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P20425

- KCY_DICDI

UniProt

P20425 - KCY_DICDI

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Protein
UMP-CMP kinase
Gene
pyrK, ctpS, DDB_G0287495
Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.UniRule annotation

Catalytic activityi

ATP + (d)CMP = ADP + (d)CDP.1 Publication
ATP + UMP = ADP + UDP.1 Publication

Cofactori

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

Kineticsi

  1. KM=25 µM for ATP1 Publication
  2. KM=0.4 mM for UMP
  3. KM=0.1 mM for CMP

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei43 – 431NMP
Binding sitei98 – 981CMP
Binding sitei132 – 1321ATP
Binding sitei138 – 1381NMP
Binding sitei149 – 1491NMP
Binding sitei177 – 1771ATP; via carbonyl oxygen

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi17 – 226ATPUniRule annotation
Nucleotide bindingi64 – 663NMPUniRule annotation
Nucleotide bindingi91 – 944NMPUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: dictyBase
  2. UMP kinase activity Source: dictyBase
  3. cytidylate kinase activity Source: dictyBase
  4. magnesium ion binding Source: dictyBase
  5. phosphotransferase activity, phosphate group as acceptor Source: dictyBase

GO - Biological processi

  1. CDP biosynthetic process Source: dictyBase
  2. UDP biosynthetic process Source: dictyBase
  3. nucleotide salvage Source: dictyBase
  4. pyrimidine nucleobase salvage Source: dictyBase
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Pyrimidine biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

SABIO-RKP20425.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:pyrK
Synonyms:ctpS
ORF Names:DDB_G0287495
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195: Chromosome 5, UP000002195: Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0287495. pyrK.

Subcellular locationi

Cytoplasm By similarity. Nucleus By similarity UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. intracellular Source: dictyBase
  3. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 195195UMP-CMP kinaseUniRule annotation
PRO_0000158948Add
BLAST

Proteomic databases

PRIDEiP20425.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi44689.DDB_0191367.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 158
Helixi20 – 3112
Beta strandi34 – 374
Helixi38 – 4710
Helixi53 – 619
Helixi68 – 8013
Beta strandi87 – 904
Helixi96 – 10611
Turni107 – 1093
Beta strandi111 – 1199
Helixi122 – 13312
Turni134 – 1363
Helixi143 – 15513
Helixi157 – 16610
Beta strandi170 – 1745
Helixi179 – 19214

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1QF9X-ray1.70A2-195[»]
1UKEX-ray2.20A2-195[»]
2UKDX-ray2.20A2-195[»]
3UKDX-ray1.90A2-195[»]
4UKDX-ray2.00A2-195[»]
5UKDX-ray1.90A2-195[»]
ProteinModelPortaliP20425.
SMRiP20425. Positions 2-195.

Miscellaneous databases

EvolutionaryTraceiP20425.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni37 – 6630NMPbindUniRule annotation
Add
BLAST
Regioni131 – 14111LIDUniRule annotation
Add
BLAST

Domaini

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.UniRule annotation

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0563.
KOiK13800.
OMAiKRPGSQY.
PhylomeDBiP20425.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00235. Adenylate_kinase_Adk.
MF_03172. Adenylate_kinase_UMP_CMP_kin.
InterProiIPR000850. Adenylat/UMP-CMP_kin.
IPR027417. P-loop_NTPase.
IPR006266. UMP_CMP_kinase.
[Graphical view]
PANTHERiPTHR23359. PTHR23359. 1 hit.
PRINTSiPR00094. ADENYLTKNASE.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR01359. UMP_CMP_kin_fam. 1 hit.
PROSITEiPS00113. ADENYLATE_KINASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P20425-1 [UniParc]FASTAAdd to Basket

« Hide

MMEKSKPNVV FVLGGPGSGK GTQCANIVRD FGWVHLSAGD LLRQEQQSGS    50
KDGEMIATMI KNGEIVPSIV TVKLLKNAID ANQGKNFLVD GFPRNEENNN 100
SWEENMKDFV DTKFVLFFDC PEEVMTQRLL KRGESSGRSD DNIESIKKRF 150
NTFNVQTKLV IDHYNKFDKV KIIPANRDVN EVYNDVENLF KSMGF 195
Length:195
Mass (Da):22,074
Last modified:December 4, 2007 - v2
Checksum:i076C6780DDC1C0F0
GO

Sequence cautioni

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

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M34568 mRNA. Translation: AAA33272.1. Different initiation.
AAFI02000102 Genomic DNA. Translation: EAL63690.1.
PIRiA35235.
RefSeqiXP_637196.1. XM_632104.1.

Genome annotation databases

EnsemblProtistsiDDB0191367; DDB0191367; DDB_G0287495.
GeneIDi8626154.
KEGGiddi:DDB_G0287495.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M34568 mRNA. Translation: AAA33272.1 . Different initiation.
AAFI02000102 Genomic DNA. Translation: EAL63690.1 .
PIRi A35235.
RefSeqi XP_637196.1. XM_632104.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1QF9 X-ray 1.70 A 2-195 [» ]
1UKE X-ray 2.20 A 2-195 [» ]
2UKD X-ray 2.20 A 2-195 [» ]
3UKD X-ray 1.90 A 2-195 [» ]
4UKD X-ray 2.00 A 2-195 [» ]
5UKD X-ray 1.90 A 2-195 [» ]
ProteinModelPortali P20425.
SMRi P20425. Positions 2-195.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 44689.DDB_0191367.

Proteomic databases

PRIDEi P20425.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblProtistsi DDB0191367 ; DDB0191367 ; DDB_G0287495 .
GeneIDi 8626154.
KEGGi ddi:DDB_G0287495.

Organism-specific databases

dictyBasei DDB_G0287495. pyrK.

Phylogenomic databases

eggNOGi COG0563.
KOi K13800.
OMAi KRPGSQY.
PhylomeDBi P20425.

Enzyme and pathway databases

SABIO-RK P20425.

Miscellaneous databases

EvolutionaryTracei P20425.
PROi P20425.

Family and domain databases

Gene3Di 3.40.50.300. 1 hit.
HAMAPi MF_00235. Adenylate_kinase_Adk.
MF_03172. Adenylate_kinase_UMP_CMP_kin.
InterProi IPR000850. Adenylat/UMP-CMP_kin.
IPR027417. P-loop_NTPase.
IPR006266. UMP_CMP_kinase.
[Graphical view ]
PANTHERi PTHR23359. PTHR23359. 1 hit.
PRINTSi PR00094. ADENYLTKNASE.
SUPFAMi SSF52540. SSF52540. 1 hit.
TIGRFAMsi TIGR01359. UMP_CMP_kin_fam. 1 hit.
PROSITEi PS00113. ADENYLATE_KINASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.

Entry informationi

Entry nameiKCY_DICDI
AccessioniPrimary (citable) accession number: P20425
Secondary accession number(s): Q54KA2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: December 4, 2007
Last modified: September 3, 2014
This is version 108 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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