Reviewed, UniProtKB/Swiss-Prot O00746 (NDKM_HUMAN)

Names and origin

Protein names

Recommended name:
    Nucleoside diphosphate kinase, mitochondrial
      Short name=NDP kinase, mitochondrial
      Short name=NDK
    EC=2.7.4.6
Alternative name(s):
    nm23-H4
    Nucleoside diphosphate kinase D
      Short name=NDPKD

Gene names

Name:	NME4
Synonyms:	NM23D

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › 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
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
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
Cellular component	mitochondrial inner membrane Ref.7 Inferred from Experiment. Source: Reactome mitochondrial intermembrane space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside diphosphate kinase activity Ref.1 Ref.7 Inferred from Experiment. Source: Reactome
Complete GO annotation...

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

Amino acid modifications

Modified residue

91

1

N6-acetyllysine Ref.8

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)
	O00746-1 [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: 9099850] [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: 11157797] [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: 15616553] [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: 15489334] [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: 10799505] [Abstract] Cited for: CHARACTERIZATION, X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
[8]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-91, MASS SPECTROMETRY.
+	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.

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	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

O00746. 2 interactions.

STRING

O00746.

Proteomic databases

PRIDE

O00746.

Genome annotation databases

Ensembl

ENST00000219479; ENSP00000219479; ENSG00000103202; Homo sapiens. [Genome view]

GeneID

4833.

KEGG

hsa:4833.

UCSC

uc002cgz.1. human.

Organism-specific databases

CTD

4833.

GeneCards

GC16P000387.

H-InvDB

HIX0012647.

HGNC

HGNC:7852. NME4.

MIM

601818. gene.

PharmGKB

PA31657.

GenAtlas

Search...

Phylogenomic databases

HOVERGEN

O00746.

PhylomeDB

O00746.

Enzyme and pathway databases

BRENDA

2.7.4.6. 247.

Reactome

REACT_1698. Metabolism of nucleotides.

Gene expression databases

ArrayExpress

O00746.

Bgee

O00746.

CleanEx

HS_NME4.

Genevestigator

O00746.

GermOnline

ENSG00000103200. Homo sapiens.

Family and domain databases

InterPro

IPR001564. Nuc_diP_kinase_core.
[Graphical view]

Gene3D

G3DSA:3.30.70.141. NDK. 1 hit.

PANTHER

PTHR11349. Nuc_diP_kinase_core. 1 hit.

Pfam

PF00334. NDK. 1 hit.
[Graphical view]

PRINTS

PR01243. NUCDPKINASE.

SMART

SM00562. NDK. 1 hit.
[Graphical view]

PROSITE

PS00469. NDP_KINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

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:	February 9, 2010
This is version 100 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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.