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P22887

- NDKC_DICDI

UniProt

P22887 - NDKC_DICDI

Protein

Nucleoside diphosphate kinase, cytosolic

Gene

ndkC-1

more
Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 131 (01 Oct 2014)
      Sequence version 1 (01 Aug 1991)
      Previous versions | rss
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    Functioni

    Major role in the synthesis of nucleoside triphosphates other than ATP.

    Catalytic activityi

    ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

    Cofactori

    Magnesium.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei16 – 161ATP
    Binding sitei64 – 641ATP
    Binding sitei92 – 921ATP
    Binding sitei98 – 981ATP
    Binding sitei109 – 1091ATP
    Binding sitei119 – 1191ATP
    Active sitei122 – 1221Pros-phosphohistidine intermediate

    GO - Molecular functioni

    1. ATP binding Source: dictyBase
    2. metal ion binding Source: UniProtKB-KW
    3. nucleoside diphosphate kinase activity Source: dictyBase

    GO - Biological processi

    1. actin cytoskeleton organization Source: dictyBase
    2. cell growth Source: dictyBase
    3. CTP biosynthetic process Source: InterPro
    4. dGDP phosphorylation Source: dictyBase
    5. dGTP biosynthetic process from dGDP Source: dictyBase
    6. G-protein coupled receptor signaling pathway Source: dictyBase
    7. GTP biosynthetic process Source: InterPro
    8. negative regulation of exocytosis Source: dictyBase
    9. negative regulation of phagocytosis Source: dictyBase
    10. negative regulation of pinocytosis Source: dictyBase
    11. nucleoside triphosphate biosynthetic process Source: dictyBase
    12. response to bacterium Source: dictyBase
    13. translational elongation Source: dictyBase
    14. UTP biosynthetic process Source: InterPro

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Nucleotide metabolism

    Keywords - Ligandi

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

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nucleoside diphosphate kinase, cytosolic (EC:2.7.4.6)
    Short name:
    NDK
    Short name:
    NDP kinase
    Gene namesi
    Name:ndkC-1
    Synonyms:gip17, ndkB
    ORF Names:DDB_G0273069
    AND
    Name:ndkC-2
    Synonyms:gip17, ndkB
    ORF Names:DDB_G0273805
    OrganismiDictyostelium discoideum (Slime mold)
    Taxonomic identifieri44689 [NCBI]
    Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
    ProteomesiUP000002195: Chromosome 2, UP000002195: Unassembled WGS sequence

    Organism-specific databases

    dictyBaseiDDB_G0273069. ndkC-1.
    DDB_G0273805. ndkC-2.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: dictyBase
    2. cytoskeleton Source: dictyBase
    3. phagocytic vesicle Source: dictyBase
    4. plasma membrane Source: dictyBase
    5. ribosome Source: dictyBase
    6. secretory granule Source: dictyBase

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 155155Nucleoside diphosphate kinase, cytosolicPRO_0000137107Add
    BLAST

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PRIDEiP22887.

    2D gel databases

    SWISS-2DPAGEP22887.

    Interactioni

    Subunit structurei

    Homohexamer.

    Protein-protein interaction databases

    STRINGi44689.DDB_0185051.

    Structurei

    Secondary structure

    1
    155
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 83
    Beta strandi10 – 156
    Helixi17 – 215
    Helixi25 – 3511
    Beta strandi38 – 458
    Helixi49 – 557
    Helixi57 – 593
    Beta strandi60 – 623
    Helixi65 – 728
    Beta strandi77 – 848
    Helixi87 – 959
    Helixi100 – 1023
    Helixi108 – 1125
    Beta strandi116 – 1183
    Beta strandi121 – 1233
    Helixi127 – 13711
    Helixi140 – 1423
    Turni151 – 1533

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1B4SX-ray2.50A/B/C1-155[»]
    1B99X-ray2.70A/B/C/D/E/F1-155[»]
    1BUXX-ray2.80A/B/C1-155[»]
    1F3FX-ray1.85A/B/C1-155[»]
    1F6TX-ray1.92A/B/C1-155[»]
    1HHQX-ray2.10A1-155[»]
    1HIYX-ray2.60A/B/C1-155[»]
    1HLWX-ray1.90A1-155[»]
    1KDNX-ray2.00A/B/C1-155[»]
    1LEOX-ray2.60A6-155[»]
    1LWXX-ray2.30A/B/C1-155[»]
    1MN7X-ray2.15A/B1-155[»]
    1MN9X-ray2.90A/B/C1-155[»]
    1NCLX-ray2.20A6-155[»]
    1NDCX-ray2.00A1-155[»]
    1NDKX-ray2.20A1-155[»]
    1NDPX-ray2.20A/B1-155[»]
    1NPKX-ray1.80A2-155[»]
    1NSPX-ray2.10A1-155[»]
    1PAEX-ray2.70X1-155[»]
    1S5ZX-ray2.00A/B/C/D/E/F1-155[»]
    2BEFX-ray2.30A/B/C1-155[»]
    3FKBX-ray1.65A/B/C/D/E/F1-155[»]
    4C6AX-ray1.25A2-155[»]
    ProteinModelPortaliP22887.
    SMRiP22887. Positions 5-155.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP22887.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the NDK family.Curated

    Phylogenomic databases

    eggNOGiCOG0105.
    KOiK00940.
    OMAiGGENWIS.
    PhylomeDBiP22887.

    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.

    P22887-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTNKVNKER TFLAVKPDGV ARGLVGEIIA RYEKKGFVLV GLKQLVPTKD    50
    LAESHYAEHK ERPFFGGLVS FITSGPVVAM VFEGKGVVAS ARLMIGVTNP 100
    LASAPGSIRG DFGVDVGRNI IHGSDSVESA NREIALWFKP EELLTEVKPN 150
    PNLYE 155
    Length:155
    Mass (Da):16,794
    Last modified:August 1, 1991 - v1
    Checksum:i426DB78B1AF2307A
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05457 mRNA. Translation: AAA33231.1.
    L23067 Genomic DNA. Translation: AAA16161.1.
    AAFI02000011 Genomic DNA. Translation: EAL70593.1.
    AAFI02000009 Genomic DNA. Translation: EAL70752.1.
    PIRiA49547.
    RefSeqiXP_644519.1. XM_639427.1.
    XP_644731.1. XM_639639.1.

    Genome annotation databases

    EnsemblProtistsiDDB0185051; DDB0185051; DDB_G0273069.
    DDB0238334; DDB0238334; DDB_G0273805.
    GeneIDi8618831.
    8619145.
    KEGGiddi:DDB_G0273069.
    ddi:DDB_G0273805.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05457 mRNA. Translation: AAA33231.1 .
    L23067 Genomic DNA. Translation: AAA16161.1 .
    AAFI02000011 Genomic DNA. Translation: EAL70593.1 .
    AAFI02000009 Genomic DNA. Translation: EAL70752.1 .
    PIRi A49547.
    RefSeqi XP_644519.1. XM_639427.1.
    XP_644731.1. XM_639639.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1B4S X-ray 2.50 A/B/C 1-155 [» ]
    1B99 X-ray 2.70 A/B/C/D/E/F 1-155 [» ]
    1BUX X-ray 2.80 A/B/C 1-155 [» ]
    1F3F X-ray 1.85 A/B/C 1-155 [» ]
    1F6T X-ray 1.92 A/B/C 1-155 [» ]
    1HHQ X-ray 2.10 A 1-155 [» ]
    1HIY X-ray 2.60 A/B/C 1-155 [» ]
    1HLW X-ray 1.90 A 1-155 [» ]
    1KDN X-ray 2.00 A/B/C 1-155 [» ]
    1LEO X-ray 2.60 A 6-155 [» ]
    1LWX X-ray 2.30 A/B/C 1-155 [» ]
    1MN7 X-ray 2.15 A/B 1-155 [» ]
    1MN9 X-ray 2.90 A/B/C 1-155 [» ]
    1NCL X-ray 2.20 A 6-155 [» ]
    1NDC X-ray 2.00 A 1-155 [» ]
    1NDK X-ray 2.20 A 1-155 [» ]
    1NDP X-ray 2.20 A/B 1-155 [» ]
    1NPK X-ray 1.80 A 2-155 [» ]
    1NSP X-ray 2.10 A 1-155 [» ]
    1PAE X-ray 2.70 X 1-155 [» ]
    1S5Z X-ray 2.00 A/B/C/D/E/F 1-155 [» ]
    2BEF X-ray 2.30 A/B/C 1-155 [» ]
    3FKB X-ray 1.65 A/B/C/D/E/F 1-155 [» ]
    4C6A X-ray 1.25 A 2-155 [» ]
    ProteinModelPortali P22887.
    SMRi P22887. Positions 5-155.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 44689.DDB_0185051.

    2D gel databases

    SWISS-2DPAGE P22887.

    Proteomic databases

    PRIDEi P22887.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblProtistsi DDB0185051 ; DDB0185051 ; DDB_G0273069 .
    DDB0238334 ; DDB0238334 ; DDB_G0273805 .
    GeneIDi 8618831.
    8619145.
    KEGGi ddi:DDB_G0273069.
    ddi:DDB_G0273805.

    Organism-specific databases

    dictyBasei DDB_G0273069. ndkC-1.
    DDB_G0273805. ndkC-2.

    Phylogenomic databases

    eggNOGi COG0105.
    KOi K00940.
    OMAi GGENWIS.
    PhylomeDBi P22887.

    Miscellaneous databases

    EvolutionaryTracei P22887.

    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. "Functional cloning of a nucleoside diphosphate kinase from Dictyostelium discoideum."
      Lacombe M.-L., Wallet V., Troll H., Veron M.
      J. Biol. Chem. 265:10012-10018(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Separate nuclear genes encode cytosolic and mitochondrial nucleoside diphosphate kinase in Dictyostelium discoideum."
      Troll H., Winckler T., Lascu I., Mueller N., Saurin W., Veron M., Mutzel R.
      J. Biol. Chem. 268:25469-25475(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: AX2.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AX4.
    4. "The genome of the social amoeba Dictyostelium discoideum."
      Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
      , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
      Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AX4.
    5. "Proteomics fingerprinting of phagosome maturation and evidence for the role of a Galpha during uptake."
      Gotthardt D., Blancheteau V., Bosserhoff A., Ruppert T., Delorenzi M., Soldati T.
      Mol. Cell. Proteomics 5:2228-2243(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: AX2.
    6. "X-ray structure of nucleoside diphosphate kinase."
      Dumas C., Lascu I., Morera S., Glaser P., Fourme R., Wallet V., Lacombe M.-L., Veron M., Janin J.
      EMBO J. 11:3203-3208(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
    7. "Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate kinase at 1.8-A resolution."
      Morera S., Lebras G., Lascu I., Lacombe M.-L., Veron M., Janin J.
      J. Mol. Biol. 243:873-890(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
    8. "Nucleoside diphosphate kinase. Investigation of the intersubunit contacts by site-directed mutagenesis and crystallography."
      Karlsson A., Mesnildrey S., Xu Y., Morera S., Janin J., Veron M.
      J. Biol. Chem. 271:19928-19934(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
    9. "X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase."
      Xu Y., Sellam O., Morera S., Sarfati S., Biondi R., Veron M., Janin J.
      Proc. Natl. Acad. Sci. U.S.A. 94:7162-7165(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
    10. "3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity."
      Schneider B., Xu Y.W., Janin J., Veron M., Deville-Bonne D.
      J. Biol. Chem. 273:28773-28778(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
    11. "Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase."
      Admiraal S.J., Schneider B., Meyer P., Janin J., Veron M., Deville-Bonne D., Herschlag D.
      Biochemistry 38:4701-4711(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
    12. "Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography."
      Gonin P., Xu Y., Milon L., Dabernat S., Morr M., Kumar R., Lacombe M.L., Janin J., Lascu I.
      Biochemistry 38:7265-7272(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).

    Entry informationi

    Entry nameiNDKC_DICDI
    AccessioniPrimary (citable) accession number: P22887
    Secondary accession number(s): Q556V0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1991
    Last sequence update: August 1, 1991
    Last modified: October 1, 2014
    This is version 131 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Caution

    The gene for this protein is duplicated in strains AX3 and AX4. These strains contain a duplication of a segment of 750 kb of chromosome 2 compared to the corresponding sequence in strain AX2.Curated

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Dictyostelium discoideum
      Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3