EzCatDB: S00550
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DB codeS00550
RLCP classification3.133.90030.392 : Transfer
CATH domainDomain 13.40.50.300 : Rossmann foldCatalytic domain
E.C.2.7.4.14

CATH domainRelated DB codes (homologues)
3.40.50.300 : Rossmann foldS00527,S00547,S00548,S00554,S00555,S00671,S00672,S00676,S00680,S00682,S00913,S00914,S00301,S00302,S00303,S00304,S00307,S00308,S00305,S00306,S00309,S00310,S00311,M00114,M00199,D00129,D00130,D00540,M00186

Enzyme Name
UniProtKBKEGG

P0A6I0P63807Q97PK6
Protein nameCytidylate kinaseCytidylate kinaseCytidylate kinasecytidylate 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
SynonymsCK
EC 2.7.4.14
Cytidine monophosphate kinase
CMP kinase
Protein mssA
p25
CK
EC 2.7.4.14
Cytidine monophosphate kinase
CMP kinase
CK
EC 2.7.4.14
Cytidine monophosphate kinase
CMP kinase
RefSeqNP_415430.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489182.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_646183.1 (Protein)
NC_003923.1 (DNA/RNA sequence)
NP_346047.1 (Protein)
NC_003028.3 (DNA/RNA sequence)
PfamPF02224 (Cytidylate_kin)
[Graphical view]
PF02224 (Cytidylate_kin)
[Graphical view]
PF02224 (Cytidylate_kin)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00240Pyrimidine metabolism

UniProtKB:Accession NumberP0A6I0P63807Q97PK6
Entry nameKCY_ECOLIKCY_STAAWKCY_STRPN
ActivityATP + (d)CMP = ADP + (d)CDP.ATP + (d)CMP = ADP + (d)CDP.ATP + (d)CMP = ADP + (d)CDP.
Subunit


Subcellular locationCytoplasm.Cytoplasm (By similarity).Cytoplasm (By similarity).
Cofactor



Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00305C00002C00055C00239C00008C00112C00705
CompoundMagnesiumATPCMPdCMPADPCDPdCDP
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamine group,nucleotideamine group,nucleotideamine group,nucleotideamine group,nucleotideamine group,nucleotide
ChEBI18420
15422
17361
15918
16761
17239
28846

PubChem888
5957
6131
13945
6022
6132
150855

                
1ckeAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1kdoAUnboundUnboundBound:__CUnboundUnboundUnboundUnboundUnbound
1kdoBUnboundUnboundBound:__CUnboundUnboundUnboundUnboundUnbound
1kdpAUnboundUnboundUnboundBound:__CUnboundUnboundUnboundUnbound
1kdpBUnboundUnboundUnboundBound:__CUnboundUnboundUnboundUnbound
1kdrAUnboundUnboundAnalogue:CARUnboundUnboundUnboundUnboundUnbound
1kdrBUnboundUnboundAnalogue:CARUnboundUnboundUnboundUnboundUnbound
1kdtAUnboundUnboundUnboundAnalogue:DOCUnboundUnboundUnboundUnbound
1kdtBUnboundUnboundUnboundAnalogue:DOCUnboundUnboundUnboundUnbound
2cmkAUnboundUnboundUnboundUnboundUnboundBound:CDPUnboundUnbound
2femAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2feoAUnboundUnboundUnboundBound:_DCUnboundUnboundUnboundUnbound
2h92AUnboundUnboundBound:C5PUnboundUnboundUnboundUnboundUnbound
2h92BUnboundUnboundBound:C5PUnboundUnboundUnboundUnboundUnbound
2h92CUnboundUnboundBound:C5PUnboundUnboundUnboundUnboundUnbound
1q3tAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
similar to S00305
pdbCatalytic residuescomment
          
1ckeALYS 18;ARG 41;ARG  92;ARG 131;ARG 158;       
invisible 180-192
1kdoALYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
1kdoBLYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
1kdpALYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
1kdpBLYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
1kdrALYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
1kdrBLYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
1kdtALYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
1kdtBLYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
2cmkALYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
2femALYS 18;ARG 41;ARG  92;ARG 131;ARG 158;       
invisible 180-192
2feoALYS 18;ARG 41;ARG  92;ARG 131;ARG 158;ARG 181
 
2h92ALYS 16;ARG 39;ARG  87;ARG 126;ARG 153;ARG 176
 
2h92BLYS 16;ARG 39;ARG  87;ARG 126;ARG 153;ARG 176
 
2h92CLYS 16;ARG 39;ARG  87;ARG 126;ARG 153;ARG 176
 
1q3tALYS 29;ARG 52;ARG 104;ARG 143;ARG 170;ARG 193
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.9724-9726
[6]Fig.1, p.9294-92952
[9]p.111-119
[10]Fig.1, Fig.22
[12]p.1106-1108

references
[1]
PubMed ID7729545
JournalFEBS Lett
Year1995
Volume363
Pages22-4
AuthorsWiesmuller L, Scheffzek K, Kliche W, Goody RS, Wittinghofer A, Reinstein J
TitleCrystallization 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).
[2]
PubMed ID7663945
JournalStructure
Year1995
Volume3
Pages483-90
AuthorsVonrhein C, Schlauderer GJ, Schulz GE
TitleMovie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases.
[3]
PubMed ID8576266
JournalJ Biol Chem
Year1996
Volume271
Pages2856-62
AuthorsBucurenci N, Sakamoto H, Briozzo P, Palibroda N, Serina L, Sarfati RS, Labesse G, Briand G, Danchin A, Barzu O, Gilles AM
TitleCMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases.
[4]
PubMed ID8703943
JournalBiochemistry
Year1996
Volume35
Pages9716-27
AuthorsScheffzek K, Kliche W, Wiesmuller L, Reinstein J
TitleCrystal 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 PDB1ukd,1uke
Related UniProtKBP20425
[5]
PubMed ID9126287
JournalArch Biochem Biophys
Year1997
Volume340
Pages144-53
AuthorsSchultz CP, Ylisastigui-Pons L, Serina L, Sakamoto H, Mantsch HH, Neuhard J, Barzu O, Gilles AM
TitleStructural and catalytic properties of CMP kinase from Bacillus subtilis: a comparative analysis with the homologous enzyme from Escherichia coli.
Related UniProtKBP0A6I0
[6]
PubMed ID9280438
JournalBiochemistry
Year1997
Volume36
Pages9290-6
AuthorsSchlichting I, Reinstein J
TitleStructures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
Related PDB2ukd,3ukd,4ukd
Related UniProtKBP20425
[7]
PubMed ID9862805
JournalStructure
Year1998
Volume6
Pages1517-27
AuthorsBriozzo P, Golinelli-Pimpaneau B, Gilles AM, Gaucher JF, Burlacu-Miron S, Sakamoto H, Janin J, Barzu O
TitleStructures 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 PDB1cke,2cmk
Related UniProtKBP0A6I0
[8]
PubMed ID10426946
JournalNat Struct Biol
Year1999
Volume6
Pages721-3
AuthorsSchlichting I, Reinstein J
TitlepH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog.
Related PDB1qf9,5ukd
[9]
PubMed ID10218107
JournalAdv Enzymol Relat Areas Mol Biol
Year1999
Volume73
Pages103-34
AuthorsYan H, Tsai MD
TitleNucleoside monophosphate kinases: structure, mechanism, and substrate specificity.
[10]
PubMed ID11152133
JournalProtein Sci
Year2000
Volume9
Pages2225-31
AuthorsHutter MC, Helms V
TitlePhosphoryl transfer by a concerted reaction mechanism in UMP/CMP-kinase.
[11]
PubMed ID11123913
JournalBiochemistry
Year2000
Volume39
Pages15870-8
AuthorsLi de La Sierra IM, Gallay J, Vincent M, Bertrand T, Briozzo P, Barzu O, Gilles AM
TitleSubstrate-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.
[12]
PubMed ID11827479
JournalJ Mol Biol
Year2002
Volume315
Pages1099-110
AuthorsBertrand T, Briozzo P, Assairi L, Ofiteru A, Bucurenci N, Munier-Lehmann H, Golinelli-Pimpaneau B, Barzu O, Gilles AM
TitleSugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme.
Related PDB1kdo,1kdp,1kdr,1kdt
[13]
PubMed ID14573872
JournalProtein Sci
Year2003
Volume12
Pages2613-21
AuthorsYu L, Mack J, Hajduk PJ, Kakavas SJ, Saiki AY, Lerner CG, Olejniczak ET
TitleSolution structure and function of an essential CMP kinase of Streptococcus pneumoniae.
Related PDB1q3t
[14]
PubMed ID16880539
JournalActa Crystallogr Sect F Struct Biol Cryst Commun
Year2006
Volume62
Pages710-5
AuthorsDhaliwal B, Ren J, Lockyer M, Charles I, Hawkins AR, Stammers DK
TitleStructure of Staphylococcus aureus cytidine monophosphate kinase in complex with cytidine 5'-monophosphate.
Related PDB2h92
[15]
PubMed ID17542990
JournalFEBS J
Year2007
Volume274
Pages3363-73
AuthorsOfiteru A, Bucurenci N, Alexov E, Bertrand T, Briozzo P, Munier-Lehmann H, Gilles AM
TitleStructural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase.
Related PDB2fem,2feo

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.

createdupdated
2002-05-312010-05-24


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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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