O00746 (NDKM_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	187 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Major role in the synthesis of nucleoside triphosphates other than ATP By similarity.
Catalytic activity	ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
Cofactor	Magnesium By similarity.
Subunit structure	Homohexamer. Interacts with CAPN8 By similarity.
Subcellular location	Mitochondrion intermembrane space.
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 process	Nucleotide metabolism
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	CTP 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 nucleoside metabolic process Traceable author statement Ref.1. Source: ProtInc
Cellular_component	mitochondrial inner membrane Traceable author statement. Source: Reactome mitochondrial intermembrane space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP 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
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
HTT	P42858	2	EBI-744871,EBI-466029

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 33

33

Mitochondrion Potential

Chain

34 – 187

154

Nucleoside diphosphate kinase, mitochondrial

PRO_0000019432

Sites

Active site

151

1

Pros-phosphohistidine intermediate By similarity

Binding site

45

1

ATP By similarity

Binding site

93

1

ATP By similarity

Binding site

121

1

ATP By similarity

Binding site

127

1

ATP By similarity

Binding site

138

1

ATP By similarity

Binding site

148

1

ATP By similarity

Secondary structure

1

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187

Helix Strand Turn

Details...

Beta strand

39 – 44

6

Helix

46 – 50

5

Helix

54 – 63

10

Beta strand

67 – 74

8

Helix

78 – 84

7

Helix

86 – 88

3

Helix

94 – 101

8

Beta strand

106 – 113

8

Helix

116 – 124

9

Helix

129 – 131

3

Helix

137 – 141

5

Beta strand

149 – 152

4

Helix

156 – 166

11

Helix

169 – 171

3

Sequences

	Sequence		Length	Mass (Da)
	O00746 [UniParc]. Last modified July 1, 1997. Version 1. Checksum: A56FEF18A7D712D4	FASTA	187	20,659
	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

References

	« Hide 'large scale' referencesShow '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], 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].
[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. , 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. , 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]. 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: EAW85820.1.
BC004880 mRNA. Translation: AAH04880.1.
BC017067 mRNA. Translation: AAH17067.1.

IPI

IPI00012972.

RefSeq

NP_005000.1. NM_005009.2.

UniGene

Hs.9235.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EHW	X-ray	2.40	A/B	36-175	[»]

ProteinModelPortal

O00746.

ModBase

Search...

Protein-protein interaction databases

IntAct

O00746. 7 interactions.

MINT

MINT-1445974.

STRING

9606.ENSP00000219479.

PTM databases

PhosphoSite

O00746.

Proteomic databases

PaxDb

O00746.

PRIDE

O00746.

Protocols and materials databases

DNASU

4833.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000219479; ENSP00000219479; ENSG00000103202.

GeneID

4833.

KEGG

hsa:4833.

UCSC

uc002cgz.3. human.

Organism-specific databases

CTD

4833.

GeneCards

GC16P000446.

H-InvDB

HIX0012647.

HGNC

HGNC:7852. NME4.

HPA

CAB045996.
CAB045997.

MIM

601818. gene.

neXtProt

NX_O00746.

PharmGKB

PA31657.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG0105.

HOGENOM

HOG000224564.

HOVERGEN

HBG000423.

KO

K00940.

Enzyme and pathway databases

Reactome

REACT_111217. Metabolism.

Gene expression databases

ArrayExpress

O00746.

Bgee

O00746.

CleanEx

HS_NME4.

Genevestigator

O00746.

GermOnline

ENSG00000103200. Homo sapiens.

Family and domain databases

Gene3D

3.30.70.141. 1 hit.

InterPro

IPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]

PANTHER

PTHR11349. PTHR11349. 1 hit.

Pfam

PF00334. NDK. 1 hit.
[Graphical view]

PRINTS

PR01243. NUCDPKINASE.

SMART

SM00562. NDK. 1 hit.
[Graphical view]

SUPFAM

SSF54919. NDK. 1 hit.

PROSITE

PS00469. NDP_KINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChEMBL

CHEMBL4488.

ChiTaRS

NME4. human.

EvolutionaryTrace

O00746.

GenomeRNAi

4833.

NextBio

18626.

SOURCE

Search...

Entry information

Entry name

NDKM_HUMAN

Accession

Primary (citable) accession number: O00746
Secondary accession number(s): Q5U0M9

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	July 1, 1997
Last modified:	May 1, 2013
This is version 131 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.