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P15700 (KCY_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 141. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | 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:
Uridylate kinase

Short name=UK
EC=2.7.4.14
Alternative name(s):
ATP:UMP phosphotransferase
Deoxycytidylate kinase
Short name=CK
Short name=dCMP kinase
Suppressor of cdc8 protein
Uridine monophosphate kinase
Short name=UMP kinase
Short name=UMPK
Gene names
Name:URA6
Synonyms:SOC8
Ordered Locus Names:YKL024C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length204 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 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. Ref.7 Ref.8 Ref.9 Ref.10

Catalytic activity

ATP + UMP = ADP + UDP. Ref.2 Ref.6 Ref.7 Ref.9 Ref.12

Cofactor

Binds 1 magnesium ion per monomer. Ref.10 Ref.12

Subunit structure

Monomer. Ref.7

Subcellular location

Cytoplasm. Nucleus. Note: Predominantly cytoplasmic. Ref.9 Ref.10

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

Miscellaneous

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

Sequence similarities

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

Caution

There is controversy about the substrate specificity of the enzyme. Next to the primary substrate UMP, Ref.9 and Ref.8 report that the enzyme accepts also CMP and AMP as nucleoside monophosphates, but not GMP, whereas Ref.7 and Ref.10 report activity with GMP and dTMP, but not AMP or CMP.

Biophysicochemical properties

Kinetic parameters:

KM=0.15 mM for UMP Ref.7 Ref.10

KM=1.0 mM for dUMP

KM=1.8 mM for dTMP

KM=0.11 mM for ATP

KM=0.53 mM for dCMP

Vmax=120 µmol/min/mg enzyme (for dCDP synthesis)

pH dependence:

Optimum pH is 6-9.5.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 204204Uridylate kinase HAMAP-Rule MF_03172
PRO_0000158947

Regions

Nucleotide binding26 – 316ATP HAMAP-Rule MF_03172
Nucleotide binding74 – 763NMP HAMAP-Rule MF_03172
Nucleotide binding104 – 1074NMP HAMAP-Rule MF_03172
Region46 – 7631NMPbind HAMAP-Rule MF_03172
Region141 – 15111LID HAMAP-Rule MF_03172

Sites

Binding site521NMP
Binding site1111NMP
Binding site1421ATP
Binding site1481NMP
Binding site1591NMP
Binding site1871ATP; via carbonyl oxygen

Experimental info

Mutagenesis291K → E: Abolishes catalytic activity. Ref.2

Secondary structure

............................... 204
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P15700 [UniParc].

Last modified April 1, 1990. Version 1.
Checksum: DDD7645EBCF4088D

FASTA20422,933
        10         20         30         40         50         60 
MTAATTSQPA FSPDQVSVIF VLGGPGAGKG TQCEKLVKDY SFVHLSAGDL LRAEQGRAGS 

        70         80         90        100        110        120 
QYGELIKNCI KEGQIVPQEI TLALLRNAIS DNVKANKHKF LIDGFPRKMD QAISFERDIV 

       130        140        150        160        170        180 
ESKFILFFDC PEDIMLERLL ERGKTSGRSD DNIESIKKRF NTFKETSMPV IEYFETKSKV 

       190        200 
VRVRCDRSVE DVYKDVQDAI RDSL 

« Hide

References

« Hide 'large scale' references
[1]"Primary structure of the S. cerevisiae gene encoding uridine monophosphokinase."
Liljelund P., Sanni A., Friesen J.D., Lacroute F.
Biochem. Biophys. Res. Commun. 165:464-473(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: FL100A.
[2]"Molecular characterization of Saccharomyces cerevisiae URA6 gene. DNA sequence, mutagenesis analysis, and cell cycle regulation relevant to its suppression mechanism to cdc8 mutation."
Jiang Z., Abaigar L.T., Huang S.-H., Cai B., Jong A.Y.
J. Biol. Chem. 266:18287-18293(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, MUTAGENESIS OF LYS-29.
[3]"Complete DNA sequence of yeast chromosome XI."
Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. expand/collapse author list , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[6]"The Saccharomyces cerevisiae SOC8-1 gene and its relationship to a nucleotide kinase."
Choi W.J., Campbell J.L., Kuo C.L., Jong A.Y.
J. Biol. Chem. 264:15593-15599(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY.
[7]"Purification and characterization of Saccharomyces cerevisiae uridine monophosphate kinase."
Ma J.J., Huang S.H., Jong A.Y.
J. Biol. Chem. 265:19122-19127(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY.
[8]"Reinigung, charakterisierung und kristallisation der uridylatkinase aus Hefe."
Mueller-Dieckmann H.-J.
Thesis (1990), Universitaet Freiburg im Breisgau, Germany
Cited for: FUNCTION, SUBSTRATE SPECIFICITY.
[9]"The adenylate kinase family in yeast: identification of URA6 as a multicopy suppressor of deficiency in major AMP kinase."
Schricker R., Magdolen V., Kaniak A., Wolf K., Bandlow W.
Gene 122:111-118(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, SUBSTRATE SPECIFICITY.
[10]"Characteristics, substrate analysis, and intracellular location of Saccharomyces cerevisiae UMP kinase."
Jong A., Yeh Y., Ma J.J.
Arch. Biochem. Biophys. 304:197-204(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, COFACTOR, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY.
[11]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]"Cloning of deoxynucleoside monophosphate kinase genes and biosynthesis of deoxynucleoside diphosphates."
Bao J., Ryu D.D.
Biotechnol. Bioeng. 93:572-580(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY, COFACTOR.
[13]"The structure of uridylate kinase with its substrates, showing the transition state geometry."
Mueller-Dieckmann H.-J., Schulz G.E.
J. Mol. Biol. 236:361-367(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 2-204 IN COMPLEX WITH ADP AND AMP.
[14]"Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase."
Mueller-Dieckmann H.-J., Schulz G.E.
J. Mol. Biol. 246:522-530(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 2-204 IN COMPLEX WITH ADP AND AMP.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA33572.
RefSeqNP_012901.3. NM_001179590.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1UKYX-ray2.13A2-204[»]
1UKZX-ray1.90A2-204[»]
ProteinModelPortalP15700.
SMRP15700. Positions 9-204.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34107. 16 interactions.
DIPDIP-4756N.
MINTMINT-529742.
STRING4932.YKL024C.

Chemistry

DrugBankDB00131. Adenosine monophosphate.

Proteomic databases

MaxQBP15700.
PaxDbP15700.
PeptideAtlasP15700.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYKL024C; YKL024C; YKL024C.
GeneID853844.
KEGGsce:YKL024C.

Organism-specific databases

CYGDYKL024c.
SGDS000001507. URA6.

Phylogenomic databases

eggNOGCOG0563.
GeneTreeENSGT00390000016215.
HOGENOMHOG000238771.
KOK13800.
OMAQAVKFEE.
OrthoDBEOG7BCNPJ.

Enzyme and pathway databases

BioCycMetaCyc:YKL024C-MONOMER.
YEAST:YKL024C-MONOMER.
BRENDA2.7.4.14. 9228.

Gene expression databases

GenevestigatorP15700.

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

EvolutionaryTraceP15700.
NextBio975061.
PROP15700.

Entry information

Entry nameKCY_YEAST
AccessionPrimary (citable) accession number: P15700
Secondary accession number(s): D6VXR0
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: April 1, 1990
Last modified: May 14, 2014
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XI

Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references