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P36010

- NDK_YEAST

UniProt

P36010 - NDK_YEAST

Protein

Nucleoside diphosphate kinase

Gene

YNK1

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 129 (01 Oct 2014)
      Sequence version 1 (01 Jun 1994)
      Previous versions | rss
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    Functioni

    Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Required for repair of UV radiation- and etoposide-induced DNA damage.1 Publication

    Catalytic activityi

    ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

    Cofactori

    Magnesium.By similarity

    Kineticsi

    1. KM=25 µM for ADP2 Publications
    2. KM=300 µM for CDP2 Publications
    3. KM=690 µM for UDP2 Publications
    4. KM=400 µM for dCDP2 Publications
    5. KM=220 µM for dGDP2 Publications
    6. KM=370 µM for dTDP2 Publications
    7. KM=530 µM for dUDP2 Publications
    8. KM=220 µM for ATP2 Publications
    9. KM=100 µM for CTP2 Publications
    10. KM=150 µM for GTP2 Publications
    11. KM=140 µM for UTP2 Publications
    12. KM=170 µM for dCTP2 Publications
    13. KM=22 µM for dGTP2 Publications
    14. KM=110 µM for dTTP2 Publications
    15. KM=130 µM for dUTP2 Publications

    Vmax=130 µmol/min/mg enzyme toward ADP2 Publications

    Vmax=220 µmol/min/mg enzyme toward CDP2 Publications

    Vmax=400 µmol/min/mg enzyme toward UDP2 Publications

    Vmax=380 µmol/min/mg enzyme toward dCDP2 Publications

    Vmax=132 µmol/min/mg enzyme toward dGDP2 Publications

    Vmax=330 µmol/min/mg enzyme toward dTDP2 Publications

    Vmax=8.6 nmol/min/mg enzyme toward dUDP2 Publications

    Vmax=170 µmol/min/mg enzyme toward ATP2 Publications

    Vmax=83 µmol/min/mg enzyme toward CTP2 Publications

    Vmax=350 µmol/min/mg enzyme toward GTP2 Publications

    Vmax=75 µmol/min/mg enzyme toward UTP2 Publications

    Vmax=110 µmol/min/mg enzyme toward dCTP2 Publications

    Vmax=38 µmol/min/mg enzyme toward dGTP2 Publications

    Vmax=105 µmol/min/mg enzyme toward dTTP2 Publications

    Vmax=90 µmol/min/mg enzyme toward dUTP2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei13 – 131ATPBy similarity
    Binding sitei61 – 611ATPBy similarity
    Binding sitei89 – 891ATPBy similarity
    Binding sitei95 – 951ATPBy similarity
    Binding sitei106 – 1061ATPBy similarity
    Binding sitei116 – 1161ATPBy similarity
    Active sitei119 – 1191Pros-phosphohistidine intermediateBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. identical protein binding Source: IntAct
    3. metal ion binding Source: UniProtKB-KW
    4. nucleoside diphosphate kinase activity Source: SGD

    GO - Biological processi

    1. cellular response to DNA damage stimulus Source: SGD
    2. CTP biosynthetic process Source: InterPro
    3. DNA repair Source: UniProtKB-KW
    4. GTP biosynthetic process Source: InterPro
    5. nucleoside diphosphate phosphorylation Source: SGD
    6. nucleoside triphosphate biosynthetic process Source: SGD
    7. UTP biosynthetic process Source: InterPro

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    DNA damage, DNA repair, Nucleotide metabolism

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:YKL067W-MONOMER.
    YEAST:YKL067W-MONOMER.
    SABIO-RKP36010.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nucleoside diphosphate kinase (EC:2.7.4.6)
    Short name:
    NDK
    Short name:
    NDP kinase
    Gene namesi
    Name:YNK1
    Synonyms:NDK1, YNK
    Ordered Locus Names:YKL067W
    ORF Names:YKL333
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XI

    Organism-specific databases

    CYGDiYKL067w.
    SGDiS000001550. YNK1.

    Subcellular locationi

    Cytoplasm 1 Publication. Mitochondrion intermembrane space 1 Publication
    Note: Localizes predominantly to the cytoplasm. A small fraction is present in the mitochondrial intermembrane space.

    GO - Cellular componenti

    1. cytosol Source: SGD
    2. mitochondrial intermembrane space Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Mitochondrion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 153153Nucleoside diphosphate kinasePRO_0000137153Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei95 – 951Phosphothreonine1 Publication

    Post-translational modificationi

    The N-terminus is blocked.

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP36010.
    PaxDbiP36010.
    PeptideAtlasiP36010.

    2D gel databases

    UCD-2DPAGEP36010.

    Expressioni

    Gene expression databases

    GenevestigatoriP36010.

    Interactioni

    Subunit structurei

    Homohexamer and homotetramer. Interacts with TOM40 preferentially in an unfolded, unphosphorylated form.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-11968,EBI-11968

    Protein-protein interaction databases

    BioGridi34067. 41 interactions.
    DIPiDIP-1969N.
    IntActiP36010. 36 interactions.
    MINTiMINT-402348.
    STRINGi4932.YKL067W.

    Structurei

    Secondary structure

    1
    153
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 126
    Helixi14 – 196
    Helixi22 – 3211
    Beta strandi35 – 428
    Helixi46 – 527
    Helixi63 – 708
    Beta strandi74 – 818
    Helixi84 – 929
    Helixi97 – 993
    Helixi105 – 1095
    Beta strandi117 – 1204
    Helixi124 – 13411
    Helixi148 – 1514

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3B54X-ray3.10A/B1-153[»]
    ProteinModelPortaliP36010.
    SMRiP36010. Positions 2-153.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP36010.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the NDK family.Curated

    Phylogenomic databases

    eggNOGiCOG0105.
    GeneTreeiENSGT00700000104244.
    HOGENOMiHOG000224564.
    KOiK00940.
    OMAiARSHSIH.
    OrthoDBiEOG7J9W2D.

    Family and domain databases

    Gene3Di3.30.70.141. 1 hit.
    HAMAPiMF_00451. NDP_kinase.
    InterProiIPR001564. Nucleoside_diP_kinase.
    IPR023005. Nucleoside_diP_kinase_AS.
    [Graphical view]
    PfamiPF00334. NDK. 1 hit.
    [Graphical view]
    PRINTSiPR01243. NUCDPKINASE.
    SMARTiSM00562. NDK. 1 hit.
    [Graphical view]
    SUPFAMiSSF54919. SSF54919. 1 hit.
    PROSITEiPS00469. NDP_KINASES. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P36010-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSSQTERTFI AVKPDGVQRG LVSQILSRFE KKGYKLVAIK LVKADDKLLE    50
    QHYAEHVGKP FFPKMVSFMK SGPILATVWE GKDVVRQGRT ILGATNPLGS 100
    APGTIRGDFG IDLGRNVCHG SDSVDSAERE INLWFKKEEL VDWESNQAKW 150
    IYE 153
    Length:153
    Mass (Da):17,167
    Last modified:June 1, 1994 - v1
    Checksum:iBE37ACED90A44D00
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D13562 Genomic DNA. Translation: BAA02758.1.
    X75780 Genomic DNA. Translation: CAA53407.1.
    Z28067 Genomic DNA. Translation: CAA81904.1.
    AY558263 Genomic DNA. Translation: AAS56589.1.
    BK006944 Genomic DNA. Translation: DAA09090.1.
    PIRiS37889.
    RefSeqiNP_012856.1. NM_001179633.1.

    Genome annotation databases

    EnsemblFungiiYKL067W; YKL067W; YKL067W.
    GeneIDi853798.
    KEGGisce:YKL067W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D13562 Genomic DNA. Translation: BAA02758.1 .
    X75780 Genomic DNA. Translation: CAA53407.1 .
    Z28067 Genomic DNA. Translation: CAA81904.1 .
    AY558263 Genomic DNA. Translation: AAS56589.1 .
    BK006944 Genomic DNA. Translation: DAA09090.1 .
    PIRi S37889.
    RefSeqi NP_012856.1. NM_001179633.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3B54 X-ray 3.10 A/B 1-153 [» ]
    ProteinModelPortali P36010.
    SMRi P36010. Positions 2-153.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34067. 41 interactions.
    DIPi DIP-1969N.
    IntActi P36010. 36 interactions.
    MINTi MINT-402348.
    STRINGi 4932.YKL067W.

    2D gel databases

    UCD-2DPAGE P36010.

    Proteomic databases

    MaxQBi P36010.
    PaxDbi P36010.
    PeptideAtlasi P36010.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YKL067W ; YKL067W ; YKL067W .
    GeneIDi 853798.
    KEGGi sce:YKL067W.

    Organism-specific databases

    CYGDi YKL067w.
    SGDi S000001550. YNK1.

    Phylogenomic databases

    eggNOGi COG0105.
    GeneTreei ENSGT00700000104244.
    HOGENOMi HOG000224564.
    KOi K00940.
    OMAi ARSHSIH.
    OrthoDBi EOG7J9W2D.

    Enzyme and pathway databases

    BioCyci MetaCyc:YKL067W-MONOMER.
    YEAST:YKL067W-MONOMER.
    SABIO-RK P36010.

    Miscellaneous databases

    EvolutionaryTracei P36010.
    NextBioi 974942.
    PROi P36010.

    Gene expression databases

    Genevestigatori P36010.

    Family and domain databases

    Gene3Di 3.30.70.141. 1 hit.
    HAMAPi MF_00451. NDP_kinase.
    InterProi IPR001564. Nucleoside_diP_kinase.
    IPR023005. Nucleoside_diP_kinase_AS.
    [Graphical view ]
    Pfami PF00334. NDK. 1 hit.
    [Graphical view ]
    PRINTSi PR01243. NUCDPKINASE.
    SMARTi SM00562. NDK. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54919. SSF54919. 1 hit.
    PROSITEi PS00469. NDP_KINASES. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Isolation, overexpression and disruption of a Saccharomyces cerevisiae YNK gene encoding nucleoside diphosphate kinase."
      Fukuchi T., Nikawa J., Kimura N., Watanabe K.
      Gene 129:141-146(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: SP1.
    2. "Sequence of a 20.7 kb region of yeast chromosome XI includes the NUP100 gene, an open reading frame (ORF) possibly representing a nucleoside diphosphate kinase gene, tRNAs for His, Val and Trp in addition to seven ORFs with weak or no significant similarity to known proteins."
      Rasmussen S.W.
      Yeast 10:S69-S74(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    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. "Nucleoside triphosphate-nucleoside diphosphate transphosphorylase (nucleoside diphosphokinase). 3. Subunit structure of the crystalline enzyme from brewers' yeast."
      Palmieri R., Yue R.H., Jacobs H.K., Maland L., Wu L., Kuby S.A.
      J. Biol. Chem. 248:4486-4499(1973) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    7. "Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity."
      Jong A.Y., Ma J.J.
      Arch. Biochem. Biophys. 291:241-246(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    8. "Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Ynk1p: localization to the mitochondrial intermembrane space."
      Amutha B., Pain D.
      Biochem. J. 370:805-815(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, INTERACTION WITH TOM40.
    9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    10. "The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for deoxypyrimidine nucleotides."
      Jeudy S., Claverie J.-M., Abergel C.
      J. Bioenerg. Biomembr. 38:247-254(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
    11. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-95, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "YNK1, the yeast homolog of human metastasis suppressor NM23, is required for repair of UV radiation- and etoposide-induced DNA damage."
      Yang M., Jarrett S.G., Craven R., Kaetzel D.M.
      Mutat. Res. 660:74-78(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    13. "Structure of Ynk1 from the yeast Saccharomyces cerevisiae."
      Wang H., Bao R., Jiang C., Yang Z., Zhou C.Z., Chen Y.
      Acta Crystallogr. F 64:572-576(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).

    Entry informationi

    Entry nameiNDK_YEAST
    AccessioniPrimary (citable) accession number: P36010
    Secondary accession number(s): D6VXM0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: June 1, 1994
    Last modified: October 1, 2014
    This is version 129 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 7130 molecules/cell in log phase SD medium.1 Publication

    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