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O00746 (NDKM_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 140. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nucleoside diphosphate kinase, mitochondrial

Short name=NDK
Short name=NDP kinase, mitochondrial
EC=2.7.4.6
Alternative name(s):
Nucleoside diphosphate kinase D
Short name=NDPKD
nm23-H4
Gene names
Name:NME4
Synonyms:NM23D
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length187 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Major role in the synthesis of nucleoside triphosphates other than ATP By similarity. HAMAP-Rule MF_00451

Catalytic activity

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. HAMAP-Rule MF_00451

Cofactor

Magnesium By similarity. HAMAP-Rule MF_00451

Subunit structure

Homohexamer. Interacts with CAPN8 By similarity. HAMAP-Rule MF_00451

Subcellular location

Mitochondrion intermembrane space HAMAP-Rule MF_00451.

Tissue specificity

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.

Sequence similarities

Belongs to the NDK family.

Ontologies

Keywords
   Biological processNucleotide metabolism
   Cellular componentMitochondrion
   Coding sequence diversityAlternative splicing
   DomainTransit peptide
   LigandATP-binding
Magnesium
Metal-binding
Nucleotide-binding
   Molecular functionKinase
Transferase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processCTP biosynthetic process

Inferred from electronic annotation. Source: InterPro

GTP biosynthetic process

Inferred from electronic annotation. Source: InterPro

UTP biosynthetic process

Inferred from electronic annotation. Source: InterPro

nucleobase-containing small molecule interconversion

Traceable author statement. Source: Reactome

nucleobase-containing small molecule metabolic process

Traceable author statement. Source: Reactome

nucleoside metabolic process

Traceable author statement Ref.1. Source: ProtInc

small molecule metabolic process

Traceable author statement. Source: Reactome

   Cellular_componentmitochondrial inner membrane

Traceable author statement. Source: Reactome

mitochondrial intermembrane space

Inferred from electronic annotation. Source: UniProtKB-SubCell

mitochondrion

Traceable author statement Ref.1. Source: ProtInc

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

nucleoside diphosphate kinase activity

Inferred from experiment. Source: Reactome

protein binding

Inferred from physical interaction PubMed 23275563. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

HTTP428582EBI-744871,EBI-466029

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O00746-1)

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.
Isoform 2 (identifier: O00746-2)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 3333Mitochondrion Potential
Chain34 – 187154Nucleoside diphosphate kinase, mitochondrial HAMAP-Rule MF_00451
PRO_0000019432

Sites

Active site1511Pros-phosphohistidine intermediate By similarity
Binding site451ATP By similarity
Binding site931ATP By similarity
Binding site1211ATP By similarity
Binding site1271ATP By similarity
Binding site1381ATP By similarity
Binding site1481ATP By similarity

Natural variations

Alternative sequence1 – 7070Missing in isoform 2.
VSP_054743

Secondary structure

............................... 187
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 1, 1997. Version 1.
Checksum: A56FEF18A7D712D4

FASTA18720,659
        10         20         30         40         50         60 
MGGLFWRSAL RGLRCGPRAP GPSLLVRHGS GGPSWTRERT LVAVKPDGVQ RRLVGDVIQR 

        70         80         90        100        110        120 
FERRGFTLVG MKMLQAPESV LAEHYQDLRR KPFYPALIRY MSSGPVVAMV WEGYNVVRAS 

       130        140        150        160        170        180 
RAMIGHTDSA EAAPGTIRGD FSVHISRNVI HASDSVEGAQ REIQLWFQSS ELVSWADGGQ 


HSSIHPA 

« Hide

Isoform 2 [UniParc].

Checksum: 3B885B828E3C1042
Show »

FASTA11712,979

References

« Hide 'large scale' references
[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]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
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. expand/collapse author list , 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).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS10408.1.
RefSeqNP_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]
UniGeneHs.9235.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1EHWX-ray2.40A/B33-175[»]
ProteinModelPortalO00746.
SMRO00746. Positions 36-175.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid110897. 14 interactions.
IntActO00746. 9 interactions.
MINTMINT-1445974.
STRING9606.ENSP00000219479.

PTM databases

PhosphoSiteO00746.

Proteomic databases

MaxQBO00746.
PaxDbO00746.
PRIDEO00746.

Protocols and materials databases

DNASU4833.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000219479; ENSP00000219479; ENSG00000103202.
ENST00000397722; ENSP00000380834; ENSG00000103202.
ENST00000450036; ENSP00000389048; ENSG00000103202.
GeneID4833.
KEGGhsa:4833.
UCSCuc002cgz.3. human. [O00746-1]

Organism-specific databases

CTD4833.
GeneCardsGC16P000446.
H-InvDBHIX0012647.
HGNCHGNC:7852. NME4.
HPACAB045996.
CAB045997.
MIM601818. gene.
neXtProtNX_O00746.
PharmGKBPA31657.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0105.
HOGENOMHOG000224564.
HOVERGENHBG000423.
KOK00940.
OrthoDBEOG7GJ6FG.
PhylomeDBO00746.
TreeFamTF106373.

Enzyme and pathway databases

ReactomeREACT_111217. Metabolism.

Gene expression databases

ArrayExpressO00746.
BgeeO00746.
CleanExHS_NME4.
GenevestigatorO00746.

Family and domain databases

Gene3D3.30.70.141. 1 hit.
HAMAPMF_00451. NDP_kinase.
InterProIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamPF00334. NDK. 1 hit.
[Graphical view]
PRINTSPR01243. NUCDPKINASE.
SMARTSM00562. NDK. 1 hit.
[Graphical view]
SUPFAMSSF54919. SSF54919. 1 hit.
PROSITEPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSNME4. human.
EvolutionaryTraceO00746.
GeneWikiNME4.
GenomeRNAi4833.
NextBio18626.
PROO00746.
SOURCESearch...

Entry information

Entry nameNDKM_HUMAN
AccessionPrimary (citable) accession number: O00746
Secondary accession number(s): A2IDD0, Q5U0M9
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 1, 1997
Last modified: July 9, 2014
This is version 140 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 16

Human chromosome 16: entries, gene names and cross-references to MIM