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P15700

- KCY_YEAST

UniProt

P15700 - KCY_YEAST

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Protein
Uridylate kinase
Gene
URA6, SOC8, YKL024C
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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 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.4 Publications

Catalytic activityi

ATP + UMP = ADP + UDP.5 Publications

Cofactori

Binds 1 magnesium ion per monomer.2 Publications

Kineticsi

  1. KM=0.15 mM for UMP2 Publications
  2. KM=1.0 mM for dUMP
  3. KM=1.8 mM for dTMP
  4. KM=0.11 mM for ATP
  5. KM=0.53 mM for dCMP

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

pH dependencei

Optimum pH is 6-9.5.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei52 – 521NMP
Binding sitei111 – 1111NMP
Binding sitei142 – 1421ATP
Binding sitei148 – 1481NMP
Binding sitei159 – 1591NMP
Binding sitei187 – 1871ATP; via carbonyl oxygen

Regions

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

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. adenylate kinase activity Source: SGD
  3. cytidylate kinase activity Source: UniProtKB-EC
  4. uridylate kinase activity Source: SGD

GO - Biological processi

  1. 'de novo' pyrimidine nucleobase biosynthetic process Source: SGD
  2. nucleobase-containing compound metabolic process Source: SGD
  3. pyrimidine nucleotide biosynthetic process Source: UniProtKB-KW
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.
BRENDAi2.7.4.14. 9228.

Names & Taxonomyi

Protein namesi
Recommended name:
Uridylate kinase (EC:2.7.4.14)
Short name:
UK
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 namesi
Name:URA6
Synonyms:SOC8
Ordered Locus Names:YKL024C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XI

Organism-specific databases

CYGDiYKL024c.
SGDiS000001507. URA6.

Subcellular locationi

Cytoplasm. Nucleus
Note: Predominantly cytoplasmic.2 Publications

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. 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 kinaseUniRule annotation
PRO_0000158947Add
BLAST

Proteomic databases

MaxQBiP15700.
PaxDbiP15700.
PeptideAtlasiP15700.

Expressioni

Gene expression databases

GenevestigatoriP15700.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi34107. 16 interactions.
DIPiDIP-4756N.
MINTiMINT-529742.
STRINGi4932.YKL024C.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UKYX-ray2.13A2-204[»]
1UKZX-ray1.90A2-204[»]
ProteinModelPortaliP15700.
SMRiP15700. Positions 9-204.

Miscellaneous databases

EvolutionaryTraceiP15700.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni46 – 7631NMPbindUniRule annotation
Add
BLAST
Regioni141 – 15111LIDUniRule 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.
GeneTreeiENSGT00390000016215.
HOGENOMiHOG000238771.
KOiK13800.
OMAiQAVKFEE.
OrthoDBiEOG7BCNPJ.

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.

P15700-1 [UniParc]FASTAAdd to Basket

« Hide

MTAATTSQPA FSPDQVSVIF VLGGPGAGKG TQCEKLVKDY SFVHLSAGDL    50
LRAEQGRAGS QYGELIKNCI KEGQIVPQEI TLALLRNAIS DNVKANKHKF 100
LIDGFPRKMD QAISFERDIV ESKFILFFDC PEDIMLERLL ERGKTSGRSD 150
DNIESIKKRF NTFKETSMPV IEYFETKSKV VRVRCDRSVE DVYKDVQDAI 200
RDSL 204
Length:204
Mass (Da):22,933
Last modified:April 1, 1990 - v1
Checksum:iDDD7645EBCF4088D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
PIRi A33572.
RefSeqi NP_012901.3. NM_001179590.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1UKY X-ray 2.13 A 2-204 [» ]
1UKZ X-ray 1.90 A 2-204 [» ]
ProteinModelPortali P15700.
SMRi P15700. Positions 9-204.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34107. 16 interactions.
DIPi DIP-4756N.
MINTi MINT-529742.
STRINGi 4932.YKL024C.

Chemistry

DrugBanki DB00131. Adenosine monophosphate.

Proteomic databases

MaxQBi P15700.
PaxDbi P15700.
PeptideAtlasi P15700.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YKL024C ; YKL024C ; YKL024C .
GeneIDi 853844.
KEGGi sce:YKL024C.

Organism-specific databases

CYGDi YKL024c.
SGDi S000001507. URA6.

Phylogenomic databases

eggNOGi COG0563.
GeneTreei ENSGT00390000016215.
HOGENOMi HOG000238771.
KOi K13800.
OMAi QAVKFEE.
OrthoDBi EOG7BCNPJ.

Enzyme and pathway databases

BioCyci MetaCyc:YKL024C-MONOMER.
YEAST:YKL024C-MONOMER.
BRENDAi 2.7.4.14. 9228.

Miscellaneous databases

EvolutionaryTracei P15700.
NextBioi 975061.
PROi P15700.

Gene expression databases

Genevestigatori P15700.

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. "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.
    , 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. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. 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. 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.

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: May 14, 2014
This is version 141 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.

Caution

There is controversy about the substrate specificity of the enzyme. Next to the primary substrate UMP, 1 Publication and 1 Publication report that the enzyme accepts also CMP and AMP as nucleoside monophosphates, but not GMP, whereas 1 Publication and 1 Publication report activity with GMP and dTMP, but not AMP or CMP.

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

External Data

Dasty 3

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