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Information on EC 2.7.4.25 - (d)CMP kinase and Organism(s) Escherichia coli and UniProt Accession P0A6I0

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IUBMB 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 .
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This record set is specific for:
Escherichia coli
UNIPROT: P0A6I0
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Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
p25 protein, dcmp kinase, bacterial cytidylate kinase, deoxycytidine monophosphate kinase, sp1603, deoxycytidine monophosphokinase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
cytidylate kinase
-
UMP-CMP kinase
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dCMP kinase
-
-
-
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deoxycytidine monophosphokinase
-
-
-
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deoxycytidylate kinase
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-
-
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prokaryotic cytidylate kinase
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
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PATHWAY SOURCE
PATHWAYS
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-, -
SYSTEMATIC NAME
IUBMB Comments
ATP:(d)CMP phosphotransferase
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].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + CMP
ADP + CDP
show the reaction diagram
ATP + dCMP
ADP + dCDP
show the reaction diagram
ATP + UMP
ADP + UDP
show the reaction diagram
ATP + 2',3'-dideoxy-CMP
ADP + ?
show the reaction diagram
2’,3’-dideoxy-CMP is a poor substrate
-
-
?
ATP + ara-CMP
ADP + ara-CDP
show the reaction diagram
ATP + CMP
ADP + CDP
show the reaction diagram
ATP + dCMP
ADP + dCDP
show the reaction diagram
ATP + dGMP
ADP + dGDP
show the reaction diagram
-
-
-
-
?
ATP + UMP
ADP + UDP
show the reaction diagram
dATP + CMP
dADP + CDP
show the reaction diagram
-
-
-
-
?
GTP + CMP
GDP + CDP
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + CMP
ADP + CDP
show the reaction diagram
-
-
-
r
ATP + dCMP
ADP + dCDP
show the reaction diagram
-
-
-
r
ATP + CMP
ADP + CDP
show the reaction diagram
-
-
-
?
ATP + dCMP
ADP + dCDP
show the reaction diagram
Escherichia coli CMPK phosphorylates dCMP nearly as well as it does CMP
-
-
?
additional information
?
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bacterial CMP kinases are specific for CMP and dCMP, whereas the related eukaryotic NMP kinase phosphorylates CMP and UMP with similar efficiency. Bacterial CMP kinase has a narrower NMP-binding pocket and a hydrogen-bonding network involving the pyrimidine moiety specific for the cytosine nucleobase compared to eukaryotic UMP?CMP kinases
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
required for activity
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.035 - 20.2
CMP
0.055 - 7.3
dCMP
0.93 - 11.3
UMP
0.15 - 0.65
2',3'-dideoxy-CMP
0.47 - 1
ara-CMP
0.36
araCMP
0.038
ATP
-
pH 7.4, reaction with CMP
0.035 - 0.47
CMP
0.087
dATP
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pH 7.4, reaction with CMP
0.094 - 0.24
dCMP
0.094
dGMP
-
reaction with ATP
0.64
GTP
-
reaction with CMP
0.93
UMP
additional information
additional information
kinetics and substrate specificities of wild-type and mutant enzymes, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
103
CMP
wild-type enzyme
108
dCMP
wild-type enzyme
0.82
UMP
wild-type enzyme
0.0083 - 0.65
2',3'-dideoxy-CMP
0.085 - 56
ara-CMP
0.08 - 103
CMP
0.071 - 109
dCMP
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
of the R188M mutant alone or with dCMP
purified recombinant mutant R188M free or in complex with CMP, X-ray diffraction structure determination and analysis at 1.9 A and 2.8 A resolution, respectively
enzyme in complex with CDP
-
hanging drop vapor diffusion technique
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in complex with substrates CMP, dCMP, ara-CMP and 2’,3’-dideoxy-CMP, hanging drop vapor diffusion method, using ammonium sulfate in a 50 mM Tris-HCl buffer (pH 7.4), at 20°C
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D132A
D132H
D132N
D132S
R110M
R188M
D185A
the mutant shows severely decreased CMP and dCMP phosphoryation activity compared to the wild type enzyme
R181M
the mutant shows severely decreased CMP and dCMP phosphoryation activity compared to the wild type enzyme
S101A
the mutation reduces CMP phosphorylation only moderately, but dramatically reduces dCMP phosphorylation
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
43
mutant D132A
45
mutant R110M
47
mutant D132N
48
mutant D132S, mutant D132H
51
mutant R188M
52
wild type, mutant S36A
48
-
midpoint denaturation temperature in absence of nucleotide substrates or in presence of ATP
49
-
midpoint denaturation temperature in presence of CMP
52
the melting temperature of the wild type enzyme is at 52°C
additional information
thermal stability of CMP kinase genetic variants, overview
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
four key amino acids interacting with the pyrimidine ring of CMP, Ser36, Asp132, Arg110 and Arg188, contribute to the stability, catalysis and substrate specificity of Escherichia coli CMP kinase
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
of the recombinant proteins
Ni-NTA column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of wild-type and mutant enzymes
overexpression in Escherichia coli
overexpression in Escherichia coli to produce CTP
expressed in Escherichia coli BL21(DE3) cells
hanging-drop method in 50 mM Tris-HCl buffer, pH 7.4, 20°C, with ammonium sulfate as a precipitant
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
CMP kinase and actetate kinase in a whole cell-biocatalysis to obtain CTP
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Li de La Sierra, I.M.; Gallay, J.; Vincent, M.; Bertrand, T.; Briozzo, P.; Barzu, O.; Gilles, A.M.
Substrate-induced fit of the ATP binding site of cytidine monophosphate kinase from Escherichia coli: time-resolved fluorescence of 3'-anthraniloyl-2'-deoxy-ADP and molecular modeling
Biochemistry
39
15870-15878
2000
Escherichia coli (P0A6I0)
Manually annotated by BRENDA team
Bucurenci, N.; Sakamoto, H.; Briozzo, P.; Palibroda, N.; Serina, L.; Sarfati, R.S.; Labesse, G.; Briand, G.; Danchin, A.; Barzu, O.; Gilles, A.M.
CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases
J. Biol. Chem.
271
2856-2862
1996
Escherichia coli, Escherichia coli K-12 (P0A6I0)
Manually annotated by BRENDA team
Schultz, C.P.; Ylisastigui-Pons, L.; Serina, L.; Sakamoto, H.; Mantsch, H.H.; Neuhard, J.; Barzu, O.; Gilles, A.M.
Structural and catalytic properties of CMP kinase from Bacillus subtilis: a comparative analysis with the homologous enzyme from Escherichia coli
Arch. Biochem. Biophys.
340
144-153
1997
Bacillus subtilis, Escherichia coli
Manually annotated by BRENDA team
Briozzo, P.; Golinelli-Pimpaneau, B.; Gilles, A.M.; Gaucher, J.F.; Burlacu-Miron, S.; Sakamoto, H.; Janin, J.; Barzu, O.
Structures of Escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity
Structure
6
1517-1527
1998
Escherichia coli
Manually annotated by BRENDA team
Lee, S.; Kim, B.
Recombinant Escherichia coli-catalyzed production of cytidine 5-triphosphate from cytidine 5-monophosphate
J. Ind. Eng. Chem.
12
757-761
2006
Escherichia coli (P0A6I0)
-
Manually annotated by BRENDA team
Alexandre, J.A.; Roy, B.; Topalis, D.; Pochet, S.; Perigaud, C.; Deville-Bonne, D.
Enantioselectivity of human AMP, dTMP and UMP-CMP kinases
Nucleic Acids Res.
35
4895-4904
2007
Escherichia coli (P0A6I0)
Manually annotated by BRENDA team
Ofiteru, A.; Bucurenci, N.; Alexov, E.; Bertrand, T.; Briozzo, P.; Munier-Lehmann, H.; Gilles, A.M.
Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase
FEBS J.
274
3363-3373
2007
Escherichia coli (P0A6I0), Escherichia coli K-12 (P0A6I0)
Manually annotated by BRENDA team
Bertrand, T.; Briozzo, P.; Assairi, L.; Ofiteru, A.; Bucurenci, N.; Munier-Lehmann, H.; Golinelli-Pimpaneau, B.; Barzu, O.; Gilles, A.M.
Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme
J. Mol. Biol.
315
1099-1110
2002
Escherichia coli (A0A140N8S7)
Manually annotated by BRENDA team