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Protein

Uridylate kinase

Gene

URA6

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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 dUMP as phosphate acceptors, but can also use CMP, dCMP, AMP, GMP, dGMP and dTMP. ATP and dATP are the best phosphate donors, but can also use GTP, dGTP, dCTP, and dTTP to some degree.UniRule annotation4 Publications

Catalytic activityi

ATP + UMP = ADP + UDP.UniRule annotation5 Publications

Cofactori

Mg2+UniRule annotation2 PublicationsNote: Binds 1 Mg2+ ion per monomer.UniRule annotation2 Publications

Kineticsi

  1. KM=0.15 mM for UMP1 Publication
  2. KM=1.0 mM for dUMP1 Publication
  3. KM=1.8 mM for dTMP1 Publication
  4. KM=0.11 mM for ATP1 Publication
  5. KM=0.53 mM for dCMP1 Publication
  1. Vmax=120 µmol/min/mg enzyme (for dCDP synthesis)1 Publication

pH dependencei

Optimum pH is 6-9.5.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei52 – 521NMPUniRule annotation2 Publications
Binding sitei111 – 1111NMPUniRule annotation2 Publications
Binding sitei142 – 1421ATPUniRule annotation2 Publications
Binding sitei148 – 1481NMPUniRule annotation2 Publications
Binding sitei159 – 1591NMPUniRule annotation2 Publications
Binding sitei187 – 1871ATP; via carbonyl oxygenUniRule annotation2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi26 – 316ATPUniRule annotation2 Publications
Nucleotide bindingi74 – 763NMPUniRule annotation2 Publications
Nucleotide bindingi104 – 1074NMPUniRule annotation2 Publications

GO - Molecular functioni

  • adenylate kinase activity Source: SGD
  • ATP binding Source: UniProtKB-KW
  • cytidylate kinase activity Source: UniProtKB-EC
  • uridylate kinase activity Source: SGD

GO - Biological processi

  • 'de novo' pyrimidine nucleobase biosynthetic process Source: SGD
  • nucleobase-containing compound metabolic process Source: SGD
  • pyrimidine nucleotide biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Pyrimidine biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:YKL024C-MONOMER.
YEAST:YKL024C-MONOMER.
BRENDAi2.7.4.B1. 984.
ReactomeiR-SCE-499943. Synthesis and interconversion of nucleotide di- and triphosphates.

Names & Taxonomyi

Protein namesi
Recommended name:
Uridylate kinaseUniRule annotation (EC:2.7.4.14UniRule annotation)
Short name:
UKUniRule annotation
Alternative name(s):
ATP:UMP phosphotransferaseUniRule annotation
Deoxycytidylate kinaseUniRule annotation
Short name:
CKUniRule annotation
Short name:
dCMP kinaseUniRule annotation
Suppressor of cdc8 protein
Uridine monophosphate kinaseUniRule annotation
Short name:
UMP kinaseUniRule annotation
Short name:
UMPKUniRule annotation
Gene namesi
Name:URA6UniRule annotation
Synonyms:SOC8
Ordered Locus Names:YKL024C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKL024C.
SGDiS000001507. URA6.

Subcellular locationi

  • Cytoplasm UniRule annotation2 Publications
  • Nucleus UniRule annotation2 Publications

  • Note: Predominantly cytoplasmic.UniRule annotation1 Publication

GO - Cellular componenti

  • cytoplasm Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi29 – 291K → E: Abolishes catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 204204Uridylate kinasePRO_0000158947Add
BLAST

Proteomic databases

MaxQBiP15700.

Interactioni

Subunit structurei

Monomer.UniRule annotation3 Publications

Protein-protein interaction databases

BioGridi34107. 15 interactions.
DIPiDIP-4756N.
MINTiMINT-529742.

Structurei

Secondary structure

1
204
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni13 – 153Combined sources
Beta strandi17 – 226Combined sources
Helixi29 – 3911Combined sources
Beta strandi43 – 464Combined sources
Helixi47 – 5610Combined sources
Helixi63 – 719Combined sources
Helixi78 – 9417Combined sources
Beta strandi99 – 1035Combined sources
Helixi109 – 11810Combined sources
Beta strandi123 – 1297Combined sources
Helixi132 – 14615Combined sources
Helixi153 – 16513Combined sources
Helixi168 – 1758Combined sources
Turni176 – 1783Combined sources
Beta strandi180 – 1845Combined sources
Helixi189 – 20315Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UKYX-ray2.13A2-204[»]
1UKZX-ray1.90A2-204[»]
ProteinModelPortaliP15700.
SMRiP15700. Positions 9-204.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP15700.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni46 – 7631NMPbindUniRule annotation2 PublicationsAdd
BLAST
Regioni141 – 15111LIDUniRule annotation2 PublicationsAdd
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 annotation2 Publications

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00390000016215.
HOGENOMiHOG000238771.
InParanoidiP15700.
KOiK13800.
OMAiEDIMLER.
OrthoDBiEOG092C5OQU.

Family and domain databases

CDDicd01428. ADK. 1 hit.
Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00235. Adenylate_kinase_Adk. 1 hit.
MF_03172. Adenylate_kinase_UMP_CMP_kin. 1 hit.
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.

P15700-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTAATTSQPA FSPDQVSVIF VLGGPGAGKG TQCEKLVKDY SFVHLSAGDL
60 70 80 90 100
LRAEQGRAGS QYGELIKNCI KEGQIVPQEI TLALLRNAIS DNVKANKHKF
110 120 130 140 150
LIDGFPRKMD QAISFERDIV ESKFILFFDC PEDIMLERLL ERGKTSGRSD
160 170 180 190 200
DNIESIKKRF NTFKETSMPV IEYFETKSKV VRVRCDRSVE DVYKDVQDAI

RDSL
Length:204
Mass (Da):22,933
Last modified:April 1, 1990 - v1
Checksum:iDDD7645EBCF4088D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M31455 Genomic DNA. Translation: AAA35194.1.
M69295 Genomic DNA. Translation: AAA35200.1.
Z28024 Genomic DNA. Translation: CAA81859.1.
AY558074 Genomic DNA. Translation: AAS56400.1.
BK006944 Genomic DNA. Translation: DAA09130.1.
PIRiA33572.
RefSeqiNP_012901.3. NM_001179590.3.

Genome annotation databases

EnsemblFungiiYKL024C; YKL024C; YKL024C.
GeneIDi853844.
KEGGisce:YKL024C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M31455 Genomic DNA. Translation: AAA35194.1.
M69295 Genomic DNA. Translation: AAA35200.1.
Z28024 Genomic DNA. Translation: CAA81859.1.
AY558074 Genomic DNA. Translation: AAS56400.1.
BK006944 Genomic DNA. Translation: DAA09130.1.
PIRiA33572.
RefSeqiNP_012901.3. NM_001179590.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UKYX-ray2.13A2-204[»]
1UKZX-ray1.90A2-204[»]
ProteinModelPortaliP15700.
SMRiP15700. Positions 9-204.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34107. 15 interactions.
DIPiDIP-4756N.
MINTiMINT-529742.

Proteomic databases

MaxQBiP15700.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYKL024C; YKL024C; YKL024C.
GeneIDi853844.
KEGGisce:YKL024C.

Organism-specific databases

EuPathDBiFungiDB:YKL024C.
SGDiS000001507. URA6.

Phylogenomic databases

GeneTreeiENSGT00390000016215.
HOGENOMiHOG000238771.
InParanoidiP15700.
KOiK13800.
OMAiEDIMLER.
OrthoDBiEOG092C5OQU.

Enzyme and pathway databases

BioCyciMetaCyc:YKL024C-MONOMER.
YEAST:YKL024C-MONOMER.
BRENDAi2.7.4.B1. 984.
ReactomeiR-SCE-499943. Synthesis and interconversion of nucleotide di- and triphosphates.

Miscellaneous databases

EvolutionaryTraceiP15700.
PROiP15700.

Family and domain databases

CDDicd01428. ADK. 1 hit.
Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00235. Adenylate_kinase_Adk. 1 hit.
MF_03172. Adenylate_kinase_UMP_CMP_kin. 1 hit.
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]
ProtoNetiSearch...

Entry informationi

Entry nameiKCY_YEAST
AccessioniPrimary (citable) accession number: P15700
Secondary accession number(s): D6VXR0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: April 1, 1990
Last modified: September 7, 2016
This is version 159 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1500 molecules/cell in log phase SD medium.1 Publication

Caution

There is controversy about the substrate specificity of the enzyme. Next to the primary substrate UMP, PubMed:1333436 and Ref. 8 report that the enzyme accepts also CMP and AMP as nucleoside monophosphates, but not GMP, whereas PubMed:2172245 and PubMed:8391780 report activity with GMP and dTMP, but not AMP or CMP.4 Publications

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.