The Enzyme Database

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EC 2.1.1.54     
Accepted name: deoxycytidylate C-methyltransferase
Reaction: 5,10-methylenetetrahydrofolate + dCMP = dihydrofolate + deoxy-5-methylcytidylate
Other name(s): deoxycytidylate methyltransferase; dCMP methyltransferase
Systematic name: 5,10-methylenetetrahydrofolate:dCMP C-methyltransferase
Comments: dCMP is methylated by formaldehyde in the presence of tetrahydrofolate. CMP, dCTP and CTP can act as acceptors, but more slowly.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 61970-01-2
References:
1.  Kuo, T.-T. and Tu, J. Enzymatic synthesis of deoxy-5-methyl-cytidylic acid replacing deoxycytidylic acid in Xanthomonas oryzae phage Xp12DNA. Nature 263 (1976) 615. [PMID: 980110]
[EC 2.1.1.54 created 1978]
 
 
EC 2.1.2.8     
Accepted name: deoxycytidylate 5-hydroxymethyltransferase
Reaction: 5,10-methylenetetrahydrofolate + H2O + deoxycytidylate = tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
Other name(s): dCMP hydroxymethylase; d-cytidine 5′-monophosphate hydroxymethylase; deoxyCMP hydroxymethylase; deoxycytidylate hydroxymethylase; deoxycytidylic hydroxymethylase
Systematic name: 5,10-methylenetetrahydrofolate:deoxycytidylate 5-hydroxymethyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9012-68-4
References:
1.  Mathews, C.K., Brown, F. and Cohen, S.S. Virus-induced acquisition of metabolic function. VII. Biosynthesis de novo of deoxycytidylate hydroxymethylase. J. Biol. Chem. 239 (1964) 2957–2963. [PMID: 14217882]
[EC 2.1.2.8 created 1972]
 
 
EC 2.7.1.74     
Accepted name: deoxycytidine kinase
Reaction: NTP + deoxycytidine = NDP + dCMP
Other name(s): deoxycytidine kinase (phosphorylating); 2′-deoxycytidine kinase; Ara-C kinase; arabinofuranosylcytosine kinase; deoxycytidine-cytidine kinase
Systematic name: NTP:deoxycytidine 5′-phosphotransferase
Comments: Cytosine arabinoside can act as acceptor; all natural nucleoside triphosphates (except dCTP) can act as donors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9039-45-6
References:
1.  Durham, J.P. and Ives, D.H. Deoxycytidine kinase. II. Purification and general properties of the calf thymus enzyme. J. Biol. Chem. 245 (1970) 2276–2284. [PMID: 5442271]
2.  Ives, D.H. and Durham, J.P. Deoxycytidine kinase. 3. Kinetics and allosteric regulation of the calf thymus enzyme. J. Biol. Chem. 245 (1970) 2285–2294. [PMID: 5462538]
3.  Kessel, D. Properties of deoxycytidine kinase partially purified from L1210 cells. J. Biol. Chem. 243 (1968) 4739–4744. [PMID: 5687717]
4.  Momparler, R.L. and Fischer, G.A. Mammalian deoxynucleoside kinase. I. Deoxycytidine kinase: purification, properties, and kinetic studies with cytosine arabinoside. J. Biol. Chem. 243 (1968) 4298–4304. [PMID: 5684726]
[EC 2.7.1.74 created 1972]
 
 
EC 2.7.4.14     
Accepted name: UMP/CMP kinase
Reaction: (1) ATP + (d)CMP = ADP + (d)CDP
(2) ATP + UMP = ADP + UDP
Other name(s): cytidylate kinase (misleading); deoxycytidylate kinase (misleading); CTP:CMP phosphotransferase (misleading); dCMP kinase (misleading); deoxycytidine monophosphokinase (misleading); UMP-CMP kinase; ATP:UMP-CMP phosphotransferase; pyrimidine nucleoside monophosphate kinase; uridine monophosphate-cytidine monophosphate phosphotransferase
Systematic name: ATP:(d)CMP/UMP phosphotransferase
Comments: This eukaryotic enzyme is a bifunctional enzyme that catalyses the phosphorylation of both CMP and UMP with similar efficiency. dCMP can also act as acceptor. Different from the monofunctional prokaryotic enzymes EC 2.7.4.25, (d)CMP kinase and EC 2.7.4.22, UMP kinase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 37278-21-0
References:
1.  Hurwitz, J. The enzymatic incorporation of ribonucleotides into polydeoxynucleotide material. J. Biol. Chem. 234 (1959) 2351–2358. [PMID: 14405566]
2.  Ruffner, B.W., Jr. and Anderson, E.P. Adenosine triphosphate: uridine monophosphate-cytidine monophosphate phosphotransferase from Tetrahymena pyriformis. J. Biol. Chem. 244 (1969) 5994–6002. [PMID: 5350952]
3.  Scheffzek, K., Kliche, W., Wiesmuller, L. and Reinstein, J. Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5′-adenosyl) P5-(5′-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 Å: implications for water-mediated specificity. Biochemistry 35 (1996) 9716–9727. [DOI] [PMID: 8703943]
4.  Zhou, L., Lacroute, F. and Thornburg, R. Cloning, expression in Escherichia coli, and characterization of Arabidopsis thaliana UMP/CMP kinase. Plant Physiol. 117 (1998) 245–254. [PMID: 9576794]
5.  Van Rompay, A.R., Johansson, M. and Karlsson, A. Phosphorylation of deoxycytidine analog monophosphates by UMP-CMP kinase: molecular characterization of the human enzyme. Mol. Pharmacol. 56 (1999) 562–569. [PMID: 10462544]
[EC 2.7.4.14 created 1961 as EC 2.7.4.5, transferred 1972 to EC 2.7.4.14, modified 1980, modified 2011]
 
 
EC 2.7.4.19     
Accepted name: 5-methyldeoxycytidine-5′-phosphate kinase
Reaction: ATP + 5-methyldeoxycytidine 5′-phosphate = ADP + 5-methyldeoxycytidine diphosphate
Systematic name: ATP:5-methyldeoxycytidine-5′-phosphate phosphotransferase
Comments: The enzyme, from phage XP-12-infected Xanthomonas oryzae, converts m5dCMP into m5dCDP and then into m5dCTP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 81032-53-3
References:
1.  Wang, R.Y.-H., Huang, L.-H. and Ehrlich, M. A bacteriophage-induced 5-methyldeoxycytidine 5′-monophosphate kinase. Biochim. Biophys. Acta 696 (1982) 31–36. [DOI] [PMID: 7082669]
[EC 2.7.4.19 created 1984]
 
 
EC 2.7.4.25     
Accepted name: (d)CMP kinase
Reaction: ATP + (d)CMP = ADP + (d)CDP
Glossary: CMP = cytidine monophosphate
dCMP = deoxycytidine monophosphate
CDP = cytidine diphosphate
dCDP = deoxycytidine diphosphate
UMP = uridine monophosphate
UDP = uridine diphosphate
Other name(s): cmk (gene name); prokaryotic cytidylate kinase; deoxycytidylate kinase (misleading); dCMP kinase (misleading); deoxycytidine monophosphokinase (misleading)
Systematic name: ATP:(d)CMP phosphotransferase
Comments: The prokaryotic cytidine monophosphate kinase specifically phosphorylates CMP (or dCMP), using ATP as the preferred phosphoryl donor. Unlike EC 2.7.4.14, a eukaryotic enzyme that phosphorylates UMP and CMP with similar efficiency, the prokaryotic enzyme phosphorylates UMP with very low rates, and this function is catalysed in prokaryotes by EC 2.7.4.22, UMP kinase. The enzyme phosphorylates dCMP nearly as well as it does CMP [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bertrand, T., Briozzo, P., Assairi, L., Ofiteru, A., Bucurenci, N., Munier-Lehmann, H., Golinelli-Pimpaneau, B., Barzu, O. and Gilles, A.M. Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme. J. Mol. Biol. 315 (2002) 1099–1110. [DOI] [PMID: 11827479]
2.  Thum, C., Schneider, C.Z., Palma, M.S., Santos, D.S. and Basso, L.A. The Rv1712 Locus from Mycobacterium tuberculosis H37Rv codes for a functional CMP kinase that preferentially phosphorylates dCMP. J. Bacteriol. 191 (2009) 2884–2887. [DOI] [PMID: 19181797]
[EC 2.7.4.25 created 2011]
 
 
EC 3.1.3.35     
Accepted name: thymidylate 5′-phosphatase
Reaction: thymidylate + H2O = thymidine + phosphate
Other name(s): thymidylate 5′-nucleotidase; deoxythymidylate 5′-nucleotidase; thymidylate nucleotidase; deoxythymidylic 5′-nucleotidase; deoxythymidylate phosphohydrolase; dTMPase
Systematic name: thymidylate 5′-phosphohydrolase
Comments: Acts on 5-methyl-dCMP and on TMP, but more slowly than on dTMP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9026-80-6
References:
1.  Aposhian, H.V. and Tremblay, G.Y. Deoxythymidylate 5′-nucleotidase. Purification and properties of an enzyme found after infection of Bacillus subtilis with phage SP5C. J. Biol. Chem. 241 (1966) 5095–5101. [PMID: 4958986]
[EC 3.1.3.35 created 1972]
 
 
EC 3.2.2.10     
Accepted name: pyrimidine-5′-nucleotide nucleosidase
Reaction: a pyrimidine 5′-nucleotide + H2O = D-ribose 5-phosphate + a pyrimidine base
Other name(s): pyrimidine nucleotide N-ribosidase; Pyr5N
Systematic name: pyrimidine-5′-nucleotide phosphoribo(deoxyribo)hydrolase
Comments: Also acts on dUMP, dTMP and dCMP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9023-31-8
References:
1.  Imada, A. Degradation of pyrimidine nucleotides by enzyme systems of Streptomyces. II. Pyrimidine 5′-nucleotide phosphoribo(deoxyribo) hydrolase of Streptomyces virginiae. J. Gen. Appl. Microbiol. 13 (1967) 267–278.
2.  Imada, A., Kuno, M. and Igarasi, S. Degradation of pyrimidine nucleotides by enzyme systems of Streptomyces. I. Ribose-5-phosphate formation from pyrimidine nucleotides. J. Gen. Appl. Microbiol. 13 (1967) 255–265.
[EC 3.2.2.10 created 1972]
 
 
EC 3.5.4.12     
Accepted name: dCMP deaminase
Reaction: dCMP + H2O = dUMP + NH3
Other name(s): deoxycytidylate deaminase; deoxy-CMP-deaminase; deoxycytidylate aminohydrolase; deoxycytidine monophosphate deaminase; deoxycytidine-5′-phosphate deaminase; deoxycytidine-5′-monophosphate aminohydrolase
Systematic name: dCMP aminohydrolase
Comments: Also acts on some 5-substituted dCMPs.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9026-92-0
References:
1.  Scarano, E. The enzymatic deamination of 6-aminopyrimidine deoxyribonucleotides. I. The enzymatic deamination of deoxycytidine 5′-phosphate and of 5-methyldeoxycytidine 5-methyldeoxycytidine 5′-phosphate. J. Biol. Chem. 235 (1960) 706–713. [PMID: 14442222]
2.  Scarano, E., Bonaduce, L. and de Petrocellis, B. The enzymatic deamination of 6-aminopyrimidine deoxyribonucleotides. II. Purification and properties of a 6-aminopyrimidine deoxyribonucleoside 5′-phosphate deaminase from unfertilized eggs of sea urchin. J. Biol. Chem. 235 (1960) 3556–3561. [PMID: 13747062]
3.  Sergott, R.C., Debeer, L.J. and Bessman, M.J. On the regulation of a bacterial deoxycytidylate deaminase. J. Biol. Chem. 246 (1971) 7755–7758. [PMID: 5002683]
[EC 3.5.4.12 created 1965]
 
 
EC 3.5.4.30     
Accepted name: dCTP deaminase (dUMP-forming)
Reaction: dCTP + 2 H2O = dUMP + diphosphate + NH3
Systematic name: dCTP aminohydrolase (dUMP-forming)
Comments: Requires Mg2+. Is highly specific for dCTP as substrate as dCMP, CTP, CDP, CMP, cytosine or deoxycytosine are not deaminated. While most bacteria require two enzymes to form dUMP from dCTP (EC 3.5.4.13, dCTP deaminase and EC 3.6.1.23, dUTP diphosphatase), the archaeon Methanocaldococcus jannaschii uses a single enzyme to carry out both functions. This enzyme can also act as a dUTP diphosphatase, but more slowly.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Li, H., Xu, H., Graham, D.E. and White, R.H. The Methanococcus jannaschii dCTP deaminase is a bifunctional deaminase and diphosphatase. J. Biol. Chem. 278 (2003) 11100–11106. [DOI] [PMID: 12538648]
[EC 3.5.4.30 created 2003]
 
 
EC 3.6.1.12     
Accepted name: dCTP diphosphatase
Reaction: dCTP + H2O = dCMP + diphosphate
Other name(s): DCTPP1 (gene name); deoxycytidine-triphosphatase; dCTPase; dCTP pyrophosphatase; deoxycytidine triphosphatase; deoxy-CTPase
Systematic name: dCTP nucleotidohydrolase
Comments: The mammalian enzyme also displays weak activity against dTTP and dATP, but none against dGTP. Activity is highest with analogs including 5-iodo-dCTP and 5-methyl-dCTP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9024-87-7
References:
1.  Zimmerman, S.B. and Kornberg, A. Deoxycytidine di- and triphosphate cleavage by an enzyme formed in bacteriophage-infected Escherichia coli. J. Biol. Chem. 236 (1961) 1480–1486. [PMID: 13788541]
2.  Moroz, O.V., Murzin, A.G., Makarova, K.S., Koonin, E.V., Wilson, K.S. and Galperin, M.Y. Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-α NTP pyrophosphohydrolases with potential "house-cleaning" functions. J. Mol. Biol. 347 (2005) 243–255. [DOI] [PMID: 15740738]
3.  Wu, B., Liu, Y., Zhao, Q., Liao, S., Zhang, J., Bartlam, M., Chen, W. and Rao, Z. Crystal structure of RS21-C6, involved in nucleoside triphosphate pyrophosphohydrolysis. J. Mol. Biol. 367 (2007) 1405–1412. [DOI] [PMID: 17320107]
4.  Nonaka, M., Tsuchimoto, D., Sakumi, K. and Nakabeppu, Y. Mouse RS21-C6 is a mammalian 2′-deoxycytidine 5′-triphosphate pyrophosphohydrolase that prefers 5-iodocytosine. FEBS J. 276 (2009) 1654–1666. [DOI] [PMID: 19220460]
5.  Requena, C.E., Perez-Moreno, G., Ruiz-Perez, L.M., Vidal, A.E. and Gonzalez-Pacanowska, D. The NTP pyrophosphatase DCTPP1 contributes to the homoeostasis and cleansing of the dNTP pool in human cells. Biochem. J. 459 (2014) 171–180. [DOI] [PMID: 24467396]
[EC 3.6.1.12 created 1965]
 
 
EC 3.6.1.65     
Accepted name: (d)CTP diphosphatase
Reaction: (1) CTP + H2O = CMP + diphosphate
(2) dCTP + H2O = dCMP + diphosphate
Other name(s): (d)CTP pyrophosphohydrolase; (d)CTP diphosphohydrolase; nudG (gene name)
Systematic name: (deoxy)cytidine 5′-triphosphate diphosphohydrolase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is specific for the pyrimidine nucleotides CTP and dCTP. It also acts on 5-methyl-dCTP, 5-hydroxy-dCTP and 8-hydroxy-dGTP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  O'Handley, S.F., Dunn, C.A. and Bessman, M.J. Orf135 from Escherichia coli is a Nudix hydrolase specific for CTP, dCTP, and 5-methyl-dCTP. J. Biol. Chem. 276 (2001) 5421–5426. [DOI] [PMID: 11053429]
2.  Fujikawa, K. and Kasai, H. The oxidized pyrimidine ribonucleotide, 5-hydroxy-CTP, is hydrolyzed efficiently by the Escherichia coli recombinant Orf135 protein. DNA Repair (Amst.) 1 (2002) 571–576. [DOI] [PMID: 12509230]
3.  Kamiya, H., Iida, E. and Harashima, H. Important amino acids in the phosphohydrolase module of Escherichia coli Orf135. Biochem. Biophys. Res. Commun. 323 (2004) 1063–1068. [DOI] [PMID: 15381107]
4.  Iida, E., Satou, K., Mishima, M., Kojima, C., Harashima, H. and Kamiya, H. Amino acid residues involved in substrate recognition of the Escherichia coli Orf135 protein. Biochemistry 44 (2005) 5683–5689. [DOI] [PMID: 15823026]
[EC 3.6.1.65 created 2013]
 
 


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