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P20425 (KCY_DICDI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 105. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
UMP-CMP kinase

EC=2.7.4.14
Alternative name(s):
Deoxycytidylate kinase
Short name=CK
Short name=dCMP kinase
Uridine monophosphate/cytidine monophosphate kinase
Short name=UMP/CMP kinase
Short name=UMP/CMPK
Gene names
Name:pyrK
Synonyms:ctpS
ORF Names:DDB_G0287495
OrganismDictyostelium discoideum (Slime mold) [Reference proteome]
Taxonomic identifier44689 [NCBI]
Taxonomic lineageEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium

Protein attributes

Sequence length195 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and CMP as phosphate acceptors. HAMAP-Rule MF_03172

Catalytic activity

ATP + (d)CMP = ADP + (d)CDP. Ref.1

ATP + UMP = ADP + UDP. Ref.1

Cofactor

Binds 1 magnesium ion per monomer. The magnesium ion binds to water and substrates. Ref.3

Subunit structure

Monomer.

Subcellular location

Cytoplasm By similarity. Nucleus By similarity HAMAP-Rule MF_03172.

Domain

Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. HAMAP-Rule MF_03172

Sequence similarities

Belongs to the adenylate kinase family. UMP-CMP kinase subfamily.

Biophysicochemical properties

Kinetic parameters:

KM=25 µM for ATP Ref.1

KM=0.4 mM for UMP

KM=0.1 mM for CMP

Sequence caution

The sequence AAA33272.1 differs from that shown. Reason: Erroneous initiation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 195195UMP-CMP kinase HAMAP-Rule MF_03172
PRO_0000158948

Regions

Nucleotide binding17 – 226ATP HAMAP-Rule MF_03172
Nucleotide binding64 – 663NMP HAMAP-Rule MF_03172
Nucleotide binding91 – 944NMP HAMAP-Rule MF_03172
Region37 – 6630NMPbind HAMAP-Rule MF_03172
Region131 – 14111LID HAMAP-Rule MF_03172

Sites

Binding site431NMP
Binding site981CMP
Binding site1321ATP
Binding site1381NMP
Binding site1491NMP
Binding site1771ATP; via carbonyl oxygen

Secondary structure

.............................. 195
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P20425 [UniParc].

Last modified December 4, 2007. Version 2.
Checksum: 076C6780DDC1C0F0

FASTA19522,074
        10         20         30         40         50         60 
MMEKSKPNVV FVLGGPGSGK GTQCANIVRD FGWVHLSAGD LLRQEQQSGS KDGEMIATMI 

        70         80         90        100        110        120 
KNGEIVPSIV TVKLLKNAID ANQGKNFLVD GFPRNEENNN SWEENMKDFV DTKFVLFFDC 

       130        140        150        160        170        180 
PEEVMTQRLL KRGESSGRSD DNIESIKKRF NTFNVQTKLV IDHYNKFDKV KIIPANRDVN 

       190 
EVYNDVENLF KSMGF 

« Hide

References

« Hide 'large scale' references
[1]"cDNA-derived sequence of UMP-CMP kinase from Dictyostelium discoideum and expression of the enzyme in Escherichia coli."
Wiesmueller L., Noegel A.A., Barzu O., Gerisch G., Schleicher M.
J. Biol. Chem. 265:6339-6345(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
[2]"The genome of the social amoeba Dictyostelium discoideum."
Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N. expand/collapse author list , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: AX4.
[3]"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."
Scheffzek K., Kliche W., Wiesmuller L., Reinstein J.
Biochemistry 35:9716-9727(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 2-195 IN COMPLEXES WITH SUBSTRATE ANALOGS, COFACTOR.
[4]"Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative."
Schlichting I., Reinstein J.
Biochemistry 36:9290-9296(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 2-195IN COMPLEX WITH ADP; CMP AND UDP.
[5]"pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog."
Schlichting I., Reinstein J.
Nat. Struct. Biol. 6:721-723(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 2-194 IN COMPLEX WITH ADP AND CMP.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M34568 mRNA. Translation: AAA33272.1. Different initiation.
AAFI02000102 Genomic DNA. Translation: EAL63690.1.
PIRA35235.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1QF9X-ray1.70A2-194[»]
1UKEX-ray2.20A2-195[»]
2UKDX-ray2.20A2-195[»]
3UKDX-ray1.90A2-195[»]
4UKDX-ray2.00A2-195[»]
5UKDX-ray1.90A2-194[»]
ProteinModelPortalP20425.
SMRP20425. Positions 2-195.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING44689.DDB_0191367.

Proteomic databases

PRIDEP20425.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsDDB0191367; DDB0191367; DDB_G0287495.
KEGGddi:DDB_G0287495.

Organism-specific databases

dictyBaseDDB_G0287495. pyrK.

Phylogenomic databases

eggNOGCOG0563.
KOK13800.
OMAKRPGSQY.
PhylomeDBP20425.

Enzyme and pathway databases

SABIO-RKP20425.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
HAMAPMF_00235. Adenylate_kinase_Adk.
MF_03172. Adenylate_kinase_UMP_CMP_kin.
InterProIPR000850. Adenylat/UMP-CMP_kin.
IPR027417. P-loop_NTPase.
IPR006266. UMP_CMP_kinase.
[Graphical view]
PANTHERPTHR23359. PTHR23359. 1 hit.
PRINTSPR00094. ADENYLTKNASE.
SUPFAMSSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR01359. UMP_CMP_kin_fam. 1 hit.
PROSITEPS00113. ADENYLATE_KINASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP20425.
PROP20425.

Entry information

Entry nameKCY_DICDI
AccessionPrimary (citable) accession number: P20425
Secondary accession number(s): Q54KA2
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: December 4, 2007
Last modified: April 16, 2014
This is version 105 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Dictyostelium discoideum

Dictyostelium discoideum: entries, gene names and cross-references to dictyBase