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P15700

- KCY_YEAST

UniProt

P15700 - KCY_YEAST

Protein

Uridylate kinase

Gene

URA6

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 142 (01 Oct 2014)
      Sequence version 1 (01 Apr 1990)
      Previous versions | rss
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    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 PublicationsUniRule annotation

    Cofactori

    Binds 1 magnesium ion per monomer.2 PublicationsUniRule annotation

    Kineticsi

    1. KM=0.15 mM for UMP2 Publications
    2. KM=1.0 mM for dUMP2 Publications
    3. KM=1.8 mM for dTMP2 Publications
    4. KM=0.11 mM for ATP2 Publications
    5. KM=0.53 mM for dCMP2 Publications

    Vmax=120 µmol/min/mg enzyme (for dCDP synthesis)2 Publications

    pH dependencei

    Optimum pH is 6-9.5.2 Publications

    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 – 316ATP
    Nucleotide bindingi74 – 763NMP
    Nucleotide bindingi104 – 1074NMP

    GO - Molecular functioni

    1. adenylate kinase activity Source: SGD
    2. ATP binding Source: UniProtKB-KW
    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-HAMAP

    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 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
    ProteomesiUP000002311: Chromosome XI

    Organism-specific databases

    CYGDiYKL024c.
    SGDiS000001507. URA6.

    Subcellular locationi

    Cytoplasm. Nucleus
    Note: Predominantly cytoplasmic.

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. nucleus Source: SGD

    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.
    PaxDbiP15700.
    PeptideAtlasiP15700.

    Expressioni

    Gene expression databases

    GenevestigatoriP15700.

    Interactioni

    Subunit structurei

    Monomer.3 PublicationsUniRule annotation

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1
    204
    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP15700.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni46 – 7631NMPbindAdd
    BLAST
    Regioni141 – 15111LIDAdd
    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.

    Sequence similaritiesi

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

    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

    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: October 1, 2014
    This is version 142 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 PubMed:1333436 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.Curated

    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