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O00746

- NDKM_HUMAN

UniProt

O00746 - NDKM_HUMAN

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Protein
Nucleoside diphosphate kinase, mitochondrial
Gene
NME4, NM23D
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.UniRule annotation

Cofactori

Magnesium By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei45 – 451ATP By similarity
Binding sitei93 – 931ATP By similarity
Binding sitei121 – 1211ATP By similarity
Binding sitei127 – 1271ATP By similarity
Binding sitei138 – 1381ATP By similarity
Binding sitei148 – 1481ATP By similarity
Active sitei151 – 1511Pros-phosphohistidine intermediate By 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. UTP biosynthetic process Source: InterPro
  4. nucleobase-containing small molecule interconversion Source: Reactome
  5. nucleobase-containing small molecule metabolic process Source: Reactome
  6. nucleoside metabolic process Source: ProtInc
  7. small molecule metabolic process Source: Reactome
Complete GO annotation...

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
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA31657.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3333Mitochondrion Reviewed prediction
Add
BLAST
Chaini34 – 187154Nucleoside diphosphate kinase, mitochondrialUniRule annotation
PRO_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.UniRule annotation

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

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.

Miscellaneous databases

EvolutionaryTraceiO00746.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.

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.
VSP_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.
ENST00000397722; ENSP00000380834; ENSG00000103202.
ENST00000450036; ENSP00000389048; ENSG00000103202.
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 .
ENST00000397722 ; ENSP00000380834 ; ENSG00000103202 .
ENST00000450036 ; ENSP00000389048 ; ENSG00000103202 .
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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 141 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

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