S00550
type: Enzyme
rlcp: p392
cath: Rossmann fold
ec: https://purl.uniprot.org/enzyme/2.7.4.14
uniprot: P0A6I0
uniprot: P63807
uniprot: Q97PK6
kegg enzyme: cytidylate kinase
kegg enzyme: deoxycytidylate kinase
kegg enzyme: CMP kinase
kegg enzyme: CTP:CMP phosphotransferase
kegg enzyme: dCMP kinase
kegg enzyme: deoxycytidine monophosphokinase
kegg enzyme: UMP-CMP kinase
kegg enzyme: ATP:UMP-CMP phosphotransferase
kegg enzyme: pyrimidine nucleoside monophosphate kinase
kegg pathway: Pyrimidine metabolism
kegg cofactor: Magnesium
kegg substrate: ATP
kegg substrate: CMP
kegg substrate: dCMP
kegg product: ADP
kegg product: CDP
kegg product: dCDP
pdb: 1ckeA
pdb: 1kdoA
pdb: 1kdoB
pdb: 1kdpA
pdb: 1kdpB
pdb: 1kdrA
pdb: 1kdrB
pdb: 1kdtA
pdb: 1kdtB
pdb: 2cmkA
pdb: 2femA
pdb: 2feoA
pdb: 2h92A
pdb: 2h92B
pdb: 2h92C
pdb: 1q3tA
pdb bound state: Unbound
  compound: ATP
  pdb: 1ckeA
pdb bound state: Unbound
  compound: ATP
  pdb: 1kdoA
pdb bound state: Unbound
  compound: ATP
  pdb: 1kdoB
pdb bound state: Unbound
  compound: ATP
  pdb: 1kdpA
pdb bound state: Unbound
  compound: ATP
  pdb: 1kdpB
pdb bound state: Unbound
  compound: ATP
  pdb: 1kdrA
pdb bound state: Unbound
  compound: ATP
  pdb: 1kdrB
pdb bound state: Unbound
  compound: ATP
  pdb: 1kdtA
pdb bound state: Unbound
  compound: ATP
  pdb: 1kdtB
pdb bound state: Unbound
  compound: ATP
  pdb: 2cmkA
pdb bound state: Unbound
  compound: ATP
  pdb: 2femA
pdb bound state: Unbound
  compound: ATP
  pdb: 2feoA
pdb bound state: Unbound
  compound: ATP
  pdb: 2h92A
pdb bound state: Unbound
  compound: ATP
  pdb: 2h92B
pdb bound state: Unbound
  compound: ATP
  pdb: 2h92C
pdb bound state: Unbound
  compound: ATP
  pdb: 1q3tA
pdb bound state: Unbound
  compound: CMP
  pdb: 1ckeA
pdb bound state: Unbound
  compound: CMP
  pdb: 1kdpA
pdb bound state: Unbound
  compound: CMP
  pdb: 1kdpB
pdb bound state: Analogue
  compound: CMP
  pdb: 1kdrA
  ligand het code: CAR
pdb bound state: Analogue
  compound: CMP
  pdb: 1kdrB
  ligand het code: CAR
pdb bound state: Unbound
  compound: CMP
  pdb: 1kdtA
pdb bound state: Unbound
  compound: CMP
  pdb: 1kdtB
pdb bound state: Unbound
  compound: CMP
  pdb: 2cmkA
references: 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).
references: Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases.
references: CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases.
references: http://ezcatdb.cbrc.jp/EzCatDB/reference/S00550#4
references: Structural and catalytic properties of CMP kinase from Bacillus subtilis: a comparative analysis with the homologous enzyme from Escherichia coli.
references: Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
references: 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.
references: pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog.
references: Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity.
references: Phosphoryl transfer by a concerted reaction mechanism in UMP/CMP-kinase.
references: 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.
references: Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme.
references: Solution structure and function of an essential CMP kinase of Streptococcus pneumoniae.
references: Structure of Staphylococcus aureus cytidine monophosphate kinase in complex with cytidine 5'-monophosphate.
references: Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase.
comment: 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.

Rossmann fold
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.50.300
catalytic domain: index.html

Pyrimidine metabolism
type: KeggPathway
references: KEGG:MAP00240

Magnesium
type: KeggCofactor
references: KEGG:C00305
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:18420
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

ATP
type: KeggSubstrate
references: KEGG:C00002
compound type: amine group
compound type: nucleotide
references: CHEBI:15422
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

CMP
type: KeggSubstrate
references: KEGG:C00055
compound type: amine group
compound type: nucleotide
references: CHEBI:17361
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

dCMP
type: KeggSubstrate
references: KEGG:C00239
compound type: amine group
compound type: nucleotide
references: CHEBI:15918
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

ADP
type: KeggProduct
references: KEGG:C00008
compound type: amine group
compound type: nucleotide
references: CHEBI:16761
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

CDP
type: KeggProduct
references: KEGG:C00112
compound type: amine group
compound type: nucleotide
references: CHEBI:17239
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

dCDP
type: KeggProduct
references: KEGG:C00705
compound type: amine group
compound type: nucleotide
references: CHEBI:28846
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1ckeA
type: Pdb
references: 1cke
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1cke
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;
comment: invisible 180-192

1kdoA
type: Pdb
references: 1kdo
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kdo
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

1kdoB
type: Pdb
references: 1kdo
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kdo
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

1kdpA
type: Pdb
references: 1kdp
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kdp
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

1kdpB
type: Pdb
references: 1kdp
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kdp
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

1kdrA
type: Pdb
references: 1kdr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kdr
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

1kdrB
type: Pdb
references: 1kdr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kdr
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

1kdtA
type: Pdb
references: 1kdt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kdt
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

1kdtB
type: Pdb
references: 1kdt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kdt
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

2cmkA
type: Pdb
references: 2cmk
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2cmk
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

2femA
type: Pdb
references: 2fem
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2fem
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;
comment: invisible 180-192

2feoA
type: Pdb
references: 2feo
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2feo
catalytic residue: LYS 18;ARG 41;ARG 92;ARG 131;ARG 158;ARG 181

2h92A
type: Pdb
references: 2h92
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2h92
catalytic residue: LYS 16;ARG 39;ARG 87;ARG 126;ARG 153;ARG 176

2h92B
type: Pdb
references: 2h92
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2h92
catalytic residue: LYS 16;ARG 39;ARG 87;ARG 126;ARG 153;ARG 176

2h92C
type: Pdb
references: 2h92
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2h92
catalytic residue: LYS 16;ARG 39;ARG 87;ARG 126;ARG 153;ARG 176

1q3tA
type: Pdb
references: 1q3t
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1q3t
catalytic residue: LYS 29;ARG 52;ARG 104;ARG 143;ARG 170;ARG 193

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).
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7729545
journal: FEBS Lett
volume: 363
pages: 22-4
published year: 1995
authors:
  item: Wiesmuller L
  item: Scheffzek K
  item: Kliche W
  item: Goody RS
  item: Wittinghofer A
  item: Reinstein J

Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7663945
journal: Structure
volume: 3
pages: 483-90
published year: 1995
authors:
  item: Vonrhein C
  item: Schlauderer GJ
  item: Schulz GE

CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8576266
journal: J Biol Chem
volume: 271
pages: 2856-62
published year: 1996
authors:
  item: Bucurenci N
  item: Sakamoto H
  item: Briozzo P
  item: Palibroda N
  item: Serina L
  item: Sarfati RS
  item: Labesse G
  item: Briand G
  item: Danchin A
  item: Barzu O
  item: Gilles AM

http://ezcatdb.cbrc.jp/EzCatDB/reference/S00550#4
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8703943
journal: Biochemistry
volume: 35
pages: 9716-27
published year: 1996
authors:
  item: Scheffzek K
  item: Kliche W
  item: Wiesmuller L
  item: 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.
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P20425

Structural and catalytic properties of CMP kinase from Bacillus subtilis: a comparative analysis with the homologous enzyme from Escherichia coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9126287
journal: Arch Biochem Biophys
volume: 340
pages: 144-53
published year: 1997
authors:
  item: Schultz CP
  item: Ylisastigui-Pons L
  item: Serina L
  item: Sakamoto H
  item: Mantsch HH
  item: Neuhard J
  item: Barzu O
  item: Gilles AM
references: P0A6I0

Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9280438
journal: Biochemistry
volume: 36
pages: 9290-6
published year: 1997
authors:
  item: Schlichting I
  item: Reinstein J
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P20425

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.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9862805
journal: Structure
volume: 6
pages: 1517-27
published year: 1998
authors:
  item: Briozzo P
  item: Golinelli-Pimpaneau B
  item: Gilles AM
  item: Gaucher JF
  item: Burlacu-Miron S
  item: Sakamoto H
  item: Janin J
  item: Barzu O
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P0A6I0

pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10426946
journal: Nat Struct Biol
volume: 6
pages: 721-3
published year: 1999
authors:
  item: Schlichting I
  item: Reinstein J
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10218107
journal: Adv Enzymol Relat Areas Mol Biol
volume: 73
pages: 103-34
published year: 1999
authors:
  item: Yan H
  item: Tsai MD

Phosphoryl transfer by a concerted reaction mechanism in UMP/CMP-kinase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11152133
journal: Protein Sci
volume: 9
pages: 2225-31
published year: 2000
authors:
  item: Hutter MC
  item: Helms V

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.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11123913
journal: Biochemistry
volume: 39
pages: 15870-8
published year: 2000
authors:
  item: Li de La Sierra IM
  item: Gallay J
  item: Vincent M
  item: Bertrand T
  item: Briozzo P
  item: Barzu O
  item: Gilles AM

Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11827479
journal: J Mol Biol
volume: 315
pages: 1099-110
published year: 2002
authors:
  item: Bertrand T
  item: Briozzo P
  item: Assairi L
  item: Ofiteru A
  item: Bucurenci N
  item: Munier-Lehmann H
  item: Golinelli-Pimpaneau B
  item: Barzu O
  item: Gilles AM
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Solution structure and function of an essential CMP kinase of Streptococcus pneumoniae.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/14573872
journal: Protein Sci
volume: 12
pages: 2613-21
published year: 2003
authors:
  item: Yu L
  item: Mack J
  item: Hajduk PJ
  item: Kakavas SJ
  item: Saiki AY
  item: Lerner CG
  item: Olejniczak ET
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Structure of Staphylococcus aureus cytidine monophosphate kinase in complex with cytidine 5'-monophosphate.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/16880539
journal: Acta Crystallogr Sect F Struct Biol Cryst Commun
volume: 62
pages: 710-5
published year: 2006
authors:
  item: Dhaliwal B
  item: Ren J
  item: Lockyer M
  item: Charles I
  item: Hawkins AR
  item: Stammers DK
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/17542990
journal: FEBS J
volume: 274
pages: 3363-73
published year: 2007
authors:
  item: Ofiteru A
  item: Bucurenci N
  item: Alexov E
  item: Bertrand T
  item: Briozzo P
  item: Munier-Lehmann H
  item: Gilles AM
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Analogue
compound: dCMP
pdb: 1kdtA
ligand het code: DOC

Analogue
compound: dCMP
pdb: 1kdtB
ligand het code: DOC

ReferenceForCatalyticMechanism
reference index: 4
reference section: p.9724-9726

ReferenceForCatalyticMechanism
reference index: 6
reference section: Fig.1, p.9294-9295
reference step: 2

ReferenceForCatalyticMechanism
reference index: 9
reference section: p.111-119

ReferenceForCatalyticMechanism
reference index: 10
reference section: Fig.1, Fig.2
reference step: 2

ReferenceForCatalyticMechanism
reference index: 12
reference section: p.1106-1108