An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: tRNA-dihydrouridine16/17 synthase [NAD(P)+]
Reaction: (1) 5,6-dihydrouracil16 in tRNA + NAD(P)+ = uracil16 in tRNA + NAD(P)H + H+
(2) 5,6-dihydrouracil17 in tRNA + NAD(P)+ = uracil17 in tRNA + NAD(P)H + H+
Other name(s): Dus1p; tRNA-dihydrouridine synthase 1
Systematic name: tRNA-5,6-dihydrouracil16/17:NAD(P)+ oxidoreductase
Comments: A flavoprotein. The enzyme specifically modifies uracil16 and uracil17 in tRNA.
References:
1. Xing, F., Hiley, S.L., Hughes, T.R. and Phizicky, E.M. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J. Biol. Chem. 279 (2004) 17850-17860. [PMID: 14970222]
2. Xing, F., Martzen, M.R. and Phizicky, E.M. A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. RNA 8 (2002) 370-381. [PMID: 12003496]
Accepted name: tRNA-dihydrouridine47 synthase [NAD(P)+]
Reaction: 5,6-dihydrouracil47 in tRNA + NAD(P)+ = uracil47 in tRNA + NAD(P)H + H+
Other name(s): Dus3p; tRNA-dihydrouridine synthase 3
Systematic name: tRNA-5,6-dihydrouracil47:NAD(P)+ oxidoreductase
Comments: A flavoenzyme. The enzyme specifically modifies uracil47 in tRNA.
References:
1. Xing, F., Hiley, S.L., Hughes, T.R. and Phizicky, E.M. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J. Biol. Chem. 279 (2004) 17850-17860. [PMID: 14970222]
Accepted name: tRNA-dihydrouridine20a/20b synthase [NAD(P)+]
Reaction: (1) 5,6-dihydrouracil20a in tRNA + NAD(P)+ = uracil20a in tRNA + NAD(P)H + H+
(2) 5,6-dihydrouracil20b in tRNA + NAD(P)+ = uracil20b in tRNA + NAD(P)H + H+
Other name(s): Dus4p
Systematic name: tRNA-5,6-dihydrouracil20a/20b:NAD(P)+ oxidoreductase
Comments: A flavoenzyme. The enzyme specifically modifies uracil20a and uracil20b in tRNA.
References:
1. Xing, F., Hiley, S.L., Hughes, T.R. and Phizicky, E.M. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J. Biol. Chem. 279 (2004) 17850-17860. [PMID: 14970222]
Accepted name: tRNA-dihydrouridine20 synthase [NAD(P)+]
Reaction: 5,6-dihydrouracil20 in tRNA + NAD(P)+ = uracil20 in tRNA + NAD(P)H + H+
Other name(s): Dus2p; tRNA-dihydrouridine synthase 2
Systematic name: tRNA-5,6-dihydrouracil20:NAD(P)+ oxidoreductase
Comments: A flavoenzyme [3]. The enzyme specifically modifies uracil20 in tRNA.
References:
1. Xing, F., Hiley, S.L., Hughes, T.R. and Phizicky, E.M. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J. Biol. Chem. 279 (2004) 17850-17860. [PMID: 14970222]
2. Xing, F., Martzen, M.R. and Phizicky, E.M. A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. RNA 8 (2002) 370-381. [PMID: 12003496]
3. Rider, L.W., Ottosen, M.B., Gattis, S.G. and Palfey, B.A. Mechanism of dihydrouridine synthase 2 from yeast and the importance of modifications for efficient tRNA reduction. J. Biol. Chem. 284 (2009) 10324-10333. [PMID: 19139092]
4. Kato, T., Daigo, Y., Hayama, S., Ishikawa, N., Yamabuki, T., Ito, T., Miyamoto, M., Kondo, S. and Nakamura, Y. A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis. Cancer Res. 65 (2005) 5638-5646. [PMID: 15994936]
Accepted name: 4,4'-diapophytoene desaturase
Reaction: 4,4'-diapophytoene + 4 FAD = 4,4'-diapolycopene + 4 FADH2 (overall reaction)
(1a) 4,4'-diapophytoene + FAD = 4,4'-diapophytofluene + FADH2
(1b) 4,4'-diapophytofluene + FAD = 4,4'-diapo-ζ-carotene + FADH2
(1c) 4,4'-diapo-ζ-carotene + FAD = 4,4'-diapolneurosporene + FADH2
(1d) 4,4'-diaponeurosporene + FAD = 4,4'-diapolycopene + FADH2
For diagram of reaction click here.
Other name(s): dehydrosqualene desaturase; CrtN
Systematic name: 4,4'-diapophytoene:FAD oxidoreductase
Comments: Typical of Staphylococcus aureus and some other bacteria such as Heliobacillus sp. Responsible for four successive dehydrogenations. In some species it only proceeds as far as 4,4'-diaponeurosporene.
References:
1. Wieland, B., Feil, C., Gloria-Maercker, E., Thumm, G., Lechner, M., Bravo, J.M., Poralla, K. and Gotz, F. Genetic and biochemical analyses of the biosynthesis of the yellow carotenoid 4,4'-diaponeurosporene of Staphylococcus aureus. J. Bacteriol. 176 (1994) 7719-7726. [PMID: 8002598]
2. Raisig, A. and Sandmann, G. 4,4'-diapophytoene desaturase: catalytic properties of an enzyme from the C30 carotenoid pathway of Staphylococcus aureus. J. Bacteriol. 181 (1999) 6184-6187. [PMID: 10498735]
3. Raisig, A. and Sandmann, G. Functional properties of diapophytoene and related desaturases of C30 to C40 carotenoid biosynthetic pathways. Biochim. Biophys. Acta 1533 (2001) 164-170. [PMID: 11566453]
[EC 1.5.1.29 Deleted entry: FMN reductase [NAD(P)H]. Now covered by EC 1.5.1.38 [FMN reductase (NADPH)], EC 1.5.1.39 [FMN reductase [NAD(P)H])] and EC 1.5.1.41 (riboflavin reductase [NAD(P)H]) (EC 1.5.1.29 created 1981 as EC 1.6.8.1, transferred 2002 to EC 1.5.1.29, modified 2002, deleted 2011)]
Accepted name: FAD reductase (NADH)
Reaction: FADH2 + NAD+ = FAD + NADH + H+
For diagram of reaction click here.
Other name(s): NADH-FAD reductase; NADH-dependent FAD reductase; NADH:FAD oxidoreductase; NADH:flavin adenine dinucleotide oxidoreductase
Systematic name: FADH2:NAD+ oxidoreductase
Comments: The enzyme from Burkholderia phenoliruptrix can reduce either FAD or flavin mononucleotide (FMN) but prefers FAD. Unlike EC 1.5.1.36, flavin reductase (NADH), the enzyme can not reduce riboflavin. The enzyme does not use NADPH as acceptor.
References:
1. Gisi, M.R. and Xun, L. Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:flavin adenine dinucleotide oxidoreductase (TftC) of Burkholderia cepacia AC1100. J. Bacteriol. 185 (2003) 2786-2792. [PMID: 12700257]
Accepted name: FMN reductase (NADPH)
Reaction: FMNH2 + NADP+ = FMN + NADPH + H+
For diagram of reaction click here.
Other name(s): FRP; flavin reductase P; SsuE
Systematic name: FMNH2:NADP+ oxidoreductase
Comments: The enzymes from bioluminescent bacteria contain FMN [4], while the enzyme from Escherichia coli does not [8]. The enzyme often forms a two-component system with monooxygenases such as luciferase. Unlike EC 1.5.1.39, this enzyme does not use NADH as acceptor [1,2]. While FMN is the preferred substrate, the enzyme can also use FAD and riboflavin with lower activity [3,6,8].
References:
1. Gerlo, E. and Charlier, J. Identification of NADH-specific and NADPH-specific FMN reductases in Beneckea harveyi. Eur. J. Biochem. 57 (1975) 461-467. [PMID: 1175652]
2. Jablonski, E. and DeLuca, M. Purification and properties of the NADH and NADPH specific FMN oxidoreductases from Beneckea harveyi. Biochemistry 16 (1977) 2932-2936. [PMID: 880288]
3. Jablonski, E. and DeLuca, M. Studies of the control of luminescence in Beneckea harveyi: properties of the NADH and NADPH:FMN oxidoreductases. Biochemistry 17 (1978) 672-678. [PMID: 23827]
4. Lei, B., Liu, M., Huang, S. and Tu, S.C. Vibrio harveyi NADPH-flavin oxidoreductase: cloning, sequencing and overexpression of the gene and purification and characterization of the cloned enzyme. J. Bacteriol. 176 (1994) 3552-3558. [PMID: 8206832]
5. Tanner, J.J., Lei, B., Tu, S.C. and Krause, K.L. Flavin reductase P: structure of a dimeric enzyme that reduces flavin. Biochemistry 35 (1996) 13531-13539. [PMID: 8885832]
6. Liu, M., Lei, B., Ding, Q., Lee, J.C. and Tu, S.C. Vibrio harveyi NADPH:FMN oxidoreductase: preparation and characterization of the apoenzyme and monomer-dimer equilibrium. Arch. Biochem. Biophys. 337 (1997) 89-95. [PMID: 8990272]
7. Lei, B. and Tu, S.C. Mechanism of reduced flavin transfer from Vibrio harveyi NADPH-FMN oxidoreductase to luciferase. Biochemistry 37 (1998) 14623-14629. [PMID: 9772191]
8. Eichhorn, E., van der Ploeg, J.R. and Leisinger, T. Characterization of a two-component alkanesulfonate monooxygenase from Escherichia coli. J. Biol. Chem. 274 (1999) 26639-26646. [PMID: 10480865]
Accepted name: FMN reductase [NAD(P)H]
Reaction: FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+
For diagram of reaction click here.
Other name(s): FRG
Systematic name: FMNH2:NAD(P)+ oxidoreductase
Comments: Contains FMN [3]. The enzyme can utilize NADH and NADPH with similar reaction rates. Different from EC 1.5.1.42, FMN reductase (NADH) and EC 1.5.1.38, FMN reductase (NADPH). The luminescent bacterium Vibrio harveyi possesses all three enzymes [2], while the bacterium Aliivibrio fischeri contains only this non-specific type [3]. Also reduces riboflavin and FAD, but more slowly.
References:
1. Tu, S.-C., Becvar, J.E. and Hastings, J.W. Kinetic studies on the mechanism of bacterial NAD(P)H:flavin oxidoreductase. Arch. Biochem. Biophys. 193 (1979) 110-116. [PMID: 222213]
2. Watanabe, H. and Hastings, J.W. Specificities and properties of three reduced pyridine nucleotide-flavin mononucleotide reductases coupling to bacterial luciferase. Mol. Cell. Biochem. 44 (1982) 181-187. [PMID: 6981058]
3. Tang, C.K., Jeffers, C.E., Nichols, J.C. and Tu, S.C. Flavin specificity and subunit interaction of Vibrio fischeri general NAD(P)H-flavin oxidoreductase FRG/FRase I. Arch. Biochem. Biophys. 392 (2001) 110-116. [PMID: 11469801]
Accepted name: 8-hydroxy-5-deazaflavin:NADPH oxidoreductase
Reaction: reduced coenzyme F420 + NADP+ = coenzyme F420 + NADPH + H+
For diagram of reaction click here.
Other name(s): 8-OH-5dFl:NADPH oxidoreductase
Systematic name: reduced coenzyme F420:NADP+ oxidoreductase
Comments: The enzyme has an absolute requirement for both the 5-deazaflavin structure and the presence of an 8-hydroxy group in the substrate [1].
References:
1. Eker, A.P., Hessels, J.K. and Meerwaldt, R. Characterization of an 8-hydroxy-5-deazaflavin:NADPH oxidoreductase from Streptomyces griseus. Biochim. Biophys. Acta 990 (1989) 80-86. [PMID: 2492438]
Accepted name: riboflavin reductase [NAD(P)H]
Reaction: reduced riboflavin + NAD(P)+ = riboflavin + NAD(P)H + H+
For diagram of reaction click here.
Other name(s): NAD(P)H-FMN reductase (ambiguous); NAD(P)H-dependent FMN reductase (ambiguous); NAD(P)H:FMN oxidoreductase (ambiguous); NAD(P)H:flavin oxidoreductase (ambiguous); NAD(P)H2 dehydrogenase (FMN) (ambiguous); NAD(P)H2:FMN oxidoreductase (ambiguous); riboflavin mononucleotide reductase (ambiguous); flavine mononucleotide reductase (ambiguous); riboflavin mononucleotide (reduced nicotinamide adenine dinucleotide (phosphate)) reductase; flavin mononucleotide reductase (ambiguous); riboflavine mononucleotide reductase (ambiguous); Fre
Systematic name: riboflavin:NAD(P)+ oxidoreductase
Comments: Catalyses the reduction of soluble flavins by reduced pyridine nucleotides. Highest activity with riboflavin. When NADH is used as acceptor, the enzyme can also utilize FMN and FAD as substrates, with lower activity than riboflavin. When NADPH is used as acceptor, the enzyme has a very low activity with FMN and no activity with FAD [1].
References:
1. Fontecave, M., Eliasson, R. and Reichard, P. NAD(P)H:flavin oxidoreductase of Escherichia coli. A ferric iron reductase participating in the generation of the free radical of ribonucleotide reductase. J. Biol. Chem. 262 (1987) 12325-12331. [PMID: 3305505]
2. Spyrou, G., Haggård-Ljungquist, E., Krook, M., Jörnvall, H., Nilsson, E. and Reichard, P. Characterization of the flavin reductase gene (fre) of Escherichia coli and construction of a plasmid for overproduction of the enzyme. J. Bacteriol. 173 (1991) 3673-3679. [PMID: 2050627]
3. Ingelman, M., Ramaswamy, S., Nivière, V., Fontecave, M. and Eklund, H. Crystal structure of NAD(P)H:flavin oxidoreductase from Escherichia coli. Biochemistry 38 (1999) 7040-7049. [PMID: 10353815]
Accepted name: FMN reductase (NADH)
Reaction: FMNH2 + NAD+ = FMN + NADH + H+
For diagram of reaction click here.
Other name(s): NADH-FMN reductase; NADH-dependent FMN reductase; NADH:FMN oxidoreductase; NADH:flavin oxidoreductase
Systematic name: FMNH2:NAD+ oxidoreductase
Comments: The enzyme often forms a two-component system with monooxygenases. Unlike EC 1.5.1.38, FMN reductase (NADPH), and EC 1.5.1.39, FMN reductase [NAD(P)H], this enzyme has a strong preference for NADH over NADPH, although some activity with the latter is observed [1,2]. While FMN is the preferred substrate, FAD can also be used with much lower activity [1,3].
References:
1. Fontecave, M., Eliasson, R. and Reichard, P. NAD(P)H:flavin oxidoreductase of Escherichia coli. A ferric iron reductase participating in the generation of the free radical of ribonucleotide reductase. J. Biol. Chem. 262 (1987) 12325-12331. [PMID: 3305505]
2. Spyrou, G., Haggård-Ljungquist, E., Krook, M., Jörnvall, H., Nilsson, E. and Reichard, P. Characterization of the flavin reductase gene (fre) of Escherichia coli and construction of a plasmid for overproduction of the enzyme. J. Bacteriol. 173 (1991) 3673-3679. [PMID: 2050627]
3. Ingelman, M., Ramaswamy, S., Nivière, V., Fontecave, M. and Eklund, H. Crystal structure of NAD(P)H:flavin oxidoreductase from Escherichia coli. Biochemistry 38 (1999) 7040-7049. [PMID: 10353815]
EC 1.7.6 With a nitrogenous group as acceptor
Accepted name: nitrite dismutase
Reaction: 3 nitrite + 2 H+ = 2 nitric oxide + nitrate + H2O
Other name(s): Prolixin S; Nitrophorin 7
Systematic name: nitrite:nitrite oxidoreductase
Comments: Contains ferriheme b. The enzyme is one of the nitrophorins from the salivary gland of the blood-feeding insect Rhodnius prolixus. Nitric oxide produced induces vasodilation after injection. Nitrophorins 2 and 4 can also catalyse this reaction.
References:
1. He, C. and Knipp, M. Formation of nitric oxide from nitrite by the ferriheme b protein nitrophorin 7. J. Am. Chem. Soc. 131 (2009) 12042-12043. [PMID: 19655755]
2. He, C., Ogata, H. and Knipp, M. Formation of the complex of nitrite with the ferriheme b β-barrel proteins nitrophorin 4 and nitrophorin 7. Biochemistry 49 (2010) 5841-5851. [PMID: 20524697]
Accepted name: nitrilotriacetate monooxygenase
Reaction: nitrilotriacetate + FMNH2 + H+ + O2 = iminodiacetate + glyoxylate + FMN + H2O
Systematic name: nitrilotriacetate,FMNH2:oxygen oxidoreductase (glyoxylate-forming)
Comments: Requires Mg2+. The enzyme from Aminobacter aminovorans (previously Chelatobacter heintzii) is part of a two component system that also includes EC 1.5.1.42 (FMN reductase), which provides reduced flavin mononucleotide for this enzyme.
References:
1. Uetz, T., Schneider, R., Snozzi, M. and Egli, T. Purification and characterization of a two-component monooxygenase that hydroxylates nitrilotriacetate from "Chelatobacter" strain ATCC 29600. J. Bacteriol. 174 (1992) 1179-1188. [PMID: 1735711]
2. Knobel, H.R., Egli, T. and van der Meer, J.R. Cloning and characterization of the genes encoding nitrilotriacetate monooxygenase of Chelatobacter heintzii ATCC 29600. J. Bacteriol. 178 (1996) 6123-6132. [PMID: 8892809]
3. Xu, Y., Mortimer, M.W., Fisher, T.S., Kahn, M.L., Brockman, F.J. and Xun, L. Cloning, sequencing, and analysis of a gene cluster from Chelatobacter heintzii ATCC 29600 encoding nitrilotriacetate monooxygenase and NADH:flavin mononucleotide oxidoreductase. J. Bacteriol. 179 (1997) 1112-1116. [PMID: 9023192]
[EC 2.1.1.31 Transferred entry: tRNA (guanine-N1-)-methyltransferase. Now covered by EC 2.1.1.221 (tRNA (guanine9-N1)-methyltransferase) and EC 2.1.1.228 (tRNA (guanine37-N1)-methyltransferase). (EC 2.1.1.31 created 1972, deleted 2011)]
[EC 2.1.1.32 Transferred entry: tRNA (guanine-N2-)-methyltransferase. Now covered by by EC 2.1.1.213 [tRNA (guanine10-N2)-dimethyltransferase], EC 2.1.1.214 [tRNA (guanine10-N2)-monomethyltransferase], EC 2.1.1.215 [tRNA (guanine26-N2/guanine27-N2)-dimethyltransferase] and EC 2.1.1.216 [tRNA (guanine26-N2)-dimethyltransferase] (EC 2.1.1.32 created 1972, deleted 2011)]
Accepted name: tRNA (guanine46-N7)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine46 in tRNA = S-adenosyl-L-homocysteine + N7-methylguanine46 in tRNA
Other name(s): Trm8/Trm82; TrmB; tRNA (m7G46) methyltransferase; transfer ribonucleate guanine 7-methyltransferase; 7-methylguanine transfer ribonucleate methylase; tRNA guanine 7-methyltransferase; N7-methylguanine methylase; S-adenosyl-L-methionine:tRNA (guanine-7-N-)-methyltransferase
Systematic name: S-adenosyl-L-methionine:tRNA (guanine-N7)-methyltransferase
Comments: The enzyme specifically methylates guanine46 at N7 in tRNA.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 37257-00-4
References:
1. Aschhoff, H.J., Elten, H., Arnold, H.H., Mahal, G., Kersten, W. and Kersten, H. 7-Methylguanine specific tRNA-methyltransferase from Escherichia coli. Nucleic Acids Res. 3 (1976) 3109-3122. [PMID: 794833]
2. Zegers, I., Gigot, D., van Vliet, F., Tricot, C., Aymerich, S., Bujnicki, J.M., Kosinski, J. and Droogmans, L. Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase. Nucleic Acids Res. 34 (2006) 1925-1934. [PMID: 16600901]
3. Purta, E., van Vliet, F., Tricot, C., De Bie, L.G., Feder, M., Skowronek, K., Droogmans, L. and Bujnicki, J.M. Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis. Proteins 59 (2005) 482-488. [PMID: 15789416]
4. Liu, Q., Gao, Y., Yang, W., Zhou, H., Gao, Y., Zhang, X., Teng, M. and Niu, L. Crystallization and preliminary crystallographic analysis of tRNA (m7G46) methyltransferase from Escherichia coli. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 743-745. [PMID: 18678947]
5. Alexandrov, A., Martzen, M.R. and Phizicky, E.M. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 8 (2002) 1253-1266. [PMID: 12403464]
Accepted name: tRNA (uracil54-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + uridine54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
Other name(s): transfer RNA uracil54 5-methyltransferase; transfer RNA uracil54 methylase; tRNA uracil54 5-methyltransferase; m5U54-methyltransferase; tRNA:m5U54-methyltransferase; RUMT; TrmA; 5-methyluridine54 tRNA methyltransferase; tRNA(uracil-54,C5)-methyltransferase; Trm2; tRNA(m5U54)methyltransferase
Systematic name: S-adenosyl-L-methionine:tRNA (uracil54-C5)-methyltransferase
Comments: Unlike this enzyme, EC 2.1.1.74 (methylenetetrahydrofolateŃtRNA-(uracil54-C5)-methyltransferase (FADH2-oxidizing)), uses 5,10-methylenetetrahydrofolate and FADH2 to supply the atoms for methylation of U54 [4].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 37257-02-6
References:
1. Björk, G.R. and Svensson, I. Studies on microbial RNA. Fractionation of tRNA methylases from Saccharomyces cerevisiae. Eur. J. Biochem. 9 (1969) 207-215. [PMID: 4896260]
2. Greenberg, R. and Dudock, B. Isolation and characterization of m5U-methyltransferase from Escherichia coli. J. Biol. Chem. 255 (1980) 8296-8302. [PMID: 6997293]
3. Hurwitz, J., Gold, M. and Anders, M. The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. 3. Purification of soluble ribonucleic acid-methylating enzymes. J. Biol. Chem. 239 (1964) 3462-3473. [PMID: 14245404]
4. Delk, A.S., Nagle, D.P., Jr. and Rabinowitz, J.C. Methylenetetrahydrofolate-dependent biosynthesis of ribothymidine in transfer RNA of Streptococcus faecalis. Evidence for reduction of the 1-carbon unit by FADH2. J. Biol. Chem. 255 (1980) 4387-4390. [PMID: 6768721]
5. Kealey, J.T., Gu, X. and Santi, D.V. Enzymatic mechanism of tRNA (m5U54)methyltransferase. Biochimie 76 (1994) 1133-1142. [PMID: 7748948]
6. Gu, X., Ivanetich, K.M. and Santi, D.V. Recognition of the T-arm of tRNA by tRNA (m5U54)-methyltransferase is not sequence specific. Biochemistry 35 (1996) 11652-11659. [PMID: 8794745]
7. Becker, H.F., Motorin, Y., Sissler, M., Florentz, C. and Grosjean, H. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨ-loop of yeast tRNAs. J. Mol. Biol. 274 (1997) 505-518. [PMID: 9417931]
8. Walbott, H., Leulliot, N., Grosjean, H. and Golinelli-Pimpaneau, B. The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity. Nucleic Acids Res. 36 (2008) 4929-4940. [PMID: 18653523]
[EC 2.1.1.36 Transferred entry: tRNA (adenine-N1-)-methyltransferase. Now covered by EC 2.1.1.217 (tRNA (adenine22-N1)-methyltransferase), EC 2.1.1.218 (tRNA (adenine9-N1)-methyltransferase), EC 2.1.1.219 (tRNA (adenine57-N1/adenine58-N1)-methyltransferase), EC 2.1.1.220 (tRNA (adenine58-N1)-methyltransferase). (EC 2.1.1.36 created 1972, deleted 2011)]
Accepted name: 23S rRNA (adenine2503-C2)-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine2503 in 23S rRNA
Other name(s): RlmN; YfgB; Cfr
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine2503-C2)-methyltransferase
Comments: Contains an [4Fe-4S] cluster [2]. This enzyme is a member of the 'AdoMet radical' (radical SAM) family. S-adenosyl-L-methionine acts as both a radical generator and as the source of the appended methyl group. RlmN is an endogenous enzyme used by the cell to refine functions of the ribosome in protein synthesis [2]. The enzyme methylates adenosine by a radical mechanism with CH2 from the S-adenosyl-L-methionine and retention of the hydrogen at C-2 of adenosine2503 of 23S rRNA. It will also methylate 8-methyladenosine2503 of 23S rRNA. cf. EC 2.1.1.224 [23S rRNA (adenine2503-C8)-methyltransferase].
Links to other databases: BRENDA, EXPASY, KEGG
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., Rhrich, 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]
3. Yan, F. and Fujimori, D.G. RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Proc. Natl. Acad. Sci. USA 108 (2011) 3930-3934. [PMID: 21368151]
4. Grove, T.L., Benner, J.S., Radle, M.I., Ahlum, J.H., Landgraf, B.J., Krebs, C. and Booker, S.J. A radically different mechanism for S-adenosylmethionine-dependent methyltransferases. Science 332 (2011) 604-607. [PMID: 21415317]
5. Boal, A.K., Grove, T.L., McLaughlin, M.I., Yennawar, N.H., Booker, S.J. and Rosenzweig, A.C. Structural basis for methyl transfer by a radical SAM enzyme. Science 332 (2011) 544-545. [PMID: 21527678]
[EC 2.1.1.194 Deleted entry: 23S rRNA (adenine2503-C2,C8)-dimethyltransferase. A mixture of EC 2.1.1.192 (23S rRNA (adenine2503-C2)-methyltransferase) and EC 2.1.1.224 (23S rRNA (adenine2503-C8)-methyltransferase) (EC 2.1.1.194 created 2010, deleted 2011)]
Accepted name: tRNASer (uridine44-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + uridine44 in tRNASer = S-adenosyl-L-homocysteine + 2'-O-methyluridine44 in tRNASer
Other name(s): TRM44
Systematic name: S-adenosyl-L-methionine:tRNASer (uridine44-2'-O)-methyltransferase
Comments: The 2'-O-methylation of uridine44 contributes to stability of tRNASer(CGA).
References:
1. Kotelawala, L., Grayhack, E.J. and Phizicky, E.M. Identification of yeast tRNA Um44 2'-O-methyltransferase (Trm44) and demonstration of a Trm44 role in sustaining levels of specific tRNASer species. RNA 14 (2008) 158-169. [PMID: 18025252]
Accepted name: 2,7,4'-trihydroxyisoflavanone 4'-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 2,7,4'-trihydroxyisoflavanone = S-adenosyl-L-homocysteine + 2,7-dihydroxy-4'-methoxyisoflavanone
Other name(s): SAM:2,7,4'-trihydroxyisoflavanone 4'-O-methyltransferase; HI4'OMT; HMM1; MtIOMT5
Systematic name: S-adenosyl-L-methionine:2,7,4'-trihydroxyisoflavanone 4'-O-methyltransferase
Comments: Specifically methylates 2,7,4'-trihydroxyisoflavanone on the 4'-position. No activity with isoflavones [2]. The enzyme is involved in formononetin biosynthesis in legumes [1].
References:
1. Akashi, T., Sawada, Y., Shimada, N., Sakurai, N., Aoki, T. and Ayabe, S. cDNA cloning and biochemical characterization of S-adenosyl-L-methionine: 2,7,4'-trihydroxyisoflavanone 4'-O-methyltransferase, a critical enzyme of the legume isoflavonoid phytoalexin pathway. Plant Cell Physiol. 44 (2003) 103-112. [PMID: 12610212]
2. Deavours, B.E., Liu, C.J., Naoumkina, M.A., Tang, Y., Farag, M.A., Sumner, L.W., Noel, J.P. and Dixon, R.A. Functional analysis of members of the isoflavone and isoflavanone O-methyltransferase enzyme families from the model legume Medicago truncatula. Plant Mol. Biol. 62 (2006) 715-733. [PMID: 17001495]
3. Liu, C.J., Deavours, B.E., Richard, S.B., Ferrer, J.L., Blount, J.W., Huhman, D., Dixon, R.A. and Noel, J.P. Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses. Plant Cell 18 (2006) 3656-3669. [PMID: 17172354]
4. Akashi, T., VanEtten, H.D., Sawada, Y., Wasmann, C.C., Uchiyama, H. and Ayabe, S. Catalytic specificity of pea O-methyltransferases suggests gene duplication for (+)-pisatin biosynthesis. Phytochemistry 67 (2006) 2525-2530.
Accepted name: tRNA (guanine10-N2)-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + guanine10 in tRNA = 2 S-adenosyl-L-homocysteine + N2-dimethylguanine10 in tRNA (overall reaction)
(1a) S-adenosyl-L-methionine + guanine10 in tRNA = S-adenosyl-L-homocysteine + N2-methylguanine10 in tRNA
(1b) S-adenosyl-L-methionine + N2-methylguanine10 in tRNA = S-adenosyl-L-homocysteine + N2-dimethylguanine10 in tRNA
Other name(s): PAB1283; N(2),N(2)-dimethylguanosine tRNA methyltransferase; Trm-G10; PabTrm-G10; PabTrm-m2 2G10 enzyme
Systematic name: S-adenosyl-L-methionine:tRNA (guanine10-N2)-dimethyltransferase
References:
1. Armengaud, J., Urbonavicius, J., Fernandez, B., Chaussinand, G., Bujnicki, J.M. and Grosjean, H. N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota. J. Biol. Chem. 279 (2004) 37142-37152. [PMID: 15210688]
Accepted name: tRNA (guanine10-N2)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine10 in tRNA = S-adenosyl-L-homocysteine + N2-methylguanine10 in tRNA
Other name(s): (m2G10) methyltransferase; Trm11-Trm112 complex
Systematic name: S-adenosyl-L-methionine:tRNA (guanine10-N2)-methyltransferase
Comments: In contrast to the archaeal enzyme tRNA (guanine10-N2)-dimethyltransferase (EC 2.1.1.213), tRNA (guanine10-N2)-methyltransferase from yeast does not catalyse the methylation from N2-methylguanine10 to N2-dimethylguanine10 in tRNA.
References:
1. Purushothaman, S.K., Bujnicki, J.M., Grosjean, H. and Lapeyre, B. Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA. Mol. Cell Biol. 25 (2005) 4359-4370. [PMID: 15899842]
Accepted name: tRNA (guanine26-N2/guanine27-N2)-dimethyltransferase
Reaction: 4 S-adenosyl-L-methionine + guanine26/guanine27 in tRNA = 4 S-adenosyl-L-homocysteine + N2-dimethylguanine26/N2-dimethylguanine27 in tRNA
Other name(s): Trm1 (ambiguous); tRNA (N2,N2-guanine)-dimethyltransferase; tRNA (m2(2G26) methyltransferase; Trm1[tRNA (m2(2)G26) methyltransferase]
Systematic name: S-adenosyl-L-methionine:tRNA (guanine26-N2/guanine27-N2)-dimethyltransferase
Comments: The enzyme from Aquifex aeolicus is similar to the TRM1 methyltransferases of archaea and eukarya (see EC 2.1.1.216, tRNA (guanine26-N2)-dimethyltransferase). However, it catalyses the double methylation of guanines at both positions 26 and 27 of tRNA.
References:
1. Awai, T., Kimura, S., Tomikawa, C., Ochi, A., Ihsanawati, Bessho, Y., Yokoyama, S., Ohno, S., Nishikawa, K., Yokogawa, T., Suzuki, T. and Hori, H. Aquifex aeolicus tRNA (N2,N2-guanine)-dimethyltransferase (Trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in tRNA. J. Biol. Chem. 284 (2009) 20467-20478. [PMID: 19491098]
Accepted name: tRNA (guanine26-N2)-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + guanine26 in tRNA = 2 S-adenosyl-L-homocysteine + N2-dimethylguanine26 in tRNA
Other name(s): Trm1p; TRM1; tRNA (m22G26)dimethyltransferase
Systematic name: S-adenosyl-L-methionine:tRNA (guanine26-N2)-dimethyltransferase
Comments: The enzyme dissociates from its tRNA substrate between the two consecutive methylation reactions. In contrast to EC 2.1.1.215, tRNA (guanine26-N2/guanine27-N2)-dimethyltransferase, this enzyme does not catalyse the methylation of guanine27 in tRNA.
References:
1. Constantinesco, F., Motorin, Y. and Grosjean, H. Characterisation and enzymatic properties of tRNA(guanine26, N2,N2-dimethyltransferase (Trm1p) from Pyrococcus furiosus. J. Mol. Biol. 291 (1999) 375-392. [PMID: 10438627]
2. Constantinesco, F., Benachenhou, N., Motorin, Y. and Grosjean, H. The tRNA(guanine-26,N2-N2) methyltransferase (Trm1) from the hyperthermophilic archaeon Pyrococcus furiosus: cloning, sequencing of the gene and its expression in Escherichia coli. Nucleic Acids Res. 26 (1998) 3753-3761. [PMID: 9685492]
3. Liu, J., Liu, J. and Straby, K.B. Point and deletion mutations eliminate one or both methyl group transfers catalysed by the yeast TRM1 encoded tRNA (m22G26)dimethyltransferase. Nucleic Acids Res. 26 (1998) 5102-5108. [PMID: 9801306]
4. Liu, J., Zhou, G.Q. and Straby, K.B. Caenorhabditis elegans ZC376.5 encodes a tRNA (m22G26)dimethyltransferance in which 246arginine is important for the enzyme activity. Gene 226 (1999) 73-81. [PMID: 10048958]
Accepted name: tRNA (adenine22-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine22 in tRNA = S-adenosyl-L-homocysteine + N1-methyladenine22 in tRNA
Other name(s): TrmK; YqfN; Sp1610 (gene name); tRNA: m1A22 methyltransferase
Systematic name: S-adenosyl-L-methionine:tRNA (adenine22-N1)-methyltransferase
Comments: The enzyme specifically methylates adenine22 in tRNA.
References:
1. Ta, H.M. and Kim, K.K. Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA methyltransferase, in complex with S-adenosyl-L-methionine. Protein Sci. 19 (2010) 617-624. [PMID: 20052680]
2. Roovers, M., Kaminska, K.H., Tkaczuk, K.L., Gigot, D., Droogmans, L. and Bujnicki, J.M. The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK). Nucleic Acids Res. 36 (2008) 3252-3262. [PMID: 18420655]
Accepted name: tRNA (adenine9-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine9 in tRNA = S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
Other name(s): Trm10p (ambiguous); tRNA(m1G9/m1A9)-methyltransferase; tRNA(m1G9/m1A9)MTase; TK0422p (gene name); tRNA m1A9-methyltransferase; tRNA m1A9 Mtase
Systematic name: S-adenosyl-L-methionine:tRNA (adenine9-N1)-methyltransferase
Comments: The enzyme from Sulfolobus acidocaldarius specifically methylates adenine9 in tRNA [1]. The bifunctional enzyme from Thermococcus kodakaraensis also catalyses the methylation of guanine9 in tRNA (cf. EC 2.1.1.221, tRNA (guanine9-N1)-methyltransferase).
References:
1. Kempenaers, M., Roovers, M., Oudjama, Y., Tkaczuk, K.L., Bujnicki, J.M. and Droogmans, L. New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. Nucleic Acids Res. 38 (2010) 6533-6543. [PMID: 20525789]
Accepted name: tRNA (adenine57-N1/adenine58-N1)-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNA = 2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNA
Other name(s): TrmI; PabTrmI; AqTrmI; MtTrmI
Systematic name: S-adenosyl-L-methionine:tRNA (adenine57/adenine58-N1)-methyltransferase
Comments: The enzyme catalyses the formation of N1-methyladenine at two adjacent positions (57 and 58) in the T-loop of certain tRNAs (e.g. tRNAAsp). Methyladenosine at position 57 is an obligatory intermediate for the synthesis of methylinosine, which is commonly found at position 57 of archaeal tRNAs.
References:
1. Roovers, M., Wouters, J., Bujnicki, J.M., Tricot, C., Stalon, V., Grosjean, H. and Droogmans, L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 32 (2004) 465-476. [PMID: 14739239]
2. Guelorget, A., Roovers, M., Guerineau, V., Barbey, C., Li, X. and Golinelli-Pimpaneau, B. Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucleic Acids Res. 38 (2010) 6206-6218. [PMID: 20483913]
Accepted name: tRNA (adenine58-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine58 in tRNA = S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
Other name(s): tRNA m1A58 methyltransferase; tRNA (m1A58) methyltransferase; TrmI; tRNA (m1A58) Mtase; Rv2118cp; Gcd10p-Gcd14p; Trm61p-Trm6p
Systematic name: S-adenosyl-L-methionine:tRNA (adenine58-N1)-methyltransferase
Comments: The enzyme specifically methylates adenine58 in tRNA. The methylation of A58 is critical for maintaining the stability of initiator tRNAMet in yeast [3].
References:
1. Droogmans, L., Roovers, M., Bujnicki, J.M., Tricot, C., Hartsch, T., Stalon, V. and Grosjean, H. Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucleic Acids Res. 31 (2003) 2148-2156. [PMID: 12682365]
2. Varshney, U., Ramesh, V., Madabushi, A., Gaur, R., Subramanya, H.S. and RajBhandary, U.L. Mycobacterium tuberculosis Rv2118c codes for a single-component homotetrameric m1A58 tRNA methyltransferase. Nucleic Acids Res. 32 (2004) 1018-1027. [PMID: 14960715]
3. Anderson, J., Phan, L. and Hinnebusch, A.G. The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 97 (2000) 5173-5178. [PMID: 10779558]
Accepted name: tRNA (guanine9-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine9 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
Other name(s): Trm10p (ambiguous); tRNA(m1G9/m1A9)-methyltransferase; tRNA(m1G9/m1A9)MTase; tRNA (guanine-N(1)-)-methyltransferase; tRNA m1G9-methyltransferase; tRNA m1G9 MTase
Systematic name: S-adenosyl-L-methionine:tRNA (guanine9-N1)-methyltransferase
Comments: The enzyme from Saccharomyces cerevisiae specifically methylates guanine9 [1,2]. The bifunctional enzyme from Thermococcus kodakaraensis also catalyses the methylation of adenine9 in tRNA (cf. EC 2.1.1.218, tRNA (adenine9-N1)-methyltransferase) [1].
References:
1. Kempenaers, M., Roovers, M., Oudjama, Y., Tkaczuk, K.L., Bujnicki, J.M. and Droogmans, L. New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. Nucleic Acids Res. 38 (2010) 6533-6543. [PMID: 20525789]
2. Jackman, J.E., Montange, R.K., Malik, H.S. and Phizicky, E.M. Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. RNA 9 (2003) 574-585. [PMID: 12702816]
Accepted name: 2-polyprenyl-6-hydroxyphenyl methylase
Reaction: S-adenosyl-L-methionine + 3-(all-trans-polyprenyl)benzene-1,2-diol = S-adenosyl-L-homocysteine + 2-methoxy-6-(all-trans-polyprenyl)phenol
For diagram of reaction click here.
Other name(s): ubiG (gene name, ambiguous); ubiG methyltransferase (ambiguous); 2-octaprenyl-6-hydroxyphenyl methylase
Systematic name: S-adenosyl-L-methionine:3-(all-trans-polyprenyl)benzene-1,2-diol 2-O-methyltransferase
Comments: UbiG catalyses both methylation steps in ubiquinone biosynthesis in Escherichia coli. The second methylation is classified as EC 2.1.1.64 (3-demethylubiquinol 3-O-methyltransferase) [2]. In eukaryotes Coq3 catalyses the two methylation steps in ubiquinone biosynthesis. However, while the second methylation is common to both enzymes, the first methylation by Coq3 occurs at a different position within the pathway, and thus involves a different substrate and is classified as EC 2.1.1.114 (polyprenyldihydroxybenzoate methyltransferase). The substrate of the eukaryotic enzyme (3,4-dihydroxy-5-all-trans-polyprenylbenzoate) differs by an additional carboxylate moiety.
References:
1. Poon, W.W., Barkovich, R.J., Hsu, A.Y., Frankel, A., Lee, P.T., Shepherd, J.N., Myles, D.C. and Clarke, C.F. Yeast and rat Coq3 and Escherichia coli UbiG polypeptides catalyze both O-methyltransferase steps in coenzyme Q biosynthesis. J. Biol. Chem. 274 (1999) 21665-21672. [PMID: 10419476]
2. Hsu, A.Y., Poon, W.W., Shepherd, J.A., Myles, D.C. and Clarke, C.F. Complementation of coq3 mutant yeast by mitochondrial targeting of the Escherichia coli UbiG polypeptide: evidence that UbiG catalyzes both O-methylation steps in ubiquinone biosynthesis. Biochemistry 35 (1996) 9797-9806. [PMID: 8703953]
Accepted name: tRNA1Val (adenine37-N6)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine37 in tRNA1Val = S-adenosyl-L-homocysteine + N6-methyladenine37 in tRNA1Val
Other name(s): YfiC
Systematic name: S-adenosyl-L-methionine:tRNA1Val (adenine37-N6)-methyltransferase
Comments: The enzyme specifically methylates adenine37 in tRNA1Val (anticodon cmo5UAC).
References:
1. Golovina, A.Y., Sergiev, P.V., Golovin, A.V., Serebryakova, M.V., Demina, I., Govorun, V.M. and Dontsova, O.A. The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val(cmo5UAC). RNA 15 (2009) 1134-1141. [PMID: 19383770]
Accepted name: 23S rRNA (adenine2503-C8)-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA
Other name(s): Cfr (gene name)
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine2503-C8)-methyltransferase
Comments: This enzyme is a member of the 'AdoMet radical' (radical SAM) family. S-adenosyl-L-methionine acts as both a radical generator and as the source of the appended methyl group. It contains an [4Fe-S] cluster [1]. Cfr is an plasmid-acquired methyltransferase that protects cells from the action of antibiotics [1]. The enzyme methylates adenosine at position 2503 of 23S rRNA by a radical mechanism, transferring a CH2 group from S-adenosyl-L-methionine while retaining the hydrogen at the C-8 position of the adenine. It will also methylate 2-methyladenine produced by the action of EC 2.1.1.192 [23S rRNA (adenine2503-C2)-methyltransferase].
References:
1. 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]
2. 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]
3. Yan, F., LaMarre, J.M., Rhrich, 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]
4. Yan, F. and Fujimori, D.G. RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Proc. Natl. Acad. Sci. USA 108 (2011) 3930-3934. [PMID: 21368151]
5. Grove, T.L., Benner, J.S., Radle, M.I., Ahlum, J.H., Landgraf, B.J., Krebs, C. and Booker, S.J. A radically different mechanism for S-adenosylmethionine-dependent methyltransferases. Science 332 (2011) 604-607. [PMID: 21415317]
6. Boal, A.K., Grove, T.L., McLaughlin, M.I., Yennawar, N.H., Booker, S.J. and Rosenzweig, A.C. Structural basis for methyl transfer by a radical SAM enzyme. Science 332 (2011) 544-545. [PMID: 21527678]
Accepted name: tRNA:m4X modification enzyme
Reaction: (1) S-adenosyl-L-methionine + cytidine4 in tRNAPro = S-adenosyl-L-homocysteine + 2'-O-methylcytidine4 in tRNAPro
(2) S-adenosyl-L-methionine + cytidine4 in tRNAGly(GCC) = S-adenosyl-L-homocysteine + 2'-O-methylcytidine4 in tRNAGly(GCC)
(3) S-adenosyl-L-methionine + adenosine4 in tRNAHis = S-adenosyl-L-homocysteine + 2'-O-methyladenosine4 in tRNAHis
Other name(s): TRM13; Trm13p; tRNA:Xm4 modification enzyme
Systematic name: S-adenosyl-L-methionine:tRNAPro/His/Gly(GCC) (cytidine/adenosine4-2'-O)-methyltransferase
Comments: The enzyme from Saccharomyces cerevisiae 2'-O-methylates cytidine4 in tRNAPro and tRNAGly(GCC), and adenosine4 in tRNAHis.
References:
1. Wilkinson, M.L., Crary, S.M., Jackman, J.E., Grayhack, E.J. and Phizicky, E.M. The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4. RNA 13 (2007) 404-413. [PMID: 17242307]
Accepted name: 23S rRNA (cytidine1920-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytidine1920 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine1920 in 23S rRNA
Other name(s): TlyA (ambiguous)
Systematic name: S-adenosyl-L-methionine:23S rRNA (cytidine1920-2'-O)-methyltransferase
Comments: The bifunctional enzyme from Mycobacterium tuberculosis 2'-O-methylates cytidine1920 in helix 69 of 23S rRNA and cytidine1409 in helix 44 of 16S rRNA (cf. EC 2.1.1.227, 16S rRNA (cytidine1409-2'-O)-methyltransferase). These methylations result in increased susceptibility to the antibiotics capreomycin and viomycin.
References:
1. Johansen, S.K., Maus, C.E., Plikaytis, B.B. and Douthwaite, S. Capreomycin binds across the ribosomal subunit interface using tlyA-encoded 2'-O-methylations in 16S and 23S rRNAs. Mol. Cell 23 (2006) 173-182. [PMID: 16857584]
2. Maus, C.E., Plikaytis, B.B. and Shinnick, T.M. Mutation of tlyA confers capreomycin resistance in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 49 (2005) 571-577. [PMID: 15673735]
Accepted name: 16S rRNA (cytidine1409-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytidine1409 in 16S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine1409 in 16S rRNA
Other name(s): TlyA (ambiguous)
Systematic name: S-adenosyl-L-methionine:16S rRNA (cytidine1409-2'-O)-methyltransferase
Comments: The bifunctional enzyme from Mycobacterium tuberculosis 2'-O-methylates cytidine1409 in helix 44 of 16S rRNA and cytidine1920 in helix 69 of 23S rRNA (cf. EC 2.1.1.226, 23S rRNA (cytidine1920-2'-O)-methyltransferase).
References:
1. Johansen, S.K., Maus, C.E., Plikaytis, B.B. and Douthwaite, S. Capreomycin binds across the ribosomal subunit interface using tlyA-encoded 2'-O-methylations in 16S and 23S rRNAs. Mol. Cell 23 (2006) 173-182. [PMID: 16857584]
2. Maus, C.E., Plikaytis, B.B. and Shinnick, T.M. Mutation of tlyA confers capreomycin resistance in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 49 (2005) 571-577. [PMID: 15673735]
Accepted name: tRNA (guanine37-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
Other name(s): TrmD; tRNA (m1G37) methyltransferase; transfer RNA (m1G37) methyltransferase; Trm5p; TRMT5; tRNA-(N1G37) methyltransferase; MJ0883 (gene name)
Systematic name: S-adenosyl-L-methionine:tRNA (guanine37-N1)-methyltransferase
Comments: This enzyme is important for the maintenance of the correct reading frame during translation. Unlike TrmD from Escherichia coli, which recognizes the G36pG37 motif preferentially, the human enzyme (encoded by TRMT5) also methylates inosine at position 37 [4].
References:
1. Takeda, H., Toyooka, T., Ikeuchi, Y., Yokobori, S., Okadome, K., Takano, F., Oshima, T., Suzuki, T., Endo, Y. and Hori, H. The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus. Genes Cells 11 (2006) 1353-1365. [PMID: 17121543]
2. Lee, C., Kramer, G., Graham, D.E. and Appling, D.R. Yeast mitochondrial initiator tRNA is methylated at guanosine 37 by the Trm5-encoded tRNA (guanine-N1-)-methyltransferase. J. Biol. Chem. 282 (2007) 27744-27753. [PMID: 17652090]
3. O'Dwyer, K., Watts, J.M., Biswas, S., Ambrad, J., Barber, M., Brule, H., Petit, C., Holmes, D.J., Zalacain, M. and Holmes, W.M. Characterization of Streptococcus pneumoniae TrmD, a tRNA methyltransferase essential for growth. J. Bacteriol. 186 (2004) 2346-2354. [PMID: 15060037]
4. Brule, H., Elliott, M., Redlak, M., Zehner, Z.E. and Holmes, W.M. Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein. Biochemistry 43 (2004) 9243-9255. [PMID: 15248782]
5. Goto-Ito, S., Ito, T., Ishii, R., Muto, Y., Bessho, Y. and Yokoyama, S. Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Proteins 72 (2008) 1274-1289. [PMID: 18384044]
6. Ahn, H.J., Kim, H.W., Yoon, H.J., Lee, B.I., Suh, S.W. and Yang, J.K. Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition. EMBO J. 22 (2003) 2593-2603. [PMID: 12773376]
Accepted name: tRNA (carboxymethyluridine34-5-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + carboxymethyluridine34 in tRNA = S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA
Glossary: 5-methoxycarboxymethyluridine = 5-(2-methoxy-2-oxoethyl)uridine
Other name(s): ALKBH8; ABH8; Trm9; tRNA methyltransferase 9
Systematic name: S-adenosyl-L-methionine:tRNA (carboxymethyluridine34-5-O)-methyltransferase
Comments: The enzyme catalyses the posttranslational modification of uridine residues at the wobble position 34 of the anticodon loop of tRNA.
References:
1. Fu, D., Brophy, J.A., Chan, C.T., Atmore, K.A., Begley, U., Paules, R.S., Dedon, P.C., Begley, T.J. and Samson, L.D. Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol. Cell Biol. 30 (2010) 2449-2459. [PMID: 20308323]
2. Songe-Moller, L., van den Born, E., Leihne, V., Vagbo, C.B., Kristoffersen, T., Krokan, H.E., Kirpekar, F., Falnes, P.O. and Klungland, A. Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding. Mol. Cell Biol. 30 (2010) 1814-1827. [PMID: 20123966]
3. Kalhor, H.R. and Clarke, S. Novel methyltransferase for modified uridine residues at the wobble position of tRNA. Mol. Cell Biol. 23 (2003) 9283-9292. [PMID: 14645538]
Accepted name: 23S rRNA (adenosine1067-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenosine1067 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methyladenosine1067 in 23S rRNA
Other name(s): 23S rRNA A1067 2'-methyltransferase; thiostrepton-resistance methylase; nosiheptide-resistance methyltransferase
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenosine1067-2'-O)-methyltransferase
Comments: The methylase that is responsible for autoimmunity in the thiostrepton producer Streptomyces azureus, renders ribosomes completely resistant to thiostrepton [2].
References:
1. Bechthold, A. and Floss, H.G. Overexpression of the thiostrepton-resistance gene from Streptomyces azureus in Escherichia coli and characterization of recognition sites of the 23S rRNA A1067 2'-methyltransferase in the guanosine triphosphatase center of 23S ribosomal RNA. Eur. J. Biochem. 224 (1994) 431-437. [PMID: 7925357]
2. Thompson, J., Schmidt, F. and Cundliffe, E. Site of action of a ribosomal RNA methylase conferring resistance to thiostrepton. J. Biol. Chem. 257 (1982) 7915-7917. [PMID: 6806287]
3. Thompson, J. and Cundliffe, E. Purification and properties of an RNA methylase produced by Streptomyces azureus and involved in resistance to thiostrepton. J. Gen. Microbiol. 124 (1981) 291-297.
4. Yang, H., Wang, Z., Shen, Y., Wang, P., Jia, X., Zhao, L., Zhou, P., Gong, R., Li, Z., Yang, Y., Chen, D., Murchie, A.I. and Xu, Y. Crystal structure of the nosiheptide-resistance methyltransferase of Streptomyces actuosus. Biochemistry 49 (2010) 6440-6450. [PMID: 20550164]
Accepted name: lipopolysaccharide N-acetylmannosaminouronosyltransferase
Reaction: UDP-N-acetyl-β-D-mannosaminouronate + N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + N-acetyl-β-D-mannosaminouronyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Glossary: N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = lipid I
N-acetyl-β-D-mannosaminouronyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = lipid II
Other name(s): ManNAcA transferase; uridine diphosphoacetylmannosaminuronate-acetylglucosaminylpyrophosphorylundecaprenol acetylmannosaminuronosyltransferase
Systematic name: UDP-N-acetyl-β-D-mannosaminouronate:lipid I N-acetyl-β-D-mannosaminouronosyltransferase
Comments: Involved in the biosynthesis of common antigen in Enterobacteriaceae.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 113478-30-1
References:
1. Barr, K., Ward, S., Meier-Dieter, U., Mayer, H. and Rick, P.D. Characterization of an Escherichia coli rff mutant defective in transfer of N-acetylmannosaminuronic acid (ManNAcA) from UDP-ManNAcA to a lipid-linked intermediate involved in enterobacterial common antigen synthesis. J. Bacteriol. 170 (1988) 228-233. [PMID: 3275612]
Accepted name: crocetin glucosyltransferase
Reaction: (1) UDP-glucose + crocetin = UDP + β-D-glucosyl crocetin
(2) UDP-glucose + β-D-glucosyl crocetin = UDP + bis(β-D-glucosyl) crocetin
(3) UDP-glucose + β-D-gentiobiosyl crocetin = UDP + β-D-gentiobiosyl β-D-glucosyl crocetin
For diagram of reaction click here.
Other name(s): crocetin GTase
Systematic name: UDP-glucose:crocetin 8-O-D-glucosyltransferase
Comments: In Crocus sativus this enzyme esterifies a free carboxyl group of crocetin or crocetin glycosyl ester. There are two isoenzymes, UGTCs2, which is mainly expressed in fully developed stigmas, and UGTCs3, which is mainly expressed in stamens.
References:
1. Côté, F., Cormier, F., Dufresne, C. and Willemot, C. Properties of a glucosyltransferase involved in crocin synthesis. Plant Sci. 153 (2000) 55-63.
2. Moraga, A.R., Nohales, P.F., Perez, J.A. and Gomez-Gomez, L. Glucosylation of the saffron apocarotenoid crocetin by a glucosyltransferase isolated from Crocus sativus stigmas. Planta 219 (2004) 955-966. [PMID: 15605174]
Accepted name: soyasapogenol B glucuronide galactosyltransferase
Reaction: UDP-galactose + soyasapogenol B 3-O-β-D-glucuronide = UDP + soyasaponin III
Glossary: soyasaponin III = 3β-(2-O-β-D-galactopyranosyl-β-D-glucopyranosyloxyuronic acid)olean-12-ene-22β,24-diol
Other name(s): UDP-galactose:SBMG-galactosyltransferase; UGT73P2; GmSGT2 (gene name)
Systematic name: UDP-galactose:soyasapogenol B 3-O-glucuronide β-D-galactosyltransferase
Comments: Part of the biosynthetic pathway for soyasaponins.
References:
1. Shibuya, M., Nishimura, K., Yasuyama, N. and Ebizuka, Y. Identification and characterization of glycosyltransferases involved in the biosynthesis of soyasaponin I in Glycine max. FEBS Lett. 584 (2010) 2258-2264. [PMID: 20350545]
Accepted name: soyasaponin III rhamnosyltransferase
Reaction: UDP-rhamnose + soyasaponin III = UDP + soyasaponin I
Other name(s): UGT91H4; GmSGT3 (gene name)
Systematic name: UDP-rhamnose:soyasaponin III rhamnosyltransferase
Comments: Part of the biosynthetic pathway for soyasaponins.
References:
1. Shibuya, M., Nishimura, K., Yasuyama, N. and Ebizuka, Y. Identification and characterization of glycosyltransferases involved in the biosynthesis of soyasaponin I in Glycine max. FEBS Lett. 584 (2010) 2258-2264. [PMID: 20350545]
Accepted name: glucosylceramide β-1,4-galactosyltransferase
Reaction: UDP-galactose + β-D-glucosyl-(1↔1)-ceramide = UDP + β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide
For diagram of reaction click here.
Other name(s): lactosylceramide synthase; uridine diphosphate-galactose:glucosyl ceramide, β 1-4 galactosyltransferase; UDP-Gal:glucosylceramide β1→4galactosyltransferase; GalT-2 (misleading)
Systematic name: UDP-galactose:β-D-glucosyl-(1↔1)-ceramide β-1,4-galactosyltransferase
Comments: Involved in the synthesis of several different major classes of glycosphingolipids.
References:
1. Chatterjee, S. and Castiglione, E. UDPgalactose:glucosylceramide β1→4-galactosyltransferase activity in human proximal tubular cells from normal and familial hypercholesterolemic homozygotes. Biochim. Biophys. Acta 923 (1987) 136-142. [PMID: 3099851]
2. Trinchera, M., Fiorilli, A. and Ghidoni, R. Localization in the Golgi apparatus of rat liver UDP-Gal:glucosylceramide β1→4galactosyltransferase. Biochemistry 30 (1991) 2719-2724. [PMID: 1900430]
3. Chatterjee, S., Ghosh, N. and Khurana, S. Purification of uridine diphosphate-galactose:glucosyl ceramide, β 1-4 galactosyltransferase from human kidney. J. Biol. Chem. 267 (1992) 7148-7153. [PMID: 1551920]
4. Nomura, T., Takizawa, M., Aoki, J., Arai, H., Inoue, K., Wakisaka, E., Yoshizuka, N., Imokawa, G., Dohmae, N., Takio, K., Hattori, M. and Matsuo, N. Purification, cDNA cloning, and expression of UDP-Gal: glucosylceramide β-1,4-galactosyltransferase from rat brain. J. Biol. Chem. 273 (1998) 13570-13577. [PMID: 9593693]
5. Takizawa, M., Nomura, T., Wakisaka, E., Yoshizuka, N., Aoki, J., Arai, H., Inoue, K., Hattori, M. and Matsuo, N. cDNA cloning and expression of human lactosylceramide synthase. Biochim. Biophys. Acta 1438 (1999) 301-304. [PMID: 10320813]
Accepted name: lactotriaosylceramide β-1,4-galactosyltransferase
Reaction: UDP-galactose + N-acetyl-β-D-galactosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide = UDP + β-D-galactosyl-(1→4)-N-acetyl-β-D-galactosaminyl-(1→3)-β-D-galactosyl-(1→4)--D-glucosyl-(1↔1)-ceramide
For diagram of reaction click here.
Glossary: lactotriaosylceramide = N-acetyl-β-D-galactosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide
Other name(s): 4Gal-T4
Systematic name: UDP-galactose:N-acetyl-β-D-galactosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide β-1,4-galactosyltransferase
References:
1. Schwientek, T., Almeida, R., Levery, S.B., Holmes, E.H., Bennett, E. and Clausen, H. Cloning of a novel member of the UDP-galactose:β-N-acetylglucosamine β1,4-galactosyltransferase family, β4Gal-T4, involved in glycosphingolipid biosynthesis. J. Biol. Chem. 273 (1998) 29331-29340. [PMID: 9792633]
Accepted name: lipid IVA 3-deoxy-D-manno-octulosonic acid transferase
Reaction: lipid IVA + CMP-α-Kdo = α-Kdo-(2→6)-lipid IVA + CMP
Glossary: lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(KDO)-lipid IVA = α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
CMP-α-Kdo = CMP-3-deoxy-α-D-manno-oct-2-ulopyranosylonate
Other name(s): KDO transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase; lipid IVA KDO transferase
Systematic name: CMP-3-deoxy-D-manno-oct-2-ulosonate:lipid IVA 3-deoxy-D-manno-oct-2-ulosonate transferase
Comments: The bifunctional enzyme from Escherichia coli transfers two 3-deoxy-D-manno-oct-2-ulosonate residues to lipid IVA (cf. EC 2.4.99.13 [(KDO)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase]) [1]. The monofunctional enzymes from Aquifex aeolicus and Haemophilus influenzae catalyse the transfer of a single 3-deoxy-D-manno-oct-2-ulosonate residue from CMP-3-deoxy-D-manno-oct-2-ulosonate to lipid IVA [2,3]. The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-oct-2-ulosonate residues and generate genus-specific epitopes [4].
Links to other databases: BRENDA, EXPASY, KEGG
References:
1. Belunis, C.J. and Raetz, C.R. Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-D-manno-octulosonic acid transferase from Escherichia coli. J. Biol. Chem. 267 (1992) 9988-9997. [PMID: 1577828]
2. Mamat, U., Schmidt, H., Munoz, E., Lindner, B., Fukase, K., Hanuszkiewicz, A., Wu, J., Meredith, T.C., Woodard, R.W., Hilgenfeld, R., Mesters, J.R. and Holst, O. WaaA of the hyperthermophilic bacterium Aquifex aeolicus is a monofunctional 3-deoxy-D-manno-oct-2-ulosonic acid transferase involved in lipopolysaccharide biosynthesis. J. Biol. Chem. 284 (2009) 22248-22262. [PMID: 19546212]
3. White, K.A., Kaltashov, I.A., Cotter, R.J. and Raetz, C.R. A mono-functional 3-deoxy-D-manno-octulosonic acid (Kdo) transferase and a Kdo kinase in extracts of Haemophilus influenzae. J. Biol. Chem. 272 (1997) 16555-16563. [PMID: 9195966]
4. Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391-399. [PMID: 8748024]
Accepted name: (KDO)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase
Reaction: α-Kdo-(2→6)-lipid IVA + CMP-α-Kdo = α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP
Glossary: (KDO)-lipid IVA = α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(KDO)2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
CMP-α-Kdo = CMP-3-deoxy-α-D-manno-oct-2-ulopyranosylonate
Other name(s): KDO transferase; waaA (gene name); kdtA (gene name); Kdo transferase; 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase
Systematic name: CMP-3-deoxy-D-manno-oct-2-ulosonate:(KDO)-lipid IVA 3-deoxy-D-manno-oct-2-ulosonate transferase
Comments: The bifunctional enzyme from Escherichia coli transfers two 3-deoxy-D-manno-oct-2-ulosonate residues to lipid IVA (cf. EC 2.4.99.12 [lipid IVA 3-deoxy-D-manno-octulosonic acid transferase]) [1]. The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-oct-2-ulosonate residues and generate genus-specific epitopes [4].
Links to other databases: BRENDA, EXPASY, KEGG
References:
1. Belunis, C.J. and Raetz, C.R. Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-D-manno-octulosonic acid transferase from Escherichia coli. J. Biol. Chem. 267 (1992) 9988-9997. [PMID: 1577828]
2. Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391-399. [PMID: 8748024]
Accepted name: (KDO)2-lipid IVA (2-8) 3-deoxy-D-manno-octulosonic acid transferase
Reaction: α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP-α-Kdo = α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP
Glossary: (KDO)2-lipid IVA = α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(KDO)3-lipid IVA = α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→8)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
CMP-α-Kdo = CMP-3-deoxy-α-D-manno-oct-2-ulopyranosylonate
Other name(s): KDO transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase
Systematic name: CMP-3-deoxy-D-manno-oct-2-ulosonate:(KDO)2-lipid IVA 3-deoxy-D-manno-oct-2-ulosonate transferase [(2→8) glycosidic bond-forming]
Comments: The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-oct-2-ulosonate residues and generate genus-specific epitopes.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1. Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391-399. [PMID: 8748024]
2. Mamat, U., Baumann, M., Schmidt, G. and Brade, H. The genus-specific lipopolysaccharide epitope of Chlamydia is assembled in C. psittaci and C. trachomatis by glycosyltransferases of low homology. Mol. Microbiol. 10 (1993) 935-941. [PMID: 7523826]
3. Belunis, C.J., Mdluli, K.E., Raetz, C.R. and Nano, F.E. A novel 3-deoxy-D-manno-octulosonic acid transferase from Chlamydia trachomatis required for expression of the genus-specific epitope. J. Biol. Chem. 267 (1992) 18702-18707. [PMID: 1382060]
Accepted name: (KDO)3-lipid IVA (2-4) 3-deoxy-D-manno-octulosonic acid transferase
Reaction: α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP-α-Kdo = α-Kdo-(2→8)-[α-Kdo-(2→4)]-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + CMP
Glossary: (KDO)3-lipid IVA = α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→8)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(KDO)4-lipid IVA = α-Kdo-(2→8)-[α-Kdo-(2→4)]-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→8)-[(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
CMP-α-Kdo = CMP-3-deoxy-α-D-manno-oct-2-ulopyranosylonate
Other name(s): KDO transferase; waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase
Systematic name: CMP-3-deoxy-D-manno-oct-2-ulosonate:(KDO)3-lipid IVA 3-deoxy-D-manno-oct-2-ulosonate transferase [(2→4) glycosidic bond-forming]
Comments: The enzyme from Chlamydia psittaci transfers four KDO residues to lipid A, forming a branched tetrasaccharide with the structure α-KDO-(2,8)-[α-KDO-(2,4)]-α-KDO-(2,4)-α-KDO (cf. EC 2.4.99.12 [lipid IVA 3-deoxy-D-manno-octulosonic acid transferase], EC 2.4.99.13 [(KDO)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase], and EC 2.4.99.14 [(KDO)2-lipid IVA (2-8) 3-deoxy-D-manno-octulosonic acid transferase]).
Links to other databases: BRENDA, EXPASY, KEGG
References:
1. Brabetz, W., Lindner, B. and Brade, H. Comparative analyses of secondary gene products of 3-deoxy-D-manno-oct-2-ulosonic acid transferases from Chlamydiaceae in Escherichia coli K-12. Eur. J. Biochem. 267 (2000) 5458-5465. [PMID: 10951204]
2. Holst, O., Bock, K., Brade, L. and Brade, H. The structures of oligosaccharide bisphosphates isolated from the lipopolysaccharide of a recombinant Escherichia coli strain expressing the gene gseA [3-deoxy-D-manno-octulopyranosonic acid (Kdo) transferase] of Chlamydia psittaci 6BC. Eur. J. Biochem. 229 (1995) 194-200. [PMID: 7744029]
Accepted name: ketal pyruvate transferase
Reaction: phosphoenolpyruvate + D-Man-β-(1→4)-D-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol = 4,6-CH3(COO-)C-D-Man-β-(1→4)-D-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol + phosphate
For diagram of reaction click here.
Other name(s): KPT
Systematic name: phosphoenolpyruvate:D-Man-β-(1→4)-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol 4,6-O-(1-carboxyethan-1,1-diyl)transferase
Comments: Involved in the biosynthesis of the polysaccharide xanthan. 30-40% of xanthan terminal mannose residues of xanthan have a 4,6-O-(1-carboxyethan-1,1-diyl) ketal group. It also acts on the 6-O-acetyl derivative of the inner mannose unit.
References:
1. Marzocca, M.P., Harding, N.E., Petroni, E.A., Cleary, J.M. and Ielpi, L. Location and cloning of the ketal pyruvate transferase gene of Xanthomonas campestris. J. Bacteriol. 173 (1991) 7519-7524. [PMID: 1657892]
Accepted name: hygromycin-B 7"-O-kinase
Reaction: ATP + hygromycin B = ADP + 7"-O-phosphohygromycin B
For diagram click here
Other name(s): hygromycin B phosphotransferase; hygromycin-B kinase (ambiguous)
Systematic name: ATP:hygromycin-B 7"-O-phosphotransferase
Comments: Phosphorylates the antibiotics hygromycin B, 1-N-hygromycin B and destomycin, but not hygromycin B2, at the 7"-hydroxy group in the destomic acid ring.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 88361-67-5
References:
1. Zalacain, M., Pardo, J.M. and Jiménez, A. Purification and characterization of a hygromycin B phosphotransferase from Streptomyces hygroscopicus. Eur. J. Biochem. 162 (1987) 419-422. [PMID: 3026811]
Accepted name: 3-deoxy-D-manno-octulosonic acid kinase
Reaction: α-Kdo-(2→6)-lipid IVA + ATP = 4-O-phospho-α-Kdo-(2→6)-lipid IVA + ADP
Glossary: (KDO)-lipid IVA = α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
(4-O-phospho-KDO)-lipid IVA = 4-O-phospho-α-Kdo-(2→6)-lipid IVA = (3-deoxy-4-O-phosphono-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): kdkA (gene name); Kdo kinase
Systematic name: ATP:(KDO)-lipid IVA 3-deoxy-α-D-manno-oct-2-ulopyranose 4-phosphotransferase
Comments: The enzyme phosphorylates the 4-OH position of KDO in (KDO)-lipid IVA.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1. Brabetz, W., Muller-Loennies, S. and Brade, H. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) transferase (WaaA) and kdo kinase (KdkA) of Haemophilus influenzae are both required to complement a waaA knockout mutation of Escherichia coli. J. Biol. Chem. 275 (2000) 34954-34962. [PMID: 10952982]
2. Harper, M., Boyce, J.D., Cox, A.D., St Michael, F., Wilkie, I.W., Blackall, P.J. and Adler, B. Pasteurella multocida expresses two lipopolysaccharide glycoforms simultaneously, but only a single form is required for virulence: identification of two acceptor-specific heptosyl I transferases. Infect. Immun. 75 (2007) 3885-3893. [PMID: 17517879]
3. White, K.A., Kaltashov, I.A., Cotter, R.J. and Raetz, C.R. A mono-functional 3-deoxy-D-manno-octulosonic acid (Kdo) transferase and a Kdo kinase in extracts of Haemophilus influenzae. J. Biol. Chem. 272 (1997) 16555-16563. [PMID: 9195966]
4. White, K.A., Lin, S., Cotter, R.J. and Raetz, C.R. A Haemophilus influenzae gene that encodes a membrane bound 3-deoxy-D-manno-octulosonic acid (Kdo) kinase. Possible involvement of kdo phosphorylation in bacterial virulence. J. Biol. Chem. 274 (1999) 31391-31400. [PMID: 10531340]
Accepted name: molybdenum cofactor guanylyltransferase
Reaction: GTP + molybdenum cofactor = diphosphate + guanylyl molybdenum cofactor
Glossary: molybdenum cofactor = MoO2(OH)Dtpp-mP = molybdenum cofactor = MoCo = {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kS)-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)molybdate
Other name(s): MobA (gene name); MoCo guanylyltransferase
Systematic name: GTP:molybdenum cofactor guanylyltransferase
Comments: Catalyses the guanylation of the molybdenum cofactor. This modification occurs only in prokaryotes.
References:
1. Lake, M.W., Temple, C.A., Rajagopalan, K.V. and Schindelin, H. The crystal structure of the Escherichia coli MobA protein provides insight into molybdopterin guanine dinucleotide biosynthesis. J. Biol. Chem. 275 (2000) 40211-40217. [PMID: 10978347]
2. Temple, C.A. and Rajagopalan, K.V. Mechanism of assembly of the bis(molybdopterin guanine dinucleotide)molybdenum cofactor in Rhodobacter sphaeroides dimethyl sulfoxide reductase. J. Biol. Chem. 275 (2000) 40202-40210. [PMID: 10978348]
3. Guse, A., Stevenson, C.E., Kuper, J., Buchanan, G., Schwarz, G., Giordano, G., Magalon, A., Mendel, R.R., Lawson, D.M. and Palmer, T. Biochemical and structural analysis of the molybdenum cofactor biosynthesis protein MobA. J. Biol. Chem. 278 (2003) 25302-25307. [PMID: 12719427]
Accepted name: GDP-D-glucose phosphorylase
Reaction: GDP-α-D-glucose + phosphate = α-D-glucose 1-phosphate + GDP
Systematic name: GDP:α-D-glucose 1-phosphate guanylyltransferase
Comments: The enzyme may be involved in prevention of misincorporation of glucose in place of mannose residues into glycoconjugates i.e. to remove accidentally produced GDP-α-D-glucose. Activities with GDP-L-galactose, GDP-D-mannose and UDP-D-glucose are all less than 3% that with GDP-D-glucose.
References:
1. Adler, L.N., Gomez, T.A., Clarke, S.G. and Linster, C.L. A novel GDP-D-glucose phosphorylase involved in quality control of the nucleoside diphosphate sugar pool in Caenorhabditis elegans and mammals. J. Biol. Chem. 286 (2011) 21511-21523. [PMID: 21507950]
Accepted name: tRNAHis guanylyltransferase
Reaction: p-tRNAHis + ATP + GTP = pppGp-tRNAHis + AMP + diphosphate (overall reaction)
(1a) p-tRNAHis + ATP = App-tRNAHis + diphosphate
(1b) App-tRNAHis + GTP = pppGp-tRNAHis + AMP
Other name(s): histidine tRNA guanylyltransferase; Thg1p (ambiguous); Thg1 (ambiguous)
Systematic name: p-tRNAHis:GTP guanylyltransferase (ATP-hydrolysing)
Comments: In eukarya an additional guanosine residue is added post-transcriptionally to the 5'-end of tRNAHis molecules. The addition occurs opposite a universally conserved adenosine73 and is thus the result of a non-templated 3'-5' addition reaction. The additional guanosine residue is an important determinant for aminoacylation by EC 6.1.1.21, histidyl-tRNA ligase. The enzyme requires a divalent cation for activity [2]. ATP activation is not required when the substrate contains a 5'-triphosphate (ppp-tRNAHis) [3].
References:
1. Jahn, D. and Pande, S. Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. II. Catalytic mechanism. J. Biol. Chem. 266 (1991) 22832-22836. [PMID: 1660462]
2. Pande, S., Jahn, D. and Soll, D. Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. I. Purification and physical properties. J. Biol. Chem. 266 (1991) 22826-22831. [PMID: 1660461]
3. Gu, W., Jackman, J.E., Lohan, A.J., Gray, M.W. and Phizicky, E.M. tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis. Genes Dev. 17 (2003) 2889-2901. [PMID: 14633974]
4. Placido, A., Sieber, F., Gobert, A., Gallerani, R., Giege, P. and Marechal-Drouard, L. Plant mitochondria use two pathways for the biogenesis of tRNAHis. Nucleic Acids Res. 38 (2010) 7711-7717. [PMID: 20660484]
5. Jackman, J.E. and Phizicky, E.M. Identification of critical residues for G-1 addition and substrate recognition by tRNA(His) guanylyltransferase. Biochemistry 47 (2008) 4817-4825. [PMID: 18366186]
6. Hyde, S.J., Eckenroth, B.E., Smith, B.A., Eberley, W.A., Heintz, N.H., Jackman, J.E. and Doublie, S. tRNA(His) guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases. Proc. Natl. Acad. Sci. USA 107 (2010) 20305-20310. [PMID: 21059936]
Accepted name: cysteine desulfurase
Reaction: L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor (overall reaction)
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
(1b) [enzyme]-S-sulfanylcysteine + acceptor = [enzyme]-cysteine + S-sulfanyl-acceptor
Other name(s): IscS; NIFS; NifS; SufS; cysteine desulfurylase
Systematic name: L-cysteine:acceptor sulfurtransferase
Comments: A pyridoxal-phosphate protein. The sulfur from free L-cysteine is first transferred to a cysteine residue in the active site, and then passed on to various other acceptors. The enzyme is involved in the biosynthesis of iron-sulfur clusters, thio-nucleosides in tRNA, thiamine, biotin, lipoate and pyranopterin (molybdopterin) [2]. In Azotobacter vinelandii, this sulfur provides the inorganic sulfide required for nitrogenous metallocluster formation [1].
Links to other databases: BRENDA, EXPASY, KEGG, METACYC, PDB, CAS registry number: 149371-08-4
References:
1. Zheng, L.M., White, R.H., Cash, V.L., Jack, R.F. and Dean, D.R. Cysteine desulfurase activity indicates a role for NIFS in metallocluster biosynthesis. Proc. Natl. Acad. Sci. USA 90 (1993) 2754-2758. [PMID: 8464885]
2. Mihara, H. and Esaki, N. Bacterial cysteine desulfurases: Their function and mechanisms. Appl. Microbiol. Biotechnol. 60 (2002) 12-23. [PMID: 12382038]
3. Frazzon, J. and Dean, D.R. Formation of iron-sulfur clusters in bacteria: An emerging field in bioinorganic chemistry. Curr. Opin. Chem. Biol. 7 (2003) 166-173. [PMID: 12714048]
Accepted name: molybdenum cofactor sulfurtransferase
Reaction: molybdenum cofactor + L-cysteine + 2 H+ = thio-molybdenum cofactor + L-alanine + H2O
Glossary: molybdenum cofactor = MoO2(OH)Dtpp-mP = MoCo = {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kS)-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)molybdate
Other name(s): molybdenum cofactor sulfurase; ABA3; HMCS; MoCo sulfurase; MoCo sulfurtransferase
Systematic name: L-cysteine:molybdenum cofactor sulfurtransferase
Comments: Contains pyridoxal phosphate. Replaces the equatorial oxo ligand of the molybdenum by sulfur via an enzyme-bound persulfide. The reaction occurs in prokaryotes and eukaryotes but MoCo sulfurtransferases are only found in eukaryotes. In prokaryotes the reaction is catalysed by two enzymes: cysteine desulfurase (EC 2.8.1.7), which is homologous to the N-terminus of eukaryotic MoCo sulfurtransferases, and a molybdo-enzyme specific chaperone which binds the MoCo and acts as an adapter protein.
References:
1. Bittner, F., Oreb, M. and Mendel, R.R. ABA3 is a molybdenum cofactor sulfurase required for activation of aldehyde oxidase and xanthine dehydrogenase in Arabidopsis thaliana. J. Biol. Chem. 276 (2001) 40381-40384. [PMID: 11553608]
2. Heidenreich, T., Wollers, S., Mendel, R.R. and Bittner, F. Characterization of the NifS-like domain of ABA3 from Arabidopsis thaliana provides insight into the mechanism of molybdenum cofactor sulfuration. J. Biol. Chem. 280 (2005) 4213-4218. [PMID: 15561708]
3. Wollers, S., Heidenreich, T., Zarepour, M., Zachmann, D., Kraft, C., Zhao, Y., Mendel, R.R. and Bittner, F. Binding of sulfurated molybdenum cofactor to the C-terminal domain of ABA3 from Arabidopsis thaliana provides insight into the mechanism of molybdenum cofactor sulfuration. J. Biol. Chem. 283 (2008) 9642-9650. [PMID: 18258600]
Accepted name: endo-1,3-β-xylanase
Reaction: Random endohydrolysis of (1→3)-β-D-glycosidic linkages in (1→3)-β-D-xylans
Other name(s): xylanase (ambiguous); endo-1,3-β-xylosidase (misleading); 1,3-β-xylanase; 1,3-xylanase; β-1,3-xylanase; endo-β-1,3-xylanase; 1,3-β-D-xylan xylanohydrolase; xylan endo-1,3-β-xylosidase
Systematic name: 3-β-D-xylan xylanohydrolase
Comments: This enzyme is found mostly in marine bacteria, which break down the β(1,3)-xylan found in the cell wall of some green and red algae. The enzyme produces mainly xylobiose, xylotriose and xylotetraose.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9025-55-2
References:
1. Chen, W.P., Matsuo, M. and Tsuneo, Y. Purification and some properties of β-1,3-xylanase from Aspergillus terreus A-07. Agric. Biol. Chem. 50 (1986) 1183-1194.
2. Aoki, T., Araki, T. and Kitamikado, M. Purification and characterization of an endo-β-1,3-xylanase from Vibrio species. Nippon Suisan Gakkaishi 54 (1988) 277-281.
3. Araki, T., Tani, S., Maeda, K., Hashikawa, S., Nakagawa, H. and Morishita, T. Purification and characterization of β-1,3-xylanase from a marine bacterium, Vibrio sp. XY-214. Biosci. Biotechnol. Biochem. 63 (1999) 2017-2019. [PMID: 10635569]
4. Araki, T., Inoue, N. and Morishita, T. Purification and characterization of β-1,3-xylanase from a marine bacterium, Alcaligenes sp. XY-234. J. Gen. Appl. Microbiol. 44 (1998) 269-274. [PMID: 12501421]
5. Okazaki, F., Shiraki, K., Tamaru, Y., Araki, T. and Takagi, M. The first thermodynamic characterization of β-1,3-xylanase from a marine bacterium. Protein J. 24 (2005) 413-421. [PMID: 16328734]
Accepted name: cellulose 1,4-β-cellobiosidase (non-reducing end)
Reaction: Hydrolysis of (1→4)-β-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains
Other name(s): exo-cellobiohydrolase; β-1,4-glucan cellobiohydrolase; β-1,4-glucan cellobiosylhydrolase; 1,4-β-glucan cellobiosidase; exoglucanase; avicelase; CBH 1; C1 cellulase; cellobiohydrolase I; cellobiohydrolase; exo-β-1,4-glucan cellobiohydrolase; 1,4-β-D-glucan cellobiohydrolase; cellobiosidase
Systematic name: 4-β-D-glucan cellobiohydrolase (non-reducing end)
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 37329-65-0
References:
1. Berghem, L.E.R. and Pettersson, L.G. The mechanism of enzymatic cellulose degradation. Purification of a cellulolytic enzyme from Trichoderma viride active on highly ordered cellulose. Eur. J. Biochem. 37 (1973) 21-30. [PMID: 4738092]
2. Eriksson, K.E. and Pettersson, B. Extracellular enzyme system utilized by the fungus Sporotrichum pulverulentum (Chrysosporium lignorum) for the breakdown of cellulose. 3. Purification and physico-chemical characterization of an exo-1,4-β-glucanase. Eur. J. Biochem. 51 (1975) 213-218. [PMID: 235428]
3. Halliwell, G., Griffin, M. and Vincent, R. The role of component C1 in cellulolytic systems. Biochem. J. 127 (1972) 43P. [PMID: 5076675]
Accepted name: arabinan endo-1,5-α-L-arabinanase
Reaction: Endohydrolysis of (1→5)-α-arabinofuranosidic linkages in (1→5)-arabinans
Other name(s): endo-1,5-α-L-arabinanase; endo-α-1,5-arabanase; endo-arabanase; 1,5-α-L-arabinan 1,5-α-L-arabinanohydrolase; arabinan endo-1,5-α-L-arabinosidase (misleading)
Systematic name: 5-α-L-arabinan 5-α-L-arabinanohydrolase
Comments: Acts best on linear 1,5-α-L-arabinan. Also acts on branched arabinan, but more slowly.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 75432-96-1
References:
1. Kaji, A. and Saheki, T. Endo-arabinanase from Bacillus subtilis F-11. Biochim. Biophys. Acta 410 (1975) 354-360. [PMID: 1096]
2. Weinstein, L. and Albersheim, P. Structure of plant cell walls. IX. Purification and partial characterization of a wall-degrading endo-arabinase and an arabinosidase from Bacillus subtilis. Plant Physiol. 63 (1979) 425-432. [PMID: 16660741]
3. Flipphi, M.J., Panneman, H., van der Veen, P., Visser, J. and de Graaff, L.H. Molecular cloning, expression and structure of the endo-1,5-α-L-arabinase gene of Aspergillus niger. Appl. Microbiol. Biotechnol. 40 (1993) 318-326. [PMID: 7764386]
4. Leal, T.F. and de Sa-Nogueira, I. Purification, characterization and functional analysis of an endo-arabinanase (AbnA) from Bacillus subtilis. FEMS Microbiol. Lett. 241 (2004) 41-48. [PMID: 15556708]
Accepted name: xyloglucan-specific exo-β-1,4-glucanase
Reaction: Hydrolysis of (1→4)-D-glucosidic linkages in xyloglucans so as to successively remove oligosaccharides from the chain end.
Other name(s): Cel74A
Systematic name: [(1→6)-α-D-xylo]-(1→4)-β-D-glucan exo-glucohydrolase
Comments: The enzyme removes XXXG heptasaccharides, XXLG/XLXG octasaccharides and XLLG nonasaccharides from the end of tamarind seed xyloglucan polymers in a processive manner. Hydrolysis occurs at the unsubstituted D-glucopyranose residue in the main backbone. It is not known whether the cleavage takes place at the reducing or non-reducing end of the polymer. Very low activity with β-D-glucans. The enzyme from Chrysosporium lucknowense shifts to an endoglucanase mode when acting on linear substrates without bulky substituents on the polymeric backbone such as barley β-glucan.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 1000598-79-7
References:
1. Grishutin, S.G., Gusakov, A.V., Markov, A.V., Ustinov, B.B., Semenova, M.V. and Sinitsyn, A.P. Specific xyloglucanases as a new class of polysaccharide-degrading enzymes. Biochim. Biophys. Acta 1674 (2004) 268-281. [PMID: 15541296]
Accepted name: cellulose 1,4-β-cellobiosidase (reducing end)
Reaction: Hydrolysis of (1→4)-β-D-glucosidic linkages in cellulose and similar substrates, releasing cellobiose from the reducing ends of the chains.
Other name(s): CelS; CelSS; endoglucanase SS; cellulase SS; cellobiohydrolase CelS; Cel48A
Systematic name: 4-β-D-glucan cellobiohydrolase (reducing end)
Comments: Some exocellulases, most of which belong to the glycoside hydrolase family 48 (GH48, formerly known as cellulase family L), act at the reducing ends of cellulose and similar substrates. The CelS enzyme from Clostridium thermocellum is the most abundant subunit of the cellulosome formed by the organism. It liberates cellobiose units from the reducing end by hydrolysis of the glycosidic bond, employing an inverting reaction mechanism [2]. Different from EC 3.2.1.91, which attacks cellulose from the non-reducing end.
References:
1. Barr, B.K., Hsieh, Y.L., Ganem, B. and Wilson, D.B. Identification of two functionally different classes of exocellulases. Biochemistry 35 (1996) 586-592. [PMID: 8555231]
2. Saharay, M., Guo, H. and Smith, J.C. Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS. PLoS One 5 (2010) e1294. [PMID: 20967294]
Accepted name: α-D-xyloside xylohydrolase
Reaction: Hydrolysis of terminal, non-reducing α-D-xylose residues with release of α-D-xylose.
Other name(s): α-xylosidase
Systematic name: α-D-xyloside xylohydrolase
Comments: The enzyme catalyses hydrolysis of a terminal, unsubstituted xyloside at the extreme reducing end of a xylogluco-oligosaccharide. Representative α-xylosidases from glycoside hydrolase family 31 utilize a two-step (double-displacement) mechanism involving a covalent glycosyl-enzyme intermediate, and retain the anomeric configuration of the product.
References:
1. Moracci, M., Cobucci Ponzano, B., Trincone, A., Fusco, S., De Rosa, M., van Der Oost, J., Sensen, C.W., Charlebois, R.L. and Rossi, M. Identification and molecular characterization of the first α -xylosidase from an archaeon. J. Biol. Chem. 275 (2000) 22082-22089. [PMID: 10801892]
2. Sampedro, J., Sieiro, C., Revilla, G., Gonzalez-Villa, T. and Zarra, I. Cloning and expression pattern of a gene encoding an α-xylosidase active against xyloglucan oligosaccharides from Arabidopsis. Plant Physiol. 126 (2001) 910-920. [PMID: 11402218]
3. Crombie, H.J., Chengappa, S., Jarman, C., Sidebottom, C. and Reid, J.S. Molecular characterisation of a xyloglucan oligosaccharide-acting α-D-xylosidase from nasturtium (Tropaeolum majus L.) cotyledons that resembles plant 'apoplastic' α-D-glucosidases. Planta 214 (2002) 406-413. [PMID: 11859845]
4. Lovering, A.L., Lee, S.S., Kim, Y.W., Withers, S.G. and Strynadka, N.C. Mechanistic and structural analysis of a family 31 α-glycosidase and its glycosyl-enzyme intermediate. J. Biol. Chem. 280 (2005) 2105-2115. [PMID: 15501829]
5. Iglesias, N., Abelenda, J.A., Rodino, M., Sampedro, J., Revilla, G. and Zarra, I. Apoplastic glycosidases active against xyloglucan oligosaccharides of Arabidopsis thaliana. Plant Cell Physiol. 47 (2006) 55-63. [PMID: 16267099]
6. Okuyama, M., Kaneko, A., Mori, H., Chiba, S. and Kimura, A. Structural elements to convert Escherichia coli α-xylosidase (YicI) into α-glucosidase. FEBS Lett. 580 (2006) 2707-2711. [PMID: 16631751]
7. Larsbrink, J., Izumi, A., Ibatullin, F., Nakhai, A., Gilbert, H.J., Davies, G.J. and Brumer, H. Structural and enzymatic characterisation of a glycoside hydrolase family 31 α-xylosidase from Cellvibrio japonicus involved in xyloglucan saccharification. Biochem. J. 436 (2011) 567-580. [PMID: 21426303]
Accepted name: β-porphyranase
Reaction: Hydrolysis of β-D-galactopyranose-(1→4)-α-L-galactopyranose-6-sulfate linkages in porphyran
Other name(s): porphyranase; PorA; PorB; endo-β-porphyranase
Systematic name: porphyran β-D-galactopyranose-(1→4)-α-L-galactopyranose-6-sulfate 4-glycanohydrolase
Comments: The backbone of porphyran consists largely (~70%) of (1→3)-linked β-D-galactopyranose followed by (1→4)-linked α-L-galactopyranose-6-sulfate [the other 30% are mostly agarobiose repeating units of (1→3)-linked β-D-galactopyranose followed by (1→4)-linked 3,6-anhydro-α-L-galactopyranose] [2]. This enzyme cleaves the (1→4) linkages between β-D-galactopyranose and α-L-galactopyranose-6-sulfate, forming mostly the disaccharide α-L-galactopyranose-6-sulfate-(1→3)-β-D-galactose, although some longer oligosaccharides of even number of residues are also observed. Since the enzyme is inactive on the non-sulfated agarose portion of the porphyran backbone, some agarose fragments are also included in the products [1]. Methylation of the D-galactose prevents its binding at position -1 [2].
References:
1. Hehemann, J.H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M. and Michel, G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464 (2010) 908-912. [PMID: 20376150]
2. Correc, G., Hehemann, J.H., Czjzek, M. and Helbert, W. Structural analysis of the degradation products of porphyran digested by Zobellia galactanivorans β-porphyranase A. Carbohydrate Polymers 83 (2011) 277-283.
Accepted name: intermediate cleaving peptidase 55
Reaction: The enzyme cleaves the Pro36-Pro37 bond of cysteine desulfurase (EC 2.8.1.7) removing three amino acid residues (Tyr-Ser-Pro) from the N-terminus after cleavage by mitochondrial processing peptidase.
Other name(s): Icp55; mitochondrial intermediate cleaving peptidase 55 kDa
Comments: Icp55 removes the destabilizing N-terminal amino acid residues that are left after cleavage by the mitochondrial processing peptidase, leading to the stabilisation of the substrate. The enzyme can remove single amino acids or a short peptide, as in the case of cysteine desulfurase (EC 2.8.1.7), where three amino acids are removed.
References:
1. Naamati, A., Regev-Rudzki, N., Galperin, S., Lill, R. and Pines, O. Dual targeting of Nfs1 and discovery of its novel processing enzyme, Icp55. J. Biol. Chem. 284 (2009) 30200-30208. [PMID: 19720832]
2. Vogtle, F.N., Wortelkamp, S., Zahedi, R.P., Becker, D., Leidhold, C., Gevaert, K., Kellermann, J., Voos, W., Sickmann, A., Pfanner, N. and Meisinger, C. Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 139 (2009) 428-439. [PMID: 19837041]
Accepted name: γ-glutamyl-γ-aminobutyrate hydrolase
Reaction: 4-(L-γ-glutamylamino)butanoate + H2O = 4-aminobutanoate + L-glutamate
Other name(s): γ-glutamyl-GABA hydrolase; PuuD; YcjL; 4-(γ-glutamylamino)butanoate amidohydrolase
Systematic name: 4-(L-γ-glutamylamino)butanoate amidohydrolase
Comments: Forms part of a putrescine-utilizing pathway in Escherichia coli, in which it has been hypothesized that putrescine is first glutamylated to form γ-glutamylputrescine, which is oxidized to 4-(γ-glutamylamino)butanal and then to 4-(γ-glutamylamino)butanoate. The enzyme can also catalyse the reactions of EC 3.5.1.35 (D-glutaminase) and EC 3.5.1.65 (theanine hydrolase).
Links to other databases: BRENDA, EXPASY, KEGG
References:
1. Kurihara, S., Oda, S., Kato, K., Kim, H.G., Koyanagi, T., Kumagai, H. and Suzuki, H. A novel putrescine utilization pathway involves γ-glutamylated intermediates of Escherichia coli K-12. J. Biol. Chem. 280 (2005) 4602-4608. [PMID: 15590624]
Accepted name: Ca2+-transporting ATPase
Reaction: ATP + H2O + Ca2+[side 1] = ADP + phosphate + Ca2+[side 2]
Other name(s): sarcoplasmic reticulum ATPase; sarco(endo)plasmic reticulum Ca2+-ATPase; calcium pump; Ca2+-pumping ATPase; plasma membrane Ca-ATPase
Systematic name: ATP phosphohydrolase (Ca2+-transporting)
Comments: A P-type ATPase that undergoes covalent phosphorylation during the transport cycle. This enzyme family comprises three types of Ca2+-transporting enzymes that are found in the plasma membrane, the sarcoplasmic reticulum and in yeast. The first and third transport one ion per ATP hydrolysed, whereas the second transports two ions. Ca2+ is transported from the cytosol [side 1] into the sarcoplasmic reticulum in muscle cells [side 2].
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1. Schatzmann, H.J. and Vicenzi, F.F. Calcium movements across the membrane of human red cells. J. Physiol. 201 (1969) 369-395. [PMID: 4238381]
2. Inesi, G., Watanabe, T., Coan, C. and Murphy, A. The mechanism of sarcoplasmic reticulum ATPase. Ann. N.Y. Acad. Sci. 402 (1982) 515-532. [PMID: 6301340]
3. Carafoli, E. The Ca2+ pump of the plasma membrane. J. Biol. Chem. 267 (1992) 2115-2118. [PMID: 1310307]
4. MacLennan, D.H., Rice, W.J. and Green, N.M. The mechanism of Ca2+ transport by sarco(endo)plasmic reticulum Ca2+-ATPases. J. Biol. Chem. 272 (1997) 28815-28818. [PMID: 9360942]
5. Toyoshima, C., Nakasako, M., Nomura, H. and Ogawa, H. Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution. Nature 405 (2000) 647-655. [PMID: 10864315]
Accepted name: 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase
Reaction: (1) (2E,4Z)-2-hydroxy-6-oxonona-2,4-dienedioate + H2O = (2E)-2-hydroxypenta-2,4-dienoate + succinate
(2) (2E,4Z,7E)-2-hydroxy-6-oxononatrienedioate + H2O = (2E)-2-hydroxypenta-2,4-dienoate + fumarate
For diagram of reaction click here and another click here.
Other name(s): mhpC (gene name)
Systematic name: (2E,4Z)-2-hydroxy-6-oxona-2,4-dienedioate succinylhydrolase
Comments: This enzyme catalyses a step in a pathway of phenylpropanoid compounds degradation.
References:
1. Burlingame, R. and Chapman, P.J. Catabolism of phenylpropionic acid and its 3-hydroxy derivative by Escherichia coli. J. Bacteriol. 155 (1983) 113-121. [PMID: 6345502]
2. Burlingame, R.P., Wyman, L. and Chapman, P.J. Isolation and characterization of Escherichia coli mutants defective for phenylpropionate degradation. J. Bacteriol. 168 (1986) 55-64. [PMID: 3531186]
3. Ferrández, A., García, J.L. and Díaz, E. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12. J. Bacteriol. 179 (1997) 2573-2581. [PMID: 9098055]
4. Díaz, E., Ferrández, A. and García, J.L. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180 (1998) 2915-2923. [PMID: 9603882]
Accepted name: 4-oxalocrotonate decarboxylase
Reaction: (2Z)-5-oxohex-2-enedioate = 2-oxopent-4-enoate + CO2
Glossary: 4-oxaloisocrotonate = (2Z)-5-oxohex-2-enedioate
4-oxalocrotonate = (2E)-5-oxohex-2-enedioate
Other name(s): 4-oxalocrotonate carboxy-lyase
Systematic name: (2Z)-5-oxohex-2-enedioate carboxy-lyase (2-oxopent-4-enoate-forming)
Comments: Involved in the meta-cleavage pathway for the degradation of phenols, modified phenols and catechols. The enzyme has been reported to accept the tautomeric forms (2Z)-5-oxohex-2-enedioate and (3Z)-2-oxohex-3-enedioate [1-3] as well as 4-oxalocrotonate and (3E)-2-oxohex-3-enedioate [4].
Links to other databases: BRENDA, EXPASY, KEGG, UM-BBD, CAS registry number: 37325-55-6
References:
1. Shingler, V., Marklund, U., Powlowski, J. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J. Bacteriol. 174 (1992) 711-724. [PMID: 1732207]
2. Takenaka, S., Murakami, S., Shinke, R. and Aoki, K. Metabolism of 2-aminophenol by Pseudomonas sp. AP-3: modified meta-cleavage pathway. Arch. Microbiol. 170 (1998) 132-137. [PMID: 9683650]
3. Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758-6768. [PMID: 19717587]
4. Stanley, T.M., Johnson, W.H., Jr., Burks, E.A., Whitman, C.P., Hwang, C.C. and Cook, P.F. Expression and stereochemical and isotope effect studies of active 4-oxalocrotonate decarboxylase. Biochemistry 39 (2000) 718-726. [PMID: 10651637]
Accepted name: pyrrole-2-carboxylate decarboxylase
Reaction: (1) pyrrole-2-carboxylate = pyrrole + CO2
(2) pyrrole-2-carboxylate + H2O = pyrrole + HCO3-
Systematic name: pyrrole-2-carboxylate carboxy-lyase
Comments: The enzyme catalyses both the carboxylation and decarboxylation reactions. However, while bicarbonate is the preferred substrate for the carboxylation reaction, decarboxylation produces carbon dioxide. The enzyme is activated by carboxylic acids.
References:
1. Wieser, M., Fujii, N., Yoshida, T. and Nagasawa, T. Carbon dioxide fixation by reversible pyrrole-2-carboxylate decarboxylase from Bacillus megaterium PYR2910. Eur. J. Biochem. 257 (1998) 495-499. [PMID: 9826198]
2. Omura, H., Wieser, M. and Nagasawa, T. Pyrrole-2-carboxylate decarboxylase from Bacillus megaterium PYR2910, an organic-acid-requiring enzyme. Eur. J. Biochem. 253 (1998) 480-484. [PMID: 9654100]
3. Wieser, M., Yoshida, T. and Nagasawa, T. Microbial synthesis of pyrrole-2-carboxylate by Bacillus megaterium PYR2910. Tetrahedron Lett. 39 (1998) 4309-4310.
Accepted name: L-threonine aldolase
Reaction: L-threonine = glycine + acetaldehyde
Other name(s): L-threonine acetaldehyde-lyase
Systematic name: L-threonine acetaldehyde-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein. This enzyme is specific for L-threonine and can not utilize L-allo-threonine. Different from EC 4.1.2.49, L-allo-threonine aldolase, and EC 4.1.2.48, low-specificity L-threonine aldolase.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 62213-23-4
References:
1. Dainty, R.H. Purification and properties of threonine aldolase from Clostridium pasteurianum. Biochem. J. 117 (1970) 585-592. [PMID: 5419751]
2. Karasek, M.A. and Greenberg, D.M. Studies on the properties of threonine aldolases. J. Biol. Chem. 227 (1957) 191-205. [PMID: 13449064]
Accepted name: low-specificity L-threonine aldolase
Reaction: (1) L-threonine = glycine + acetaldehyde
(2) L-allo-threonine = glycine + acetaldehyde
Other name(s): LtaE
Systematic name: L-threonine/L-allo-threonine acetaldehyde-lyase (glycine-forming)
Comments: Requires pyridoxal phosphate. The low-specificity L-threonine aldolase can act on both L-threonine and L-allo-threonine [1,2]. The enzyme from Escherichia coli can also act on L-threo-phenylserine and L-erythro-phenylserine [4]. The enzyme can also catalyse the aldol condensation of glycolaldehyde and glycine to form 4-hydroxy-L-threonine, an intermediate of pyridoxal phosphate biosynthesis [3]. Different from EC 4.1.2.5, L-threonine aldolase, and EC 4.1.2.49, L-allo-threonine aldolase.
References:
1. Yamada, H., Kumagai, H., Nagate, T. and Yoshida, H. Crystalline threonine aldolase from Candida humicola. Biochem. Biophys. Res. Commun. 39 (1970) 53-58. [PMID: 5438301]
2. Kumagai, H., Nagate, T., Yoshida, H. and Yamada, H. Threonine aldolase from Candida humicola. II. Purification, crystallization and properties. Biochim. Biophys. Acta 258 (1972) 779-790. [PMID: 5017702]
3. Liu, J.Q., Nagata, S., Dairi, T., Misono, H., Shimizu, S. and Yamada, H. The GLY1 gene of Saccharomyces cerevisiae encodes a low-specific L-threonine aldolase that catalyzes cleavage of L-allo-threonine and L-threonine to glycine—expression of the gene in Escherichia coli and purification and characterization of the enzyme. Eur. J. Biochem. 245 (1997) 289-293. [PMID: 9151955]
4. Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. Gene cloning, biochemical characterization and physiological role of a thermostable low-specificity L-threonine aldolase from Escherichia coli. Eur. J. Biochem. 255 (1998) 220-226. [PMID: 9692922]
5. Kim, J., Kershner, J.P., Novikov, Y., Shoemaker, R.K. and Copley, S.D. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis. Mol. Syst. Biol. 6 (2010) 436. [PMID: 21119630]
Accepted name: L-allo-threonine aldolase
Reaction: L-allo-threonine = glycine + acetaldehyde
Systematic name: L-allo-threonine acetaldehyde-lyase (glycine-forming)
Comments: Requires pyridoxal phosphate. This enzyme, characterized from the bacterium Aeromonas jandaei, is specific for L-allo-threonine and can not act on either L-threonine or L-serine. Different from EC 4.1.2.5, L-threonine aldolase, and EC 4.1.2.48, low-specificity L-threonine aldolase. A previously listed enzyme with this name, EC 4.1.2.6, was deleted in 1971 after it was found to be identical to EC 2.1.2.1, glycine hydroxymethyltransferase.
References:
1. Kataoka, M., Wada, M., Nishi, K., Yamada, H. and Shimizu, S. Purification and characterization of L-allo-threonine aldolase from Aeromonas jandaei DK-39. FEMS Microbiol. Lett. 151 (1997) 245-248. [PMID: 9228760]
Accepted name: phosphomethylpyrimidine synthase
Reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-phosphomethylpyrimidine + 5'-deoxyadenosine + L-methionine + formate + CO
Other name(s): thiC (gene name)
Systematic name: 5-amino-1-(5-phospho-D-ribosyl)imidazole formate-lyase (decarboxylating, 4-amino-2-methyl-5-phosphomethylpyrimidine-forming)
Comments: Binds a 4Fe-4S cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce L-methionine and a 5-deoxyadenosin-5-yl radical that is crucial for the conversion of the substrate. Part of the pathway for thiamine biosynthesis.
References:
1. Chatterjee, A., Li, Y., Zhang, Y., Grove, T.L., Lee, M., Krebs, C., Booker, S.J., Begley, T.P. and Ealick, S.E. Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat. Chem. Biol. 4 (2008) 758-765. [PMID: 18953358]
2. Martinez-Gomez, N.C., Poyner, R.R., Mansoorabadi, S.O., Reed, G.H. and Downs, D.M. Reaction of AdoMet with ThiC generates a backbone free radical. Biochemistry 48 (2009) 217-219. [PMID: 19113839]
3. Chatterjee, A., Hazra, A.B., Abdelwahed, S., Hilmey, D.G. and Begley, T.P. A "radical dance" in thiamin biosynthesis: mechanistic analysis of the bacterial hydroxymethylpyrimidine phosphate synthase. Angew. Chem. Int. Ed. Engl. 49 (2010) 8653-8656. [PMID: 20886485]
Accepted name: cyclic pyranopterin monophosphate synthase
Reaction: GTP = cyclic pyranopterin monophosphate + diphosphate
Glossary: cyclic pyranopterin monophosphate = cPMP = precursor Z = 8-amino-2,12,12-trihydroxy-4a,5a,6,9,11,11a,12,12a-octahydro[1,3,2]dioxaphosphinino[4',5':5,6]pyrano[3,2-g]pteridin-10(4H)-one 2-oxide = 8-amino-2,12,12-trihydroxy-4,4a,5a,6,9,10,11,11a,12,12a-decahydro-[1,3,2]dioxaphosphinino[4',5':5,6]pyrano[3,2-g]pteridine 2-oxide
Other name(s): MOCS1A; MoaA; MoaC; molybdenum cofactor biosynthesis protein 1
Systematic name: GTP 8,9-lyase (cyclic pyranopterin monophosphate-forming)
Comments: The enzyme catalyses an early step in the biosynthesis of the molybdenum cofactor (MoCo). The enzyme MoaA from bacteria and the human enzyme MOCS1A each contain two oxygen-sensitive FeS clusters. The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes. In bacteria, the reaction is catalysed by MoaA and requires the action of MoaC. The latter protein is equivalent to the C-terminal domain of the eukaryotic enzyme MOCS1A which does not need further protein components to perform the reaction.
References:
1. Rieder, C., Eisenreich, W., O'Brien, J., Richter, G., Götze, E., Boyle, P., Blanchard, S., Bacher, A. and Simon, H. Rearrangement reactions in the biosynthesis of molybdopterin - an NMR study with multiply 13C/15N labelled precursors. Eur. J. Biochem. 255 (1998) 24-36. [PMID: 9692897]
2. Wuebbens, M.M. and Rajagopalan, K.V. Investigation of the early steps of molybdopterin biosynthesis in Escherichia coli through the use of in vivo labeling studies. J. Biol. Chem. 270 (1995) 1082-1087. [PMID: 7836363]
3. Hänzelmann, P., Hernandez, H.L., Menzel, C., Garcia-Serres, R., Huynh, B.H., Johnson, M.K., Mendel, R.R. and Schindelin, H. Characterization of MOCS1A, an oxygen-sensitive iron-sulfur protein involved in human molybdenum cofactor biosynthesis. J. Biol. Chem. 279 (2004) 34721-34732. [PMID: 15180982]
4. Hänzelmann, P. and Schindelin, H. Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans. Proc. Natl. Acad. Sci. USA 101 (2004) 12870-12875. [PMID: 15317939]
5. Sanishvili, R., Beasley, S., Skarina, T., Glesne, D., Joachimiak, A., Edwards, A. and Savchenko, A. The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis. J. Biol. Chem. 279 (2004) 42139-42146. [PMID: 15269205]
6. Hänzelmann, P. and Schindelin, H. Binding of 5'-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism. Proc. Natl. Acad. Sci. USA 103 (2006) 6829-6834. [PMID: 16632608]
7. Lees, N.S., Hänzelmann, P., Hernandez, H.L., Subramanian, S., Schindelin, H., Johnson, M.K. and Hoffman, B.M. ENDOR spectroscopy shows that guanine N1 binds to [4Fe-4S] cluster II of the S-adenosylmethionine-dependent enzyme MoaA: mechanistic implications. J. Am. Chem. Soc. 131 (2009) 9184-9185. [PMID: 19566093]
Accepted name: 2-iminoacetate synthase
Reaction: L-tyrosine + S-adenosyl-L-methionine + reduced acceptor = 2-iminoacetate + 4-methylphenol + 5'-deoxyadenosine + L-methionine + acceptor + 2 H+
Glossary: 4-methylphenol = 4-cresol = p-cresol
Other name(s): thiH (gene name)
Systematic name: L-tyrosine 4-methylphenol-lyase (2-iminoacetate-forming)
Comments: Binds a 4Fe-4S cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce methionine and a 5-deoxyadenosin-5-yl radical that is crucial for the conversion of the substrate. Part of the pathway for thiamine biosynthesis.
References:
1. Leonardi, R., Fairhurst, S.A., Kriek, M., Lowe, D.J. and Roach, P.L. Thiamine biosynthesis in Escherichia coli: isolation and initial characterisation of the ThiGH complex. FEBS Lett. 539 (2003) 95-99. [PMID: 12650933]
2. Kriek, M., Martins, F., Challand, M.R., Croft, A. and Roach, P.L. Thiamine biosynthesis in Escherichia coli: identification of the intermediate and by-product derived from tyrosine. Angew. Chem. Int. Ed. Engl. 46 (2007) 9223-9226. [PMID: 17969213]
3. Kriek, M., Martins, F., Leonardi, R., Fairhurst, S.A., Lowe, D.J. and Roach, P.L. Thiazole synthase from Escherichia coli: an investigation of the substrates and purified proteins required for activity in vitro. J. Biol. Chem. 282 (2007) 17413-17423. [PMID: 17403671]
Accepted name: tryptophan synthase
Reaction: L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O (overall reaction)
(1a) 1-C-(indol-3-yl)glycerol 3-phosphate = indole + glyceraldehyde 3-phosphate
(1b) L-serine + indole = L-tryptophan + H2O
For diagram of reaction click here and mechanism click here
Other name(s): L-tryptophan synthetase; indoleglycerol phosphate aldolase; tryptophan desmolase; tryptophan synthetase; L-serine hydro-lyase (adding indoleglycerol-phosphate)
Systematic name: L-serine hydro-lyase [adding 1-C-(indol-3-yl)glycerol 3-phosphate, L-tryptophan and glyceraldehyde-3-phosphate-forming]
Comments: A pyridoxal-phosphate protein. The α-subunit catalyses the conversion of 1-C-(indol-3-yl)glycerol 3-phosphate to indole and glyceraldehyde 3-phosphate (this reaction was listed formerly as EC 4.1.2.8). The indole migrates to the β-subunit where, in the presence of pyridoxal 5'-phosphate, it is combined with L-serine to form L-tryptophan. In some organisms this enzyme is part of a multifunctional protein that also includes one or more of the enzymes EC 2.4.2.18 (anthranilate phosphoribosyltransferase), EC 4.1.1.48 (indole-3-glycerol-phosphate synthase), EC 4.1.3.27 (anthranilate synthase) and EC 5.3.1.24 (phosphoribosylanthranilate isomerase). In thermophilic organisms, where the high temperature enhances diffusion and causes the loss of indole, a protein similar to the β subunit can be found (EC 4.2.1.122). That enzyme cannot combine with the α unit of EC 4.2.1.20 to form a complex.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, PDB, CAS registry number: 9014-52-2
References:
1. Crawford, I.P. and Yanofsky, C. On the separation of the tryptophan synthetase of Escherichia coli into two protein components. Proc. Natl. Acad. Sci. USA 44 (1958) 1161-1170. [PMID: 16590328]
2. Creighton, T.E. and Yanofsky, C. Chorismate to tryptophan (Escherichia coli) - anthranilate synthetase, PR transferase, PRA isomerase, InGP synthetase, tryptophan synthetase. Methods Enzymol. 17A (1970) 365-380.
3. Hütter, R., Niederberger, P. and DeMoss, J.A. Tryptophan synthetic genes in eukaryotic microorganisms. Annu. Rev. Microbiol. 40 (1986) 55-77. [PMID: 3535653]
4. Hyde, C.C., Ahmed, S.A., Padlan, E.A., Miles, E.W. and Davies, D.R. Three-dimensional structure of the tryptophan synthase α2β2 multienzyme complex from Salmonella typhimurium. J. Biol. Chem. 263 (1988) 17857-17871. [PMID: 3053720]
5. Woehl, E. and Dunn, M.F. Mechanisms of monovalent cation action in enzyme catalysis: the tryptophan synthase α-, β-, and αβ-reactions. Biochemistry 38 (1999) 7131-7141. [PMID: 10353823]
Accepted name: D-lactate dehydratase
Reaction: (R)-lactate = methylglyoxal + H2O
Other name(s): glyoxylase III
Systematic name: (R)-lactate hydro-lyase
Comments: The enzyme converts methylglyoxal to D-lactate in a single glutathione (GSH)-independent step. The other known route for this conversion is the two-step GSH-dependent pathway catalysed by EC 4.4.1.5 (lactoylglutathione lyase) and EC 3.1.2.6 (hydroxyacylglutathione hydrolase).
References:
1. Misra, K., Banerjee, A.B., Ray, S. and Ray, M. Glyoxalase III from Escherichia coli: a single novel enzyme for the conversion of methylglyoxal into D-lactate without reduced glutathione. Biochem. J. 305 ( Pt 3) (1995) 999-1003. [PMID: 7848303]
2. Subedi, K.P., Choi, D., Kim, I., Min, B. and Park, C. Hsp31 of Escherichia coli K-12 is glyoxalase III. Mol. Microbiol. 81 (2011) 926-936. [PMID: 21696459]
Accepted name: gellan lyase
Reaction: Eliminative cleavage of β-D-glucopyranosyl-(1→4)-β-D-glucopyranosyluronate bonds of gellan backbone releasing tetrasaccharides containing a 4-deoxy-4,5-unsaturated D-glucopyranosyluronic acid at the non-reducing end. The tetrasaccharide produced from deacetylated gellan is β-D-4-deoxy-Δ4-GlcAp-(1→4)-β-D-Glcp-(1→4)-α-L-Rhap-(1→3)-β-D-Glcp.
Systematic name: gellan β-D-glucopyranosyl-(1→4)-D-glucopyranosyluronate lyase
Comments: The enzyme is highly specific to gellan, especially deacetylated gellan.
References:
1. Hashimoto, W., Maesaka, K., Sato, N., Kimura, S., Yamamoto, K., Kumagai, H. and Murata, K. Microbial system for polysaccharide depolymerization: enzymatic route for gellan depolymerization by Bacillus sp. GL1. Arch. Biochem. Biophys. 339 (1997) 17-23. [PMID: 9056228]
2. Hashimoto, W., Sato, N., Kimura, S. and Murata, K. Polysaccharide lyase: molecular cloning of gellan lyase gene and formation of the lyase from a huge precursor protein in Bacillus sp. GL1. Arch. Biochem. Biophys. 354 (1998) 31-39. [PMID: 9633595]
3. Miyake, O., Kobayashi, E., Nankai, H., Hashimoto, W., Mikami, B. and Murata, K. Posttranslational processing of polysaccharide lyase: maturation route for gellan lyase in Bacillus sp. GL1. Arch. Biochem. Biophys. 422 (2004) 211-220. [PMID: 14759609]
Accepted name: β-chamigrene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-β-chamigrene + diphosphate
For diagram of reaction click here and mechanism click here.
Systematic name: (2E,6E)-farnesyl diphosphate lyase (cyclizing, (+)-β-chamigrene-forming)
Comments: The recombinant enzyme from the plant Arabidopsis thaliana produces 27.3% (+)-α-barbatene, 17.8% (+)-thujopsene and 9.9% (+)-β-chamigrene [1] plus traces of other sesquiterpenoids [2]. See EC 4.2.3.69 (+)-α-barbatene synthase, and EC 4.2.3.79 thujopsene synthase.
References:
1. Wu, S., Schoenbeck, M.A., Greenhagen, B.T., Takahashi, S., Lee, S., Coates, R.M. and Chappell, J. Surrogate splicing for functional analysis of sesquiterpene synthase genes. Plant Physiol. 138 (2005) 1322-1333. [PMID: 15965019]
2. Tholl, D., Chen, F., Petri, J., Gershenzon, J. and Pichersky, E. Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J. 42 (2005) 757-771. [PMID: 15918888]
Accepted name: thujopsene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-thujopsene + diphosphate
For diagram of reaction click here and mechanism click here.
Systematic name: (2E,6E)-farnesyl diphosphate lyase (cyclizing, (+)-thujopsene-forming)
Comments: The recombinant enzyme from the plant Arabidopsis thaliana produces 27.3% (+)-α-barbatene, 17.8% (+)-thujopsene and 9.9% (+)-β-chamigrene [1] plus traces of other sesquiterpenoids [2]. See EC 4.2.3.69 (+)-α-barbatene synthase, and EC 4.2.3.78 β-chamigrene synthase.
References:
1. Wu, S., Schoenbeck, M.A., Greenhagen, B.T., Takahashi, S., Lee, S., Coates, R.M. and Chappell, J. Surrogate splicing for functional analysis of sesquiterpene synthase genes. Plant Physiol. 138 (2005) 1322-1333. [PMID: 15965019]
2. Tholl, D., Chen, F., Petri, J., Gershenzon, J. and Pichersky, E. Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J. 42 (2005) 757-771. [PMID: 15918888]
Accepted name: α-longipinene synthase
Reaction: (2E,6E)-farnesyl diphosphate = α-longipinene + diphosphate
For diagram of reaction click here and mechanism click here.
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (α-longipinene-forming)
Comments: The enzyme from Norway spruce produces longifolene as the main product (c.f. EC 4.2.3.58, longifolene synthase). α-Longipinene constitutes about 15% of the total products.
References:
1. Martin, D.M., Faldt, J. and Bohlmann, J. Functional characterization of nine Norway Spruce TPS genes and evolution of gymnosperm terpene synthases of the TPS-d subfamily. Plant Physiol. 135 (2004) 1908-1927. [PMID: 15310829]
2. Köpke, D., Schröder, R., Fischer, H.M., Gershenzon, J., Hilker, M. and Schmidt, A. Does egg deposition by herbivorous pine sawflies affect transcription of sesquiterpene synthases in pine? Planta 228 (2008) 427-438. [PMID: 18493792]
Accepted name: exo-α-bergamotene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (–)-exo-α-bergamotene + diphosphate
For diagram of reaction click here and mechanism click here.
Glossary: (–)-exo-α-bergamotene = (–)-trans-α-bergamotene = (1S,5S,6R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]hept-2-ene
Other name(s): trans-α-bergamotene synthase; LaBERS (gene name)
Systematic name: (2E,6E)-farnesyl diphosphate lyase (cyclizing, (–)-exo-α-bergamotene-forming)
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2E,6E)-farnesyl diphosphate. As well as (–)-exo-α-bergamotene (74%) there were (E)-nerolidol (10%), (Z)-α-bisabolene (6%), (E)-β-farnesene (5%) and β-sesquiphellandrene (1%).
References:
1. Schnee, C., Kollner, T.G., Held, M., Turlings, T.C., Gershenzon, J. and Degenhardt, J. The products of a single maize sesquiterpene synthase form a volatile defense signal that attracts natural enemies of maize herbivores. Proc. Natl. Acad. Sci. USA 103 (2006) 1129-1134. [PMID: 16418295]
2. Landmann, C., Fink, B., Festner, M., Dregus, M., Engel, K.H. and Schwab, W. Cloning and functional characterization of three terpene synthases from lavender (Lavandula angustifolia). Arch. Biochem. Biophys. 465 (2007) 417-429. [PMID: 17662687]
Accepted name: α-santalene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-α-santalene + diphosphate
For diagram of reaction click here and mechanism click here.
Glossary: (–)-exo-α-bergamotene = (–)-trans-α-bergamotene = (1S,5S,6R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]hept-2-ene
Systematic name: (2E,6E)-farnesyl diphosphate lyase (cyclizing, (+)-α-santalene-forming)
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2E,6E)-farnesyl diphosphate. As well as (+)-α-santalene, (–)-β-santalene and (–)-exo-α-bergamotene are formed with traces of (+)-epi-β-santalene. See EC 4.2.3.83 [(–)-β-santalene synthase], and EC 4.2.3.81 [(–)-exo-α-bergamotene synthase]. cf. EC 4.2.3.50 α-santalene synthase [(2Z,6Z)-farnesyl diphosphate cyclizing]
References:
1. Jones, C.G., Moniodis, J., Zulak, K.G., Scaffidi, A., Plummer, J.A., Ghisalberti, E.L., Barbour, E.L. and Bohlmann, J. Sandalwood fragrance biosynthesis involves sesquiterpene synthases of both the terpene synthase (TPS)-a and TPS-b subfamilies, including santalene synthases. J. Biol. Chem. 286 (2011) 17445-17454. [PMID: 21454632]
Accepted name: β-santalene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (-)-β-santalene + diphosphate
For diagram of reaction click here and mechanism click here.
Glossary: (–)-exo-α-bergamotene = (–)-trans-α-bergamotene = (1S,5S,6R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]hept-2-ene
Systematic name: (2E,6E)-farnesyl diphosphate lyase (cyclizing, (–)-β-santalene-forming)
Comments: The enzyme synthesizes a mixture of sesquiterpenoids from (2E,6E)-farnesyl diphosphate. As well as (–)-β-santalene (+)-α-santalene and (–)-exo-α-bergamotene are formed with traces of (+)-epi-β-santalene. See EC 4.2.3.82 [(+)-α-santalene synthase], and EC 4.2.3.81 [(–)-exo-α-bergamotene synthase].
References:
1. Jones, C.G., Moniodis, J., Zulak, K.G., Scaffidi, A., Plummer, J.A., Ghisalberti, E.L., Barbour, E.L. and Bohlmann, J. Sandalwood fragrance biosynthesis involves sesquiterpene synthases of both the terpene synthase (TPS)-a and TPS-b subfamilies, including santalene synthases. J. Biol. Chem. 286 (2011) 17445-17454. [PMID: 21454632]
Accepted name: pyridoxal 5'-phosphate synthase (glutamine hydrolyzing)
Reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5'-phosphate + 4 H2O + phosphate
Other name(s): PdxST
Systematic name: D-ribose 5-phosphate,D-glyceraldehyde 3-phosphate pyridoxal 5'-phosphate-lyase
Comments: The ammonia is provided by the glutaminase subunit and channeled to the active site of the lyase subunit by a 100 Å tunnel. The enzyme can also use ribulose 5-phosphate and dihydroxyacetone phosphate. The enzyme complex is found in aerobic bacteria, archeae, fungi and plants.
References:
1. Burns, K.E., Xiang, Y., Kinsland, C.L., McLafferty, F.W. and Begley, T.P. Reconstitution and biochemical characterization of a new pyridoxal-5'-phosphate biosynthetic pathway. J. Am. Chem. Soc. 127 (2005) 3682-3683. [PMID: 15771487]
2. Raschle, T., Amrhein, N. and Fitzpatrick, T.B. On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis. J. Biol. Chem. 280 (2005) 32291-32300. [PMID: 16030023]
3. Strohmeier, M., Raschle, T., Mazurkiewicz, J., Rippe, K., Sinning, I., Fitzpatrick, T.B. and Tews, I. Structure of a bacterial pyridoxal 5'-phosphate synthase complex. Proc. Natl. Acad. Sci. USA 103 (2006) 19284-19289. [PMID: 17159152]
4. Raschle, T., Arigoni, D., Brunisholz, R., Rechsteiner, H., Amrhein, N. and Fitzpatrick, T.B. Reaction mechanism of pyridoxal 5'-phosphate synthase. Detection of an enzyme-bound chromophoric intermediate. J. Biol. Chem. 282 (2007) 6098-6105. [PMID: 17189272]
5. Hanes, J.W., Keresztes, I. and Begley, T.P. Trapping of a chromophoric intermediate in the Pdx1-catalyzed biosynthesis of pyridoxal 5'-phosphate. Angew. Chem. Int. Ed. Engl. 47 (2008) 2102-2105. [PMID: 18260082]
6. Hanes, J.W., Burns, K.E., Hilmey, D.G., Chatterjee, A., Dorrestein, P.C. and Begley, T.P. Mechanistic studies on pyridoxal phosphate synthase: the reaction pathway leading to a chromophoric intermediate. J. Am. Chem. Soc. 130 (2008) 3043-3052. [PMID: 18271580]
7. Hanes, J.W., Keresztes, I. and Begley, T.P. 13C NMR snapshots of the complex reaction coordinate of pyridoxal phosphate synthase. Nat. Chem. Biol. 4 (2008) 425-430. [PMID: 18516049]
8. Wallner, S., Neuwirth, M., Flicker, K., Tews, I. and Macheroux, P. Dissection of contributions from invariant amino acids to complex formation and catalysis in the heteromeric pyridoxal 5-phosphate synthase complex from Bacillus subtilis. Biochemistry 48 (2009) 1928-1935. [PMID: 19152323]
Accepted name: N-acetylneuraminate epimerase
Reaction: N-acetyl-α-neuraminate = N-acetyl-β-neuraminate
Other name(s): sialic acid epimerase; N-acetylneuraminate mutarotase; YjhT
Systematic name: N-acetyl-α-neuraminate 2-epimerase
Comments: Sialoglycoconjugates present in vertebrates are linked exclusively by α-linkages and are released in α form during degradation. This enzyme accelerates maturotation to the β form (which also occurs as a slow spontaneous reaction), which is necessary for further metabolism by the bacteria.
References:
1. Severi, E., Müller, A., Potts, J.R., Leech, A., Williamson, D., Wilson, K.S. and Thomas, G.H. Sialic acid mutarotation is catalyzed by the Escherichia coli β-propeller protein YjhT. J. Biol. Chem. 283 (2008) 4841-4849. [PMID: 18063573]
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.
References:
1. Ansmant, I., Motorin, Y., Massenet, S., Grosjean, H. and Branlant, C. Identification and characterization of the tRNA:Ψ 31-synthase (Pus6p) of Saccharomyces cerevisiae. J. Biol. Chem. 276 (2001) 34934-34940. [PMID: 11406626]
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.
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 psi(2819) in 21S mitochondrial ribosomal RNA. Nucleic Acids Res. 28 (2000) 1941-1946. [PMID: 10756195]
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].
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]
Accepted name: lycopene ε-cyclase
Reaction: carotenoid ψ-end group = carotenoid ε-end group
For diagram of reaction click here and mechanism click here.
Other name(s): CrtL-e; LCYe
Systematic name: carotenoid ψ-end group lyase (decyclizing)
Comments: The carotenoid lycopene has the ψ-end group at both ends. When acting on one end, this enzyme forms δ-carotene. When acting on both ends, it forms ε-carotene.
References:
1. Cunningham, F.X., Jr. and Gantt, E. One ring or two? Determination of ring number in carotenoids by lycopene ε-cyclases. Proc. Natl. Acad. Sci. USA 98 (2001) 2905-2910. [PMID: 11226339]
2. Stickforth, P., Steiger, S., Hess, W.R. and Sandmann, G. A novel type of lycopene ε-cyclase in the marine cyanobacterium Prochlorococcus marinus MED4. Arch. Microbiol. 179 (2003) 409-415. [PMID: 12712234]
Accepted name: lycopene β-cyclase
Reaction: carotenoid ψ-end group = carotenoid β-end group
For diagram of reaction click here and mechanism click here.
Other name(s): CrtL; CrtL-b: CrtY
Systematic name: carotenoid β-end group lyase (decyclizing)
Comments: Requires NAD(P)H. Lycopene has a ψ-end group at both ends. When acting on one end, this enzyme forms γ-carotene. When acting on both ends it forms β-carotene. It also acts on neurosporene to give β-zeacarotene. The hydrogen introduced at C-2 originates from water, not from NAD(P)H.
References:
1. Cunningham, F.X., Jr., Chamovitz, D., Misawa, N., Gantt, E. and Hirschberg, J. Cloning and functional expression in Escherichia coli of a cyanobacterial gene for lycopene cyclase, the enzyme that catalyzes the biosynthesis of β-carotene. FEBS Lett. 328 (1993) 130-138. [PMID: 8344419]
2. Cunningham, F.X., Jr., Sun, Z., Chamovitz, D., Hirschberg, J. and Gantt, E. Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942. Plant Cell 6 (1994) 1107-1121. [PMID: 7919981]
3. Hugueney, P., Badillo, A., Chen, H.C., Klein, A., Hirschberg, J., Camara, B. and Kuntz, M. Metabolism of cyclic carotenoids: a model for the alteration of this biosynthetic pathway in Capsicum annuum chromoplasts. Plant J. 8 (1995) 417-424. [PMID: 7550379]
4. Pecker, I., Gabbay, R., Cunningham, F.X., Jr. and Hirschberg, J. Cloning and characterization of the cDNA for lycopene β-cyclase from tomato reveals decrease in its expression during fruit ripening. Plant Mol. Biol. 30 (1996) 807-819. [PMID: 8624411]
5. Hornero-Mendez, D. and Britton, G. Involvement of NADPH in the cyclization reaction of carotenoid biosynthesis. FEBS Lett. 515 (2002) 133-136. [PMID: 11943208]
6. Maresca, J.A., Graham, J.E., Wu, M., Eisen, J.A. and Bryant, D.A. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc. Natl. Acad. Sci. USA 104 (2007) 11784-11789. [PMID: 17606904]