1,4-dihydroxy-2-naphthoyl-CoA hydrolase
Reaction: 1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA
Systematic name: 1,4-dihydroxy-2-naphthoyl-CoA hydrolase
Comments: This enzyme participates in the synthesis of menaquinones, phyloquinone [1], as well as several plant pigments [2,3]. The enzyme from the cyanobacterium Synechocystis sp. PCC 6803 does not accept benzoyl-CoA or phenylacetyl-CoA as substrates [1].
References:
1. Widhalm, J.R., van Oostende, C., Furt, F. and Basset, G.J. A dedicated thioesterase of the Hotdog-fold family is required for the biosynthesis of the naphthoquinone ring of vitamin K1. Proc. Natl. Acad. Sci. USA 106 (2009) 5599-5603. [PMID: 19321747]
2. Muller, W and Leistner, E 1,4-naphthoquinone, an intermediate in juglone (5-hydroxy-1,4-naphthoquinone) biosynthesis. Phytochemistry 15 (1976) 407-410.
3. Eichinger D, Bacher A., Zenk M.H. and Eisenreich W. Quantitative Assessment of Metabolic Flux by 13C NMR Analysis. Biosynthesis of Anthraquinones in Rubia tinctorum. J. Am. Chem. Soc. 121 (1999) 7469-7475.
Accepted name: heparanase
Reaction: endohydrolysis of (1→4)-β-D-glycosidic bonds of heparan sulfate chains in heparan sulfate proteoglycan
Other name(s): Hpa1 heparanase; Hpa1; heparanase 1; heparanase-1; C1A heparanase; HPSE
Systematic name: heparan sulfate N-sulfo-D-glucosamine endoglucanase
Comments: Heparanase cleaves the linkage between a glucuronic acid unit and an N-sulfo glucosamine unit carrying either a 3-O-sulfo or a 6-O-sulfo group [2]. Heparanase-1 cuts macromolecular heparin into fragments of 5000-20000 Da [5]. The enzyme cleaves the heparan sulfate glycosaminoglycans from proteoglycan core proteins and degrades them to small oligosaccharides. Inside cells, the enzyme is important for the normal catabolism of heparan sulfate proteoglycans, generating glycosaminoglycan fragments that are then transported to lysosomes and completely degraded. When secreted, heparanase degrades basement membrane heparan sulfate glycosaminoglycans at sites of injury or inflammation, allowing extravasion of immune cells into nonvascular spaces and releasing factors that regulate cell proliferation and angiogenesis [1].
References:
1. Bame, K.J. Heparanases: endoglycosidases that degrade heparan sulfate proteoglycans. Glycobiology 11 (2001) 91R-98R. [PMID: 11445547]
2. Peterson, S.B. and Liu, J. Unraveling the specificity of heparanase utilizing synthetic substrates. J. Biol. Chem. 285 (2010) 14504-14513. [PMID: 20181948]
3. Pikas, D.S., Li, J.P., Vlodavsky, I. and Lindahl, U. Substrate specificity of heparanases from human hepatoma and platelets. J. Biol. Chem. 273 (1998) 18770-18777. [PMID: 9668050]
4. Okada, Y., Yamada, S., Toyoshima, M., Dong, J., Nakajima, M. and Sugahara, K. Structural recognition by recombinant human heparanase that plays critical roles in tumor metastasis. Hierarchical sulfate groups with different effects and the essential target disulfated trisaccharide sequence. J. Biol. Chem. 277 (2002) 42488-42495. [PMID: 12213822]
5. Vreys, V. and David, G. Mammalian heparanase: what is the message. J Cell Mol Med 11 (2007) 427-452. [PMID: 17635638]
6. Gong, F., Jemth, P., Escobar Galvis, M.L., Vlodavsky, I., Horner, A., Lindahl, U. and Li, J.P. Processing of macromolecular heparin by heparanase. J. Biol. Chem. 278 (2003) 35152-35158. [PMID: 12837765]
7. Toyoshima, M. and Nakajima, M. Human heparanase. Purification, characterization, cloning, and expression. J. Biol. Chem. 274 (1999) 24153-24160. [PMID: 10446189]
8. Miao, H.Q., Navarro, E., Patel, S., Sargent, D., Koo, H., Wan, H., Plata, A., Zhou, Q., Ludwig, D., Bohlen, P. and Kussie, P. Cloning, expression, and purification of mouse heparanase. Protein Expr. Purif. 26 (2002) 425-431. [PMID: 12460766]
9. Hammond, E., Li, C.P. and Ferro, V. Development of a colorimetric assay for heparanase activity suitable for kinetic analysis and inhibitor screening. Anal. Biochem. 396 (2010) 112-116. [PMID: 19748475]
Accepted name: HslU—HslV peptidase
Reaction: ATP-dependent cleavage of peptide bonds with broad specificity.
Other name(s): HslUV; HslV-HslU; HslV peptidase; ATP-dependent HslV-HslU proteinase; caseinolytic protease X; caseinolytic proteinase X; ClpXP ATP-dependent protease; ClpXP protease; ClpXP serine proteinase; Escherichia coli ClpXP serine proteinase; HslUV protease; HslUV proteinase; HslVU protease; HslVU proteinase; protease HslVU; proteinase HslUV
Comments: The HslU subunit of the HslU—HslV complex functions as an ATP dependent “unfoldase”. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolysed by HslV [5]. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis [7]. In peptidase family T1.
Links to other databases: BRENDA, EXPASY, KEGG, MEROPS CAS registry number:
References:
1. Wang, J., Rho, S.H., Park, H.H. and Eom, S.H. Correction of X-ray intensities from an HslV-HslU co-crystal containing lattice-translocation defects. Acta Crystallogr. D Biol. Crystallogr. 61 (2005) 932-941. [PMID: 15983416]
2. Nishii, W. and Takahashi, K. Determination of the cleavage sites in SulA, a cell division inhibitor, by the ATP-dependent HslVU protease from Escherichia coli. FEBS Lett. 553 (2003) 351-354. [PMID: 14572649]
3. Ramachandran, R., Hartmann, C., Song, H.K., Huber, R. and Bochtler, M. Functional interactions of HslV (ClpQ) with the ATPase HslU (ClpY). Proc. Natl. Acad. Sci. USA 99 (2002) 7396-7401. [PMID: 12032294]
4. Yoo, S.J., Seol, J.H., Shin, D.H., Rohrwild, M., Kang, M.S., Tanaka, K., Goldberg, A.L. and Chung, C.H. Purification and characterization of the heat shock proteins HslV and HslU that form a new ATP-dependent protease in Escherichia coli. J. Biol. Chem. 271 (1996) 14035-14040. [PMID: 8662828]
5. Yoo, S.J., Seol, J.H., Seong, I.S., Kang, M.S. and Chung, C.H. ATP binding, but not its hydrolysis, is required for assembly and proteolytic activity of the HslVU protease in Escherichia coli. Biochem. Biophys. Res. Commun. 238 (1997) 581-585. [PMID: 9299555]
6. Kanemori, M., Nishihara, K., Yanagi, H. and Yura, T. Synergistic roles of HslVU and other ATP-dependent proteases in controlling in vivo turnover of σ32 and abnormal proteins in Escherichia coli. J. Bacteriol. 179 (1997) 7219-7225. [PMID: 9393683]
7. Burton, R.E., Baker, T.A. and Sauer, R.T. Nucleotide-dependent substrate recognition by the AAA+ HslUV protease. Nat Struct Mol Biol 12 (2005) 245-251. [PMID: 15696175]
Accepted name: guanosine-5'-triphosphate,3'-diphosphate phosphatase
Reaction: guanosine 5'-triphosphate 3'-diphosphate + H2O = guanosine 3',5'-bis(diphosphate) + phosphate
Other name(s): pppGpp 5'-phosphohydrolase; guanosine 5'-triphosphate-3'-diphosphate 5'-phosphohydrolase; guanosine pentaphosphatase; guanosine pentaphosphate phosphatase; guanosine 5'-triphosphate 3'-diphosphate 5'-phosphatase; guanosine pentaphosphate phosphohydrolase
Systematic name: guanosine-5'-triphosphate-3'-diphosphate 5'-phosphohydrolase
Comments: Also hydrolyses other guanosine 5'-triphosphate derivatives with at least one unsubstituted phosphate group on the 3'-position, but not GTP, ATP or adenosine 5'-triphosphate 3'-diphosphate.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 85130-44-5
References:
1. Hara, A. and Sy, J. Guanosine 5'-triphosphate, 3'-diphosphate 5'-phosphohydrolase. Purification and substrate specificity. J. Biol. Chem. 258 (1983) 1678-1683. [PMID: 6130093]
Accepted name: cobalt-precorrin 5A hydrolase
Reaction: cobalt-precorrin-5A + H2O = cobalt-precorrin-5B + acetaldehyde + 2 H+
Other name(s): CbiG (gene name)
Systematic name: obalt-precorrin 5A acylhydrolase
Comments: This enzyme hydrolyses the ring A acetate δ-lactone of cobalt-precorrin-5A resulting in the loss of the C-20 carbon and its attached methyl group in the form of acetaldehyde. This is a key reaction in the contraction of the porphyrin-type tetrapyrrole ring and its conversion to a corrin ring in the anaerobic (early cobalt insertion) adenosylcobalamin biosynthesis pathway.
References:
1. Kajiwara, Y., Santander, P.J., Roessner, C.A., Perez, L.M. and Scott, A.I. Genetically engineered synthesis and structural characterization of cobalt-precorrin 5A and -5B, two new intermediates on the anaerobic pathway to vitamin B12: definition of the roles of the CbiF and CbiG enzymes. J. Am. Chem. Soc. 128 (2006) 9971-9978. [PMID: 16866557]
Accepted name: 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase
Reaction: (2E,4E)-6-(2-aminophenyl)-2-hydroxy-6-oxohexa-2,4-dienoate + H2O = anthranilate + (2E)-2-hydroxypenta-2,4-dienoate
Other name(s): CarC
Systematic name: (2E,4E)-6-(2-aminophenyl)-2-hydroxy-6-oxohexa-2,4-dienoate acylhydrolase
Comments: This enzyme catalyses the third step in the aerobic degradation pathway of carbazole. The effect of the presence of an amino group or hydroxyl group at the 2'-position of the substrate is small. The enzyme has no cofactor requirement [2].
References:
1. Nojiri, H., Taira, H., Iwata, K., Morii, K., Nam, J.W., Yoshida, T., Habe, H., Nakamura, S., Shimizu, K., Yamane, H. and Omori, T. Purification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans strain CA10. Biosci. Biotechnol. Biochem. 67 (2003) 36-45. [PMID: 12619671]
2. Riddle, R.R., Gibbs, P.R., Willson, R.C. and Benedik, M.J. Purification and properties of 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid hydrolase involved in microbial degradation of carbazole. Protein Expr. Purif. 28 (2003) 182-189. [PMID: 12651123]
Accepted name: UDP-sulfoquinovose synthase
Reaction: UDP-α-D-glucose + sulfite = UDP-α-D-sulfoquinovopyranose + H2O
For diagram of the reaction, click here
Other name(s): sulfite:UDP-glucose sulfotransferase; UDPsulfoquinovose synthase
Systematic name: UDP-6-sulfo-6-deoxyglucose sulfohydrolase
Comments: Requires NAD+, which appears to oxidize the substrate to UDP-4-dehydroglucose, which dehydrates to UDP-4-dehydro-6-deoxygluc-5-enose, to which sulfite can add; the reaction is completed when the substrate is rehydrogenated at C-4. The enzyme from Arabidopsis thaliana is specific for UDP-Glc and sulfite.
Links to other databases: BRENDA, EXPASY, KEGG, PDB CAS registry number:
References:
1. Essigmann, B., Gler, S., Narang, R.A., Linke, D. and Benning, C. Phosphate availability affects the thylakoid lipid composition and the expression of SQD1, a gene required for sulfolipid biosynthesis in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 95 (1998) 1950-1955. [PMID: 9465123]
2. Essigmann, B., Hespenheide, B.M., Kuhn, L.A. and Benning, C. Prediction of the active-site structure and NAD+ binding in SQD1, a protein essential for sulfolipid biosynthesis in Arabidopsis. Arch. Biochem. Biophys. 369 (1999) 30-41. [PMID: 10462438]
3. Mulichak, A.M., Theisen, M.J., Essigmann, B., Benning, C. and Garavito, R.M. Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose. Proc. Natl. Acad. Sci. USA 96 (1999) 13097-13102. [PMID: 10557279]
4. Sanda, S., Leustek, T., Theisen, M., Garavito, R.M. and Benning, C. Recombinant Arabidopsis SQD1 converts UDP-glucose and sulfite to the sulfolipid head group precursor UDP-sulfoquinovose in vitro. J. Biol. Chem. 276 (2001) 3941-3946. [PMID: 11073956]
Accepted name: 1,4-dihydroxy-2-naphthoyl-CoA synthase
Reaction: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
For diagram of reaction, click here.
Other name(s): naphthoate synthase; 1,4-dihydroxy-2-naphthoate synthase; dihydroxynaphthoate synthase; o-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase (cyclizing); MenB; o-succinylbenzoyl-CoA dehydratase (cyclizing)
Systematic name: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA dehydratase (cyclizing)
Comments: This enzyme is involved in the synthesis of 1,4-dihydroxy-2-naphthoate, a branch point metabolite leading to the biosynthesis of menaquinone (vitamin K2, in bacteria), phylloquinone (vitamin K1 in plants), and many plant pigments. The coenzyme A group is subsequently removed from the product by EC 3.1.2.28, 1,4-dihydroxy-2-naphthoyl-CoA hydrolase.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 61328-42-5
References:
1. Meganathan, R. and Bentley, R. Menaquinone (vitamin K2) biosynthesis: conversion of o-succinylbenzoic acid to 1,4-dihydroxy-2-naphthoic acid by Mycobacterium phlei enzymes. J. Bacteriol. 140 (1979) 92-98. [PMID: 500558]
2. Kolkmann, R. and Leistner, E. 4-(2'-Carboxyphenyl)-4-oxobutyryl coenzyme A ester, an intermediate in vitamin K2 (menaquinone) biosynthesis. Z. Naturforsch. C: Sci. 42 (1987) 1207-1214. [PMID: 2966501]
3. Johnson, T.W., Shen, G., Zybailov, B., Kolling, D., Reategui, R., Beauparlant, S., Vassiliev, I.R., Bryant, D.A., Jones, A.D., Golbeck, J.H. and Chitnis, P.R. Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. pcc 6803. J. Biol. Chem. 275 (2000) 8523-8530. [PMID: 10722690]
4. Truglio, J.J., Theis, K., Feng, Y., Gajda, R., Machutta, C., Tonge, P.J. and Kisker, C. Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis. J. Biol. Chem. 278 (2003) 42352-42360. [PMID: 12909628]
Accepted name: spore photoproduct lyase
Reaction: (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'→5')-thymidylate (in double-helical DNA)
For diagram click here
Other name(s): SAM; SP lyase; SPL; SplB; SplG
Systematic name: spore photoproduct pyrimidine-lyase
Comments: This enzyme is a member of the 'AdoMet radical' (radical SAM) family. The enzyme binds a [4Fe-4S] cluster. The cluster is coordinated by 3 cysteines and an exchangeable SAM molecule [3]. The 5'-deoxy-adenosine radical formed after electron transfer from the [4Fe-4S] cluster to the S-adenosyl-L-methionine, initiates the repair by abstracting the C-6 hydrogen of the spore photoproduct lesion. During the second part of the repair process the SAM molecule is regenerated [3].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 37290-70-3
References:
1. Chandor, A., Berteau, O., Douki, T., Gasparutto, D., Sanakis, Y., Ollagnier-de-Choudens, S., Atta, M. and Fontecave, M. Dinucleotide spore photoproduct, a minimal substrate of the DNA repair spore photoproduct lyase enzyme from Bacillus subtilis. J. Biol. Chem. 281 (2006) 26922-26931. [PMID: 16829676]
2. Pieck, J.C., Hennecke, U., Pierik, A.J., Friedel, M.G. and Carell, T. Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrates. J. Biol. Chem. 281 (2006) 36317-36326. [PMID: 16968710]
3. Buis, J.M., Cheek, J., Kalliri, E. and Broderick, J.B. Characterization of an active spore photoproduct lyase, a DNA repair enzyme in the radical S-adenosylmethionine superfamily. J. Biol. Chem. 281 (2006) 25994-26003. [PMID: 16829680]
4. Mantel, C., Chandor, A., Gasparutto, D., Douki, T., Atta, M., Fontecave, M., Bayle, P.-A., Mouesca, J.-M. and Bardet, M. Combined NMR and DFT studies for the absolute configuration elucidation of the spore photoproduct, a UV-induced DNA lesion. J. Am. Chem. Soc. 130 (2008) 16978-16984. [PMID: 19012397]
5. Silver, S.C., Chandra, T., Zilinskas, E., Ghose, S., Broderick, W.E. and Broderick, J.B. Complete stereospecific repair of a synthetic dinucleotide spore photoproduct by spore photoproduct lyase. J. Biol. Inorg. Chem. 15 (2010) 943-955. [PMID: 20405152]
Accepted name: chondroitin-sulfate-ABC exolyase
Reaction: Exolytic removal of Δ4-unsaturated disaccharide residues from the non-reducing ends of both polymeric chondroitin/dermatan sulfates and their oligosaccharide fragments.
For diagram of reaction click here
Glossary: chondroitin sulfate A = chondroitin 4-sulfate
chondroitin sulfate B = dermatan sulfate
chondroitin sulfate C = chondroitin 6-sulfate
For the nomenclature of glycoproteins, glycopeptides and peptidoglycans, click here
Other name(s): chondroitinase (ambiguous); chondroitin ABC eliminase (ambiguous); chondroitinase ABC (ambiguous); chondroitin ABC lyase (ambiguous); chondroitin sulfate ABC lyase (ambiguous); ChS ABC lyase (ambiguous); chondroitin sulfate ABC exoeliminase; chondroitin sulfate ABC exolyase; ChS ABC lyase II
Systematic name: chondroitin-sulfate-ABC exolyase
Comments: This enzyme degrades a variety of glycosaminoglycans of the chondroitin-sulfate- and dermatan-sulfate type. Chondroitin sulfate, chondroitin-sulfate proteoglycan and dermatan sulfate are the best substrates but the enzyme can also act on hyaluronan at a much lower rate. Keratan sulfate, heparan sulfate and heparin are not substrates. The related enzyme EC 4.2.2.20, chondroitin-sulfate-ABC endolyase, has the same substrate specificity but produces a mixture of oligosaccharides of different sizes that are ultimately degraded to tetra- and disaccharides [4]. Both enzymes act by the removal of a relatively acidic C-5 proton of the uronic acid followed by the elimination of a 4-linked hexosamine, resulting in the formation of an unsaturated C4—C5 bond on the hexuronic acid moiety of the products [4,6].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 1000607-06-6
References:
1. Yamagata, T., Saito, H., Habuchi, O. and Suzuki, S. Purification and properties of bacterial chondroitinases and chondrosulfatases. J. Biol. Chem. 243 (1968) 1523-1535. [PMID: 5647268]
2. Saito, H., Yamagata, T. and Suzuki, S. Enzymatic methods for the determination of small quantities of isomeric chondroitin sulfates. J. Biol. Chem. 243 (1968) 1536-1542. [PMID: 4231029]
3. Suzuki, S., Saito, H., Yamagata, T., Anno, K., Seno, N., Kawai, Y. and Furuhashi, T. Formation of three types of disulfated disaccharides from chondroitin sulfates by chondroitinase digestion. J. Biol. Chem. 243 (1968) 1543-1550. [PMID: 5647269]
4. Hamai, A., Hashimoto, N., Mochizuki, H., Kato, F., Makiguchi, Y., Horie, K. and Suzuki, S. Two distinct chondroitin sulfate ABC lyases. An endoeliminase yielding tetrasaccharides and an exoeliminase preferentially acting on oligosaccharides. J. Biol. Chem. 272 (1997) 9123-9130. [PMID: 9083041]
5. Huckerby, T.N., Nieduszynski, I.A., Giannopoulos, M., Weeks, S.D., Sadler, I.H. and Lauder, R.M. Characterization of oligosaccharides from the chondroitin/dermatan sulfates. 1H-NMR and 13C-NMR studies of reduced trisaccharides and hexasaccharides. FEBS J. 272 (2005) 6276-6286. [PMID: 16336265]
6. Zhang, Z., Park, Y., Kemp, M.M., Zhao, W., Im, A.R., Shaya, D., Cygler, M., Kim, Y.S. and Linhardt, R.J. Liquid chromatography-mass spectrometry to study chondroitin lyase action pattern. Anal. Biochem. 385 (2009) 57-64. [PMID: 18992215]
Accepted name: (+)-α-santalene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = (+)-α-santalene
Other name(s): SBS
Systematic name: (2Z,6Z)-farnesyl diphosphate lyase (cyclizing; (+)-α-santalene-forming)
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2Z,6Z)-farnesyl diphosphate. Following dephosphorylation of (2Z,6Z)-farnesyl diphosphate, the (2Z,6Z)-farnesyl carbocation is converted to either the (6R)- or the (6S)-bisabolyl cations depending on the stereochemistry of the 6,1 closure. The (6R)-bisabolyl cation will then lead to the formation of (+)-α-santalene, while the (6S)-bisabolyl cation will give rise to (–)-endo-α-bergamotene (see EC 4.2.3.54) and (+)-endo-β-bergamotene (see EC 4.2.3.53). Small amounts of (–)-epi-β-santalene are also formed from the (6R)-bisabolyl cation and small amounts of (–)-exo-α-bergamotene are formed from the (6S)-bisabolyl cation [1].
References:
1. Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301-317. [PMID: 19155349]
Accepted name: β-phellandrene synthase (neryl-diphosphate-cyclizing)
Reaction: neryl diphosphate = β-phellandrene + diphosphate
Other name(s): phellandrene synthase 1; PHS1; monoterpene synthase PHS1
Systematic name: neryl-diphosphate diphosphate-lyase [cyclizing; β-phellandrene-forming]
Comments: The enzyme from Solanum lycopersicum has very poor affinity with geranyl diphosphate as substrate. Catalyses the formation of the acyclic myrcene and ocimene as major products in addition to β-phellandrene [1].
References:
1. Schilmiller, A.L., Schauvinhold, I., Larson, M., Xu, R., Charbonneau, A.L., Schmidt, A., Wilkerson, C., Last, R.L. and Pichersky, E. Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate. Proc. Natl. Acad. Sci. USA 106 (2009) 10865-10870. [PMID: 19487664]
Accepted name: (4S)-β-phellandrene synthase (geranyl-diphosphate-cyclizing)
Reaction: geranyl diphosphate = (4S)-β-phellandrene + diphosphate
Other name(s): phellandrene synthase; (#150;)-β-phellandrene synthase; (–)-(4S)-β-phellandrene synthase
Systematic name: geranyl-diphosphate diphosphate-lyase [cyclizing; (4S)-β-phellandrene-forming)
Comments: Requires Mn2+. Mg2+ is not effective [1]. Some (–)-α-phellandrene is also formed [3]. The reaction involves a 1,3-hydride shift [4].
References:
1. Savage, T.J., Hatch, M.W. and Croteau, R. Monoterpene synthases of Pinus contorta and related conifers. A new class of terpenoid cyclase. J. Biol. Chem. 269 (1994) 4012-4020. [PMID: 8307957]
2. Bohlmann, J., Phillips, M., Ramachandiran, V., Katoh, S. and Croteau, R. cDNA cloning, characterization, and functional expression of four new monoterpene synthase members of the Tpsd gene family from grand fir (Abies grandis). Arch. Biochem. Biophys. 368 (1999) 232-243. [PMID: 10441373]
3. Wagschal, K., Savage, T.J. and Croteau, R. Isotopically sensitive branching as a tool for evaluating multiple product formation by monoterpene cyclases. Tetrahedron 31 (1991) 5933-5944.
4. LaFever, R.E. and Croteau, R. Hydride shifts in the biosynthesis of the p-menthane monoterpenes α-terpinene, γ-terpinene, and β-phellandrene. Arch. Biochem. Biophys. 301 (1993) 361-366. [PMID: 8460944]
Accepted name: (+)-endo-β-bergamotene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = (+)-endo-β-bergamotene
Other name(s): SBS
Systematic name: (2Z,6Z)-farnesyl diphosphate lyase (cyclizing; (+)-endo-β-bergamotene-forming)
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2Z,6Z)-farnesyl diphosphate. Following dephosphorylation of (2Z,6Z)-farnesyl diphosphate, the (2Z,6Z)-farnesyl carbocation is converted to either the (6R)- or the (6S)-bisabolyl cations depending on the stereochemistry of the 6,1 closure. The (6R)-bisabolyl cation will then lead to the formation of (+)-α-santalene (see EC 4.2.3.50), while the (6S)-bisabolyl cation will give rise to (–)-endo-α-bergamotene (see EC 4.2.3.54), as well as (+)-endo-β-bergamotene. Small amounts of (–)-epi-β-santalene are also formed from the (6R)-bisabolyl cation and small amounts of (–)-exo-α-bergamotene are formed from the (6S)-bisabolyl cation [1].
References:
1. Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301-317. [PMID: 19155349]
Accepted name: (–)-endo-α-bergamotene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6Z)-farnesyl diphosphate = (–)-endo-α-bergamotene
Other name(s): SBS
Systematic name: (2Z,6Z)-farnesyl diphosphate lyase (cyclizing; (–)-endo-α-bergamotene-forming)
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2Z,6Z)-farnesyl diphosphate. Following dephosphorylation of (2Z,6Z)-farnesyl diphosphate, the (2Z,6Z)-farnesyl carbocation is converted to either the (6R)- or the (6S)-bisabolyl cations depending on the stereochemistry of the 6,1 closure. The (6R)-bisabolyl cation will then lead to the formation of (+)-α-santalene (see EC 4.2.3.50), while the (6S)-bisabolyl cation will give rise to (+)-endo-β-bergamotene (EC 4.2.3.53) as well as (–)-endo-α-bergamotene. Small amounts of (–)-epi-β-santalene are also formed from the (6R)-bisabolyl cation and small amounts of (–)-exo-α-bergamotene are formed from the (6S)-bisabolyl cation [1].
References:
1. Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301-317. [PMID: 19155349]
Accepted name: isochorismate lyase
Reaction: isochorismate = salicylate + pyruvate
Other name(s): salicylate biosynthesis protein pchB; pyochelin biosynthetic protein PchB; isochorismate pyruvate lyase
Systematic name: isochorismate pyruvate-lyase (salicylate-forming)
Comments: This enzyme is part of the pathway of salicylate formation from chorismate, and forms an integral part of pathways that produce salicylate-derived siderophores, such as pyochelin and yersiniabactin.
References:
1. Serino, L., Reimmann, C., Baur, H., Beyeler, M., Visca, P. and Haas, D. Structural genes for salicylate biosynthesis from chorismate in Pseudomonas aeruginosa. Mol. Gen. Genet. 249 (1995) 217-228. [PMID: 7500944]
2. Kerbarh, O., Ciulli, A., Howard, N.I. and Abell, C. Salicylate biosynthesis: overexpression, purification, and characterization of Irp9, a bifunctional salicylate synthase from Yersinia enterocolitica. J. Bacteriol. 187 (2005) 5061-5066. [PMID: 16030197]
EC 6.1.2 acid—alcohol ligases (ester synthases)
Accepted name: D-alanine—(R)-lactate ligase
Reaction: D-alanine + (R)-lactate + ATP = D-alanyl-(R)-lactate + ADP + phosphate
Glossary: (R)-lactate = D-lactate
D-alanyl-(R)-lactate = D-alanyl-D-lactate = (2R)-2-(D-alanyloxy)propanoic acid = (R)-2-[(R)-2-aminopropanoyloxy]propanoic acid
Other name(s): VanA; VanB; VanD
Systematic name: D-alanine:(R)-lactate ligase (ADP-forming)
Comments: The product of this enzyme, the depsipeptide D-alanyl-(R)-lactate, can be incorporated into the peptidoglycan pentapeptide instead of the usual D-alanyl-D-alanine dipeptide, which is formed by EC 6.3.2.4, D-alanine—D-alanine ligase. The resulting peptidoglycan does not bind the glycopeptide antibiotics vancomycin and teicoplanin, conferring resistance on the bacteria.
References:
1. Bugg, T.D., Wright, G.D., Dutka-Malen, S., Arthur, M., Courvalin, P. and Walsh, C.T. Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA. Biochemistry 30 (1991) 10408-10415. [PMID: 1931965]
2. Meziane-Cherif, D., Badet-Denisot, M.A., Evers, S., Courvalin, P. and Badet, B. Purification and characterization of the VanB ligase associated with type B vancomycin resistance in Enterococcus faecalis V583. FEBS Lett. 354 (1994) 140-142. [PMID: 7957913]
3. Perichon, B., Reynolds, P. and Courvalin, P. VanD-type glycopeptide-resistant Enterococcus faecium BM4339. Antimicrob. Agents Chemother. 41 (1997) 2016-2018. [PMID: 9303405]
Accepted name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—2,6-diaminopimelate ligase
Reaction: ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diaminoheptanedioate
For diagram of reaction, (click here.
Other name(s): MurE synthetase [ambiguous]; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-2,6-diamino-heptanedioate ligase (ADP-forming); UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase; UDP-N-acetylmuramoylalanyl-D-glutamate—2,6-diaminopimelate ligase
Systematic name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-2,6-diaminoheptanedioate γ-ligase (ADP-forming)
Comments: Involved with EC 6.3.2.4 (D-alanine—D-alanine ligase), EC 6.3.2.8 (UDP-N-acetylmuramate—L-alanine ligase), EC 6.3.2.9 (UDP-N-acetylmuramoyl-L-alanine—D-glutamate ligase) and EC 6.3.2.10 (UDP-N-acetylmuramoyl-tripeptide—D-alanyl-D-alanine ligase) in the synthesis of a cell-wall peptide (click here for diagram). This enzyme adds diaminopimelate in Gram-negative organisms and in some Gram-positive organisms; in others EC 6.3.2.7 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase) adds lysine instead. It is the amino group of the L-centre of the diaminopimelate that is acylated.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9075-09-6
References:
1. Mizuno, Y. and Ito, E. Purification and properties of uridine diphosphate N-acetylmuramyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate ligase. J. Biol. Chem. 243 (1968) 2665-2672. [PMID: 4967958]
2. van Heijenoort, J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18 (2001) 503-519. [PMID: 11699883]
Accepted name: cobyrinate a,c-diamide synthase
Reaction: 2 ATP + cobyrinate + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + cobyrinate a,c-diamide + 2 L-glutamate
(1a) ATP + cobyrinate + L-glutamine + H2O = ADP + phosphate + cobyrinate c-monamide + L-glutamate
(1b) ATP + cobyrinate c-monamide + L-glutamine + H2O = ADP + phosphate + cobyrinate a,c-diamide + L-glutamate
Other name(s): cobyrinic acid a,c-diamide synthetase; CbiA (gene name)
Comments: This enzyme is the first glutamine amidotransferase that participates in the anaerobic (early cobalt insertion) biosynthetic pathway of adenosylcobalamin, and catalyses the ATP-dependent synthesis of cobyrinate a,c-diamide from cobyrinate using either L-glutamine or ammonia as the nitrogen source. It is proposed that the enzyme first catalyses the amidation of the c-carboxylate, and then the intermediate is released into solution and binds to the same catalytic site for the amidation of the a-carboxylate. The Km for ammonia is substantially higher than that for L-glutamine.
References:
1. Fresquet, V., Williams, L. and Raushel, F.M. Mechanism of cobyrinic acid a,c-diamide synthetase from Salmonella typhimurium LT2. Biochemistry 43 (2004) 10619-10627. [PMID: 15311923]