DB code: S00308

RLCP classification 3.133.90030.392 : Transfer
CATH domain 3.40.50.300 : Rossmann fold Catalytic domain
E.C. 2.7.4.14
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.300 : Rossmann fold S00527 S00547 S00548 S00550 S00554 S00555 S00671 S00672 S00676 S00680 S00682 S00913 S00914 S00301 S00302 S00303 S00304 S00307 S00305 S00306 S00309 S00310 S00311 M00114 M00199 D00129 D00130 D00540 M00186

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P20425 Cytidylate kinase
EC 2.7.4.14
Deoxycytidylate kinase
UMP-CMP kinase
XP_637196.1 (Protein)
XM_632104.1 (DNA/RNA sequence)
PF00406 (ADK)
[Graphical View]
P30085 UMP-CMP kinase
EC 2.7.4.14
Cytidylate kinase
Deoxycytidylate kinase
Cytidine monophosphate kinase
Uridine monophosphate kinase
Uridine monophosphate/cytidine monophosphate kinase
UMP/CMP kinase
UMP/CMPK
NP_001129612.1 (Protein)
NM_001136140.1 (DNA/RNA sequence)
NP_057392.1 (Protein)
NM_016308.2 (DNA/RNA sequence)
PF00406 (ADK)
[Graphical View]

KEGG enzyme name
cytidylate kinase
deoxycytidylate kinase
deoxycytidylate kinase
CMP kinase
CTP:CMP phosphotransferase
dCMP kinase
deoxycytidine monophosphokinase
UMP-CMP kinase
ATP:UMP-CMP phosphotransferase
pyrimidine nucleoside monophosphate kinase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P30085 KCY_HUMAN ATP + (d)CMP = ADP + (d)CDP. Nucleus. Cytoplasm. Note=Mainly nuclear. Magnesium.
P20425 KCY_DICDI ATP + (d)CMP = ADP + (d)CDP. Monomer.

KEGG Pathways
Map code Pathways E.C.
MAP00240 Pyrimidine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00055 C00239 C00008 C00112 C00705
E.C.
Compound Magnesium ATP CMP dCMP ADP CDP dCDP
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amine group,nucleotide amine group,nucleotide amine group,nucleotide amine group,nucleotide amine group,nucleotide
ChEBI 18420
15422
17361
15918
16761
17239
28846
PubChem 888
5957
6131
13945
6022
6132
150855
1qf9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Bound:C5P Unbound Bound:ADP Unbound Unbound Transition-state-analogue:ALF
1ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:UP5(ATP) Analogue:UP5(CMP) Unbound Unbound Unbound Unbound Unbound
1ukeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Analogue:UP5(ATP) Analogue:UP5(CMP) Unbound Unbound Unbound Unbound Unbound
2ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Bound:C5P Unbound Bound:ADP Unbound Unbound Unbound
3ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Bound:C5P Unbound Bound:ADP Unbound Unbound Transition-state-analogue:AF3
4ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Bound:ADP Analogue:UDP Unbound Transition-state-analogue:BF2
5ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Bound:C5P Unbound Bound:ADP Unbound Unbound Transition-state-analogue:AF3
1tevA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
similar to S00305

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1qf9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 19;ARG 42;ARG 93;ARG 131;ARG 137;ARG 148
1ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 19;ARG 42;ARG 93;ARG 131;ARG 137;ARG 148
1ukeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 19;ARG 42;ARG 93;ARG 131;ARG 137;ARG 148
2ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 19;ARG 42;ARG 93;ARG 131;ARG 137;ARG 148
3ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 19;ARG 42;ARG 93;ARG 131;ARG 137;ARG 148
4ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 19;ARG 42;ARG 93;ARG 131;ARG 137;ARG 148
5ukdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 19;ARG 42;ARG 93;ARG 131;ARG 137;ARG 148
1tevA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 16;ARG 39;ARG 96;ARG 134;ARG 140;ARG 151

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.9724-9726
[6]
Fig.1, p.9294-9295 2
[9]
p.111-119
[10]
Fig.1, Fig.2 2
[12]
p.1106-1108

References
[1]
Resource
Comments
Medline ID
PubMed ID 7729545
Journal FEBS Lett
Year 1995
Volume 363
Pages 22-4
Authors Wiesmuller L, Scheffzek K, Kliche W, Goody RS, Wittinghofer A, Reinstein J
Title Crystallization and preliminary X-ray analysis of UMP/CMP-kinase from Dictyostelium discoideum with the specific bisubstrate inhibitor P1-(adenosine 5')-P5-(uridine 5')-pentaphosphate (UP5A).
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 7663945
Journal Structure
Year 1995
Volume 3
Pages 483-90
Authors Vonrhein C, Schlauderer GJ, Schulz GE
Title Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8576266
Journal J Biol Chem
Year 1996
Volume 271
Pages 2856-62
Authors Bucurenci N, Sakamoto H, Briozzo P, Palibroda N, Serina L, Sarfati RS, Labesse G, Briand G, Danchin A, Barzu O, Gilles AM
Title CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8703943
Journal Biochemistry
Year 1996
Volume 35
Pages 9716-27
Authors Scheffzek K, Kliche W, Wiesmuller L, Reinstein J
Title 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 A: implications for water-mediated specificity.
Related PDB 1ukd 1uke
Related UniProtKB P20425
[5]
Resource
Comments
Medline ID
PubMed ID 9126287
Journal Arch Biochem Biophys
Year 1997
Volume 340
Pages 144-53
Authors Schultz CP, Ylisastigui-Pons L, Serina L, Sakamoto H, Mantsch HH, Neuhard J, Barzu O, Gilles AM
Title Structural and catalytic properties of CMP kinase from Bacillus subtilis: a comparative analysis with the homologous enzyme from Escherichia coli.
Related PDB
Related UniProtKB P0A6I0
[6]
Resource
Comments
Medline ID
PubMed ID 9280438
Journal Biochemistry
Year 1997
Volume 36
Pages 9290-6
Authors Schlichting I, Reinstein J
Title Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
Related PDB 2ukd 3ukd 4ukd
Related UniProtKB P20425
[7]
Resource
Comments
Medline ID
PubMed ID 9862805
Journal Structure
Year 1998
Volume 6
Pages 1517-27
Authors Briozzo P, Golinelli-Pimpaneau B, Gilles AM, Gaucher JF, Burlacu-Miron S, Sakamoto H, Janin J, Barzu O
Title 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.
Related PDB 1cke 2cmk
Related UniProtKB P0A6I0
[8]
Resource
Comments
Medline ID
PubMed ID 10426946
Journal Nat Struct Biol
Year 1999
Volume 6
Pages 721-3
Authors Schlichting I, Reinstein J
Title pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog.
Related PDB 1qf9 5ukd
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10218107
Journal Adv Enzymol Relat Areas Mol Biol
Year 1999
Volume 73
Pages 103-34
Authors Yan H, Tsai MD
Title Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 11152133
Journal Protein Sci
Year 2000
Volume 9
Pages 2225-31
Authors Hutter MC, Helms V
Title Phosphoryl transfer by a concerted reaction mechanism in UMP/CMP-kinase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11123913
Journal Biochemistry
Year 2000
Volume 39
Pages 15870-8
Authors Li de La Sierra IM, Gallay J, Vincent M, Bertrand T, Briozzo P, Barzu O, Gilles AM
Title 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.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11827479
Journal J Mol Biol
Year 2002
Volume 315
Pages 1099-110
Authors Bertrand T, Briozzo P, Assairi L, Ofiteru A, Bucurenci N, Munier-Lehmann H, Golinelli-Pimpaneau B, Barzu O, Gilles AM
Title Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 15163660
Journal J Biol Chem
Year 2004
Volume 279
Pages 33882-9
Authors Segura-Pena D, Sekulic N, Ort S, Konrad M, Lavie A
Title Substrate-induced conformational changes in human UMP/CMP kinase.
Related PDB 1tev
Related UniProtKB

Comments
Literature [6] concluded that the mechanism of phosphoryl transfer has a strong associative character rather than dissociative character.
According to the literature [6] & [10], the positions of the catalytic Mg2+ ion and the conserved lysine residue, Lys19, of the P-loop are invariant during the reaction, suggesting that they just provide a structural template for phosphoryl transfer. In contrast, catalytic arginine residues move to stabilize negative charges that develop during the reaction [6].
The paper [10] proposed a concerted reaction mechanism, in which a proton shifts synchronously from the monophosphate of the acceptor substrate to the transferred phosphate group.

Created Updated
2002-05-31 2010-05-24