The Enzyme Database

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EC 2.1.1.61     
Accepted name: tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase
Reaction: S-adenosyl-L-methionine + tRNA containing 5-(aminomethyl)-2-thiouridine = S-adenosyl-L-homocysteine + tRNA containing 5-[(methylamino)methyl]-2-thiouridylate
Other name(s): transfer ribonucleate 5-methylaminomethyl-2-thiouridylate 5-methyltransferase; tRNA 5-methylaminomethyl-2-thiouridylate 5′-methyltransferase; S-adenosyl-L-methionine:tRNA (5-methylaminomethyl-2-thio-uridylate)-methyltransferase; tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase
Systematic name: S-adenosyl-L-methionine:tRNA 5-(aminomethyl)-2-thiouridylate N-methyltransferase
Comments: This enzyme specifically adds the terminal methyl group of 5-[(methylamino)methyl]-2-thiouridylate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 39391-17-8
References:
1.  Taya, Y. and Nishimura, S. Biosynthesis of 5-methylaminomethyl-2-thiouridylate. I. Isolation of a new tRNA-methylase specific for 5-methylaminomethyl-2-thiouridylate. Biochem. Biophys. Res. Commun. 51 (1973) 1062–1068. [DOI] [PMID: 4703553]
2.  Taya, Y. and Nishimura, S. In: Salvatore, F., Borek, E., Zappia, V., Williams-Ashman, H.G. and Schlenk, F. (Ed.), The Biochemistry of Adenosylmethionine, Columbia University Press, New York, 1977, p. 251.
3.  Bujnicki, J.M., Oudjama, Y., Roovers, M., Owczarek, S., Caillet, J. and Droogmans, L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA 10 (2004) 1236–1242. [DOI] [PMID: 15247431]
4.  Kim, J. and Almo, S.C. Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC. BMC Struct Biol 13:5 (2013). [DOI] [PMID: 23617613]
[EC 2.1.1.61 created 1982, modified 2012, modified 2021]
 
 
EC 2.4.2.9     
Accepted name: uracil phosphoribosyltransferase
Reaction: UMP + diphosphate = uracil + 5-phospho-α-D-ribose 1-diphosphate
Other name(s): UMP pyrophosphorylase; UPRTase; UMP:pyrophosphate phosphoribosyltransferase; uridine 5′-phosphate pyrophosphorylase; uridine monophosphate pyrophosphorylase; uridylate pyrophosphorylase; uridylic pyrophosphorylase
Systematic name: UMP:diphosphate phospho-α-D-ribosyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9030-24-4
References:
1.  Crawford, I., Kornberg, A. and Simms, E.S. Conversion of uracil and orotate to uridine 5′-phosphate by enzymes in lactobacilli. J. Biol. Chem. 226 (1967) 1093–1101. [PMID: 13438895]
2.  Flaks, J.G. Nucleotide synthesis from 5-phosphoribosylpyrophosphate. Methods Enzymol. 6 (1963) 136–158.
[EC 2.4.2.9 created 1961]
 
 
EC 2.7.4.22     
Accepted name: UMP kinase
Reaction: ATP + UMP = ADP + UDP
Other name(s): uridylate kinase; UMPK; uridine monophosphate kinase; PyrH; UMP-kinase; SmbA
Systematic name: ATP:UMP phosphotransferase
Comments: This enzyme is strictly specific for UMP as substrate and is used by prokaryotes in the de novo synthesis of pyrimidines, in contrast to eukaryotes, which use the dual-specificity enzyme UMP/CMP kinase (EC 2.7.4.14) for the same purpose [2]. This enzyme is the subject of feedback regulation, being inhibited by UTP and activated by GTP [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9036-23-1
References:
1.  Serina, L., Blondin, C., Krin, E., Sismeiro, O., Danchin, A., Sakamoto, H., Gilles, A.M. and Bârzu, O. Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry 34 (1995) 5066–5074. [PMID: 7711027]
2.  Marco-Marín, C., Gil-Ortiz, F. and Rubio, V. The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis. J. Mol. Biol. 352 (2005) 438–454. [DOI] [PMID: 16095620]
[EC 2.7.4.22 created 2006]
 
 
EC 2.8.1.4     
Accepted name: tRNA uracil 4-sulfurtransferase
Reaction: ATP + [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + uracil in tRNA + 2 reduced ferredoxin [iron-sulfur] cluster = AMP + diphosphate + 4-thiouracil in tRNA + [ThiI sulfur-carrier protein]-L-cysteine + 2 oxidized ferredoxin [iron-sulfur] cluster
Other name(s): thiI (gene name); transfer ribonucleate sulfurtransferase (ambiguous); RNA sulfurtransferase (ambiguous); ribonucleate sulfurtransferase (ambiguous); transfer RNA sulfurtransferase (ambiguous); transfer RNA thiolase (ambiguous); L-cysteine:tRNA sulfurtransferase (incorrect); tRNA sulfurtransferase (ambiguous)
Systematic name: [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine:uracil in tRNA sulfurtransferase
Comments: The enzyme, found in bacteria and archaea, is activated by EC 2.8.1.7, cysteine desulfurase, which transfers a sulfur atom to an internal L-cysteine residue, forming a cysteine persulfide. The activated enzyme then transfers the sulfur to a uridine in a tRNA chain in a reaction that requires ATP. The enzyme from the bacterium Escherichia coli forms 4-thiouridine only at position 8 of tRNA. The enzyme also participates in the biosynthesis of the thiazole moiety of thiamine, but different domains are involved in the two processes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9055-57-6
References:
1.  Abrell, J.W., Kaufman, E.E. and Lipsett, M.N. The biosynthesis of 4-thiouridylate. Separation and purification of two enzymes in the transfer ribonucleic acid-sulfurtransferase system. J. Biol. Chem. 246 (1971) 294–301. [PMID: 5541999]
2.  Hayward, R.S. and Weiss, S.B. RNA thiolase: the enzymatic transfer of sulfur from cysteine to sRNA in Escherichia coli extracts. Proc. Natl. Acad. Sci. USA 55 (1966) 1161–1168. [DOI] [PMID: 5334200]
3.  Lipsett, M.N. and Peterkofsky, A. Enzymatic thiolation of E. coli sRNA. Proc. Natl. Acad. Sci. USA 55 (1966) 1169–1174. [DOI] [PMID: 5334201]
4.  Wong, T., Weiss, S.B., Eliceiri, G.L. and Bryant, J. Ribonucleic acid sulfurtransferase from Bacillus subtilis W168. Sulfuration with β-mercaptopyruvate and properties of the enzyme system. Biochemistry 9 (1970) 2376–2386. [PMID: 4987417]
5.  Kambampati, R. and Lauhon, C.T. Evidence for the transfer of sulfane sulfur from IscS to ThiI during the in vitro biosynthesis of 4-thiouridine in Escherichia coli tRNA. J. Biol. Chem. 275 (2000) 10727–10730. [DOI] [PMID: 10753862]
6.  Mueller, E.G., Palenchar, P.M. and Buck, C.J. The role of the cysteine residues of ThiI in the generation of 4-thiouridine in tRNA. J. Biol. Chem. 276 (2001) 33588–33595. [DOI] [PMID: 11443125]
7.  Lauhon, C.T., Erwin, W.M. and Ton, G.N. Substrate specificity for 4-thiouridine modification in Escherichia coli. J. Biol. Chem. 279 (2004) 23022–23029. [DOI] [PMID: 15037613]
8.  Neumann, P., Lakomek, K., Naumann, P.T., Erwin, W.M., Lauhon, C.T. and Ficner, R. Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification. Nucleic Acids Res. 42 (2014) 6673–6685. [DOI] [PMID: 24705700]
9.  Liu, Y., Vinyard, D.J., Reesbeck, M.E., Suzuki, T., Manakongtreecheep, K., Holland, P.L., Brudvig, G.W. and Soll, D. A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes. Proc. Natl. Acad. Sci. USA 113 (2016) 12703–12708. [DOI] [PMID: 27791189]
[EC 2.8.1.4 created 1984, modified 2017]
 
 
EC 3.1.26.9     
Accepted name: ribonuclease [poly-(U)-specific]
Reaction: Endonucleolytic cleavage of poly(U) to fragments terminated by 3′-hydroxy and 5′-phosphate groups
Other name(s): ribonuclease (uracil-specific); uracil-specific endoribonuclease; uracil-specific RNase
Comments: Forms oligonucleotides with chain lengths of 6 to 12.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bachmann, M., Trautmann, F., Messer, R., Zahn, R.K., Meyer zum Büschenfelde, K.H. and Müller, W.E.G. Association of a polyuridylate-specific endoribonuclease with small nuclear ribonucleo-proteins which had been isolated by affinity chromatography using antibodies from a patient with systemic lupus erythematosus. Eur. J. Biochem. 136 (1983) 447–451. [DOI] [PMID: 6227485]
[EC 3.1.26.9 created 1986]
 
 
EC 3.1.27.8     
Accepted name: ribonuclease V
Reaction: Hydrolysis of poly(A), forming oligoribonucleotides and ultimately 3′-AMP
Other name(s): endoribonuclease V
Comments: Also hydrolyses poly(U).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 74505-36-5
References:
1.  Schröder, H.C., Dose, K., Zahn, R.K. and Müller, E.G. Isolation and characterization of the novel polyadenylate- and polyuridylate-degrading acid endoribonuclease V from calf thymus. J. Biol. Chem. 255 (1980) 5108–5112. [PMID: 6246098]
[EC 3.1.27.8 created 1984]
 
 
EC 3.6.1.23     
Accepted name: dUTP diphosphatase
Reaction: dUTP + H2O = dUMP + diphosphate
Other name(s): DUT (gene name); deoxyuridine-triphosphatase; dUTPase; dUTP pyrophosphatase; desoxyuridine 5′-triphosphate nucleotidohydrolase; desoxyuridine 5′-triphosphatase
Systematic name: dUTP nucleotidohydrolase
Comments: The enzyme catalyses the Mg2+-dependent hydrolysis of dUTP to dUMP, providing the substrate for EC 2.1.1.45, thymidylate synthase, leading to production of thymidine nucleotides. By reducing the effective ratio of dUTP to TTP, the enzyme also reduces the possibility of dUTP incorporation into DNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37289-34-2
References:
1.  Greenberg, G.R. and Somerville, R.L. Deoxyuridylate kinase activity and deoxyuridinetriphosphatase in Escherichia coli. Proc. Natl. Acad. Sci. USA 48 (1962) 247–257. [PMID: 13901467]
2.  Bertani, L.E., Häggmark, A. and Reichard, P. Enzymatic synthesis of deoxyribonucleotides. II. Formation and interconversion of deoxyuridine phosphates. J. Biol. Chem. 238 (1963) 3407–3413. [PMID: 14085395]
3.  Grindey, G.B. and Nichol, C.A. Mammalian deoxyuridine 5′-triphosphate pyrophosphatase. Biochim. Biophys. Acta 240 (1971) 180–183. [DOI] [PMID: 5105331]
4.  Shlomai, J. and Kornberg, A. Deoxyuridine triphosphatase of Escherichia coli. Purification, properties, and use as a reagent to reduce uracil incorporation into DNA. J. Biol. Chem. 253 (1978) 3305–3312. [PMID: 346589]
5.  Giroir, L.E. and Deutsch, W.A. Drosophila deoxyuridine triphosphatase. Purification and characterization. J. Biol. Chem. 262 (1987) 130–134. [PMID: 3025197]
6.  Cedergren-Zeppezauer, E.S., Larsson, G., Nyman, P.O., Dauter, Z. and Wilson, K.S. Crystal structure of a dUTPase. Nature 355 (1992) 740–743. [DOI] [PMID: 1311056]
7.  Ladner, R.D., McNulty, D.E., Carr, S.A., Roberts, G.D. and Caradonna, S.J. Characterization of distinct nuclear and mitochondrial forms of human deoxyuridine triphosphate nucleotidohydrolase. J. Biol. Chem. 271 (1996) 7745–7751. [DOI] [PMID: 8631816]
8.  Bajaj, M. and Moriyama, H. Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63 (2007) 409–411. [DOI] [PMID: 17565183]
9.  Varga, B., Barabas, O., Kovari, J., Toth, J., Hunyadi-Gulyas, E., Klement, E., Medzihradszky, K.F., Tolgyesi, F., Fidy, J. and Vertessy, B.G. Active site closure facilitates juxtaposition of reactant atoms for initiation of catalysis by human dUTPase. FEBS Lett. 581 (2007) 4783–4788. [DOI] [PMID: 17880943]
[EC 3.6.1.23 created 1972]
 
 
EC 4.2.1.70     
Accepted name: pseudouridylate synthase
Reaction: uracil + D-ribose 5-phosphate = pseudouridine 5′-phosphate + H2O
Other name(s): pseudouridylic acid synthetase; pseudouridine monophosphate synthetase; 5-ribosyluracil 5-phosphate synthetase; pseudouridylate synthetase; upsilonUMP synthetase; uracil hydro-lyase (adding D-ribose 5-phosphate); YeiN; pseudouridine-5′-phosphate glycosidase
Systematic name: uracil hydro-lyase (adding D-ribose 5-phosphate; pseudouridine-5′-phosphate-forming)
Comments: The reaction it readily reversible. While the enzymes from Tetrahymena pyriformis and Agrobacterium tumefaciens produce pseudouridine 5′-phosphate the enzyme from Escherichia coli functions as a pseudouridine-5′-phosphate glycosidase in vivo [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-35-2
References:
1.  Heinrikson, R.L. and Goldwasser, E. Studies on the biosynthesis of 5-ribosyluracil 5′-monophosphate in Tetrahymena pyriformis. J. Biol. Chem. 239 (1964) 1177–1187. [PMID: 14165924]
2.  Matsushita, T. and Davis, F.F. Studies on pseudouridylic acid synthetase from various sources. Biochim. Biophys. Acta 238 (1971) 165–173. [DOI] [PMID: 4936431]
3.  Rensen, J.F., Matsushita, T., Chirikjian, J.G. and Davis, F.F. Enzymatic synthesis of deoxypseudouridylic acid and a study of certain of its properties. Biochim. Biophys. Acta 281 (1972) 481–487. [DOI] [PMID: 4569284]
4.  Suzuki, T. and Hochater, R.M. On the biosynthesis of pseudouridine and of pseudouridylic acid in Agrobacterium tumefaciens. Can. J. Biochem. 44 (1966) 259–272. [PMID: 5942965]
5.  Preumont, A., Snoussi, K., Stroobant, V., Collet, J.F. and Van Schaftingen, E. Molecular identification of pseudouridine-metabolizing enzymes. J. Biol. Chem. 283 (2008) 25238–25246. [DOI] [PMID: 18591240]
[EC 4.2.1.70 created 1978]
 
 
EC 4.6.1.26     
Accepted name: uridylate cyclase
Reaction: UTP = 3′,5′-cyclic UMP + diphosphate
Glossary: 3′,5′-cyclic UMP = cUMP
uridylate = CMP
Other name(s): pycC (gene name) (ambiguous)
Systematic name: UTP diphosphate-lyase (cyclizing; 3′,5′-cyclic-UMP-forming)
Comments: The enzyme, found in bacteria and archaea, forms cUMP, which functions as a second messenger in bacterial immunity against viruses. The enzyme is synthesized following phage infection and activates immune effectors that execute an antiviral response.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB
References:
1.  Tal, N., Morehouse, B.R., Millman, A., Stokar-Avihail, A., Avraham, C., Fedorenko, T., Yirmiya, E., Herbst, E., Brandis, A., Mehlman, T., Oppenheimer-Shaanan, Y., Keszei, A.FA., Shao, S., Amitai, G., Kranzusch, P.J. and Sorek, R. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell 184 (2021) 5728–5739.e16. [DOI] [PMID: 34644530]
[EC 4.6.1.26 created 2022]
 
 
EC 5.4.99.12     
Accepted name: tRNA pseudouridine38-40 synthase
Reaction: tRNA uridine38-40 = tRNA pseudouridine38-40
Other name(s): TruA; tRNA pseudouridine synthase I; PSUI; hisT (gene name)
Systematic name: tRNA-uridine38-40 uracil mutase
Comments: The uridylate residues at positions 38, 39 and 40 of nearly all tRNAs are isomerized to pseudouridine. TruA specifically modifies uridines at positions 38, 39, and/or 40 in the anticodon stem loop of tRNAs with highly divergent sequences and structures [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 61506-89-6
References:
1.  Hur, S. and Stroud, R.M. How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA. Mol. Cell 26 (2007) 189–203. [DOI] [PMID: 17466622]
2.  Huang, L., Pookanjanatavip, M., Gu, X. and Santi, D.V. A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst. Biochemistry 37 (1998) 344–351. [DOI] [PMID: 9425056]
3.  Kammen, H.O., Marvel, C.C., Hardy, L. and Penhoet, E.E. Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. J. Biol. Chem. 263 (1988) 2255–2263. [PMID: 3276686]
4.  Turnbough, C.L., Jr., Neill, R.J., Landsberg, R. and Ames, B.N. Pseudouridylation of tRNAs and its role in regulation in Salmonella typhimurium. J. Biol. Chem. 254 (1979) 5111–5119. [PMID: 376505]
5.  Zhao, X. and Horne, D.A. The role of cysteine residues in the rearrangement of uridine to pseudouridine catalyzed by pseudouridine synthase I. J. Biol. Chem. 272 (1997) 1950–1955. [DOI] [PMID: 8999885]
6.  Foster, P.G., Huang, L., Santi, D.V. and Stroud, R.M. The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I. Nat. Struct. Biol. 7 (2000) 23–27. [DOI] [PMID: 10625422]
7.  Dong, X., Bessho, Y., Shibata, R., Nishimoto, M., Shirouzu, M., Kuramitsu, S. and Yokoyama, S. Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8. RNA Biol. 3 (2006) 115–122. [PMID: 17114947]
8.  Arena, F., Ciliberto, G., Ciampi, S. and Cortese, R. Purification of pseudouridylate synthetase I from Salmonella typhimurium. Nucleic Acids Res. 5 (1978) 4523–4536. [DOI] [PMID: 370771]
[EC 5.4.99.12 created 1990, modified 2011]
 
 


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