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O00746

- NDKM_HUMAN

UniProt

O00746 - NDKM_HUMAN

Protein

Nucleoside diphosphate kinase, mitochondrial

Gene

NME4

Organism
Homo sapiens (Human)
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 Jul 1997)
      Previous versions | rss
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    Functioni

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

    Catalytic activityi

    ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

    Cofactori

    Magnesium.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei45 – 451ATPBy similarity
    Binding sitei93 – 931ATPBy similarity
    Binding sitei121 – 1211ATPBy similarity
    Binding sitei127 – 1271ATPBy similarity
    Binding sitei138 – 1381ATPBy similarity
    Binding sitei148 – 1481ATPBy similarity
    Active sitei151 – 1511Pros-phosphohistidine intermediateBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

    1. CTP biosynthetic process Source: InterPro
    2. GTP biosynthetic process Source: InterPro
    3. nucleobase-containing small molecule interconversion Source: Reactome
    4. nucleobase-containing small molecule metabolic process Source: Reactome
    5. nucleoside metabolic process Source: ProtInc
    6. small molecule metabolic process Source: Reactome
    7. UTP biosynthetic process Source: InterPro

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Nucleotide metabolism

    Keywords - Ligandi

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

    Enzyme and pathway databases

    ReactomeiREACT_21330. Synthesis and interconversion of nucleotide di- and triphosphates.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nucleoside diphosphate kinase, mitochondrial (EC:2.7.4.6)
    Short name:
    NDK
    Short name:
    NDP kinase, mitochondrial
    Alternative name(s):
    Nucleoside diphosphate kinase D
    Short name:
    NDPKD
    nm23-H4
    Gene namesi
    Name:NME4
    Synonyms:NM23D
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 16

    Organism-specific databases

    HGNCiHGNC:7852. NME4.

    Subcellular locationi

    GO - Cellular componenti

    1. mitochondrial inner membrane Source: Reactome
    2. mitochondrial intermembrane space Source: UniProtKB-SubCell
    3. mitochondrion Source: ProtInc

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA31657.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 3333MitochondrionSequence AnalysisAdd
    BLAST
    Chaini34 – 187154Nucleoside diphosphate kinase, mitochondrialPRO_0000019432Add
    BLAST

    Proteomic databases

    MaxQBiO00746.
    PaxDbiO00746.
    PRIDEiO00746.

    PTM databases

    PhosphoSiteiO00746.

    Expressioni

    Tissue specificityi

    Widely distributed. Found at very high levels in prostate, heart, liver, small intestine, and skeletal muscle tissues, and in low amounts in the brain and in blood leukocytes.

    Gene expression databases

    ArrayExpressiO00746.
    BgeeiO00746.
    CleanExiHS_NME4.
    GenevestigatoriO00746.

    Organism-specific databases

    HPAiCAB045996.
    CAB045997.

    Interactioni

    Subunit structurei

    Homohexamer. Interacts with CAPN8 By similarity.By similarity

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    HTTP428582EBI-744871,EBI-466029

    Protein-protein interaction databases

    BioGridi110897. 14 interactions.
    IntActiO00746. 9 interactions.
    MINTiMINT-1445974.
    STRINGi9606.ENSP00000219479.

    Structurei

    Secondary structure

    1
    187
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi35 – 373
    Beta strandi39 – 446
    Helixi46 – 505
    Helixi54 – 6310
    Beta strandi67 – 748
    Helixi78 – 847
    Helixi86 – 883
    Helixi94 – 1018
    Beta strandi106 – 1138
    Helixi116 – 1249
    Helixi129 – 1313
    Helixi137 – 1415
    Beta strandi149 – 1524
    Helixi156 – 16611
    Helixi169 – 1713

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EHWX-ray2.40A/B33-175[»]
    ProteinModelPortaliO00746.
    SMRiO00746. Positions 36-175.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO00746.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the NDK family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0105.
    HOGENOMiHOG000224564.
    HOVERGENiHBG000423.
    KOiK00940.
    OrthoDBiEOG7GJ6FG.
    PhylomeDBiO00746.
    TreeFamiTF106373.

    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]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: O00746-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MGGLFWRSAL RGLRCGPRAP GPSLLVRHGS GGPSWTRERT LVAVKPDGVQ    50
    RRLVGDVIQR FERRGFTLVG MKMLQAPESV LAEHYQDLRR KPFYPALIRY 100
    MSSGPVVAMV WEGYNVVRAS RAMIGHTDSA EAAPGTIRGD FSVHISRNVI 150
    HASDSVEGAQ REIQLWFQSS ELVSWADGGQ HSSIHPA 187
    Length:187
    Mass (Da):20,659
    Last modified:July 1, 1997 - v1
    Checksum:iA56FEF18A7D712D4
    GO
    Isoform 2 (identifier: O00746-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-70: Missing.

    Note: No experimental confirmation available. Gene prediction based on EST data.

    Show »
    Length:117
    Mass (Da):12,979
    Checksum:i3B885B828E3C1042
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 7070Missing in isoform 2. CuratedVSP_054743Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y07604 mRNA. Translation: CAA68877.1.
    BT019438 mRNA. Translation: AAV38245.1.
    AE006463 Genomic DNA. Translation: AAK61230.1.
    Z97634 Genomic DNA. Translation: CAC37288.1.
    CH471112 Genomic DNA. Translation: EAW85818.1.
    CH471112 Genomic DNA. Translation: EAW85819.1.
    CH471112 Genomic DNA. Translation: EAW85820.1.
    BC004880 mRNA. Translation: AAH04880.1.
    BC017067 mRNA. Translation: AAH17067.1.
    CCDSiCCDS10408.1. [O00746-1]
    CCDS66886.1. [O00746-2]
    RefSeqiNP_001273362.1. NM_001286433.1.
    NP_001273364.1. NM_001286435.1.
    NP_001273365.1. NM_001286436.1. [O00746-2]
    NP_001273367.1. NM_001286438.1. [O00746-2]
    NP_001273368.1. NM_001286439.1. [O00746-2]
    NP_001273369.1. NM_001286440.1. [O00746-2]
    NP_005000.1. NM_005009.2. [O00746-1]
    UniGeneiHs.9235.

    Genome annotation databases

    EnsembliENST00000219479; ENSP00000219479; ENSG00000103202. [O00746-1]
    ENST00000397722; ENSP00000380834; ENSG00000103202. [O00746-2]
    ENST00000450036; ENSP00000389048; ENSG00000103202. [O00746-2]
    GeneIDi4833.
    KEGGihsa:4833.
    UCSCiuc002cgz.3. human. [O00746-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y07604 mRNA. Translation: CAA68877.1 .
    BT019438 mRNA. Translation: AAV38245.1 .
    AE006463 Genomic DNA. Translation: AAK61230.1 .
    Z97634 Genomic DNA. Translation: CAC37288.1 .
    CH471112 Genomic DNA. Translation: EAW85818.1 .
    CH471112 Genomic DNA. Translation: EAW85819.1 .
    CH471112 Genomic DNA. Translation: EAW85820.1 .
    BC004880 mRNA. Translation: AAH04880.1 .
    BC017067 mRNA. Translation: AAH17067.1 .
    CCDSi CCDS10408.1. [O00746-1 ]
    CCDS66886.1. [O00746-2 ]
    RefSeqi NP_001273362.1. NM_001286433.1.
    NP_001273364.1. NM_001286435.1.
    NP_001273365.1. NM_001286436.1. [O00746-2 ]
    NP_001273367.1. NM_001286438.1. [O00746-2 ]
    NP_001273368.1. NM_001286439.1. [O00746-2 ]
    NP_001273369.1. NM_001286440.1. [O00746-2 ]
    NP_005000.1. NM_005009.2. [O00746-1 ]
    UniGenei Hs.9235.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EHW X-ray 2.40 A/B 33-175 [» ]
    ProteinModelPortali O00746.
    SMRi O00746. Positions 36-175.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 110897. 14 interactions.
    IntActi O00746. 9 interactions.
    MINTi MINT-1445974.
    STRINGi 9606.ENSP00000219479.

    PTM databases

    PhosphoSitei O00746.

    Proteomic databases

    MaxQBi O00746.
    PaxDbi O00746.
    PRIDEi O00746.

    Protocols and materials databases

    DNASUi 4833.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000219479 ; ENSP00000219479 ; ENSG00000103202 . [O00746-1 ]
    ENST00000397722 ; ENSP00000380834 ; ENSG00000103202 . [O00746-2 ]
    ENST00000450036 ; ENSP00000389048 ; ENSG00000103202 . [O00746-2 ]
    GeneIDi 4833.
    KEGGi hsa:4833.
    UCSCi uc002cgz.3. human. [O00746-1 ]

    Organism-specific databases

    CTDi 4833.
    GeneCardsi GC16P000446.
    H-InvDB HIX0012647.
    HGNCi HGNC:7852. NME4.
    HPAi CAB045996.
    CAB045997.
    MIMi 601818. gene.
    neXtProti NX_O00746.
    PharmGKBi PA31657.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG0105.
    HOGENOMi HOG000224564.
    HOVERGENi HBG000423.
    KOi K00940.
    OrthoDBi EOG7GJ6FG.
    PhylomeDBi O00746.
    TreeFami TF106373.

    Enzyme and pathway databases

    Reactomei REACT_21330. Synthesis and interconversion of nucleotide di- and triphosphates.

    Miscellaneous databases

    ChiTaRSi NME4. human.
    EvolutionaryTracei O00746.
    GeneWikii NME4.
    GenomeRNAii 4833.
    NextBioi 18626.
    PROi O00746.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O00746.
    Bgeei O00746.
    CleanExi HS_NME4.
    Genevestigatori O00746.

    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. "nm23-H4, a new member of the family of human nm23/nucleoside diphosphate kinase genes localised on chromosome 16p13."
      Milon L., Rousseau-Merck M.-F., Munier A., Erent M., Lascu I., Capeau J., Lacombe M.-L.
      Hum. Genet. 99:550-557(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PARTIAL PROTEIN SEQUENCE.
      Tissue: Stomach.
    2. "Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
      Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
      Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    3. "Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16."
      Daniels R.J., Peden J.F., Lloyd C., Horsley S.W., Clark K., Tufarelli C., Kearney L., Buckle V.J., Doggett N.A., Flint J., Higgs D.R.
      Hum. Mol. Genet. 10:339-352(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "The sequence and analysis of duplication-rich human chromosome 16."
      Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J.
      , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
      Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Skin and Uterus.
    7. "The human nm23-H4 gene product is a mitochondrial nucleoside diphosphate kinase."
      Milon L., Meyer P., Chiadmi M., Munier A., Johansson M., Karlsson A., Lascu I., Capeau J., Janin J., Lacombe M.-L.
      J. Biol. Chem. 275:14264-14272(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).

    Entry informationi

    Entry nameiNDKM_HUMAN
    AccessioniPrimary (citable) accession number: O00746
    Secondary accession number(s): A2IDD0, Q5U0M9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: July 1, 1997
    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 programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome 16
      Human chromosome 16: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3