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Protein

Nucleoside diphosphate kinase 3

Gene

NME3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Probably has a role in normal hematopoiesis by inhibition of granulocyte differentiation and induction of apoptosis.

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei29ATPBy similarity1
Binding sitei77ATPBy similarity1
Binding sitei105ATPBy similarity1
Binding sitei111ATPBy similarity1
Binding sitei122ATPBy similarity1
Binding sitei132ATPBy similarity1
Active sitei135Pros-phosphohistidine intermediateBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Apoptosis, Nucleotide metabolism

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciZFISH:HS02442-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase 3 (EC:2.7.4.6)
Short name:
NDK 3
Short name:
NDP kinase 3
Alternative name(s):
DR-nm23
Nucleoside diphosphate kinase C
Short name:
NDPKC
nm23-H3
Gene namesi
Name:NME3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:7851. NME3.

Subcellular locationi

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • intracellular Source: GO_Central
  • mitochondrion Source: Ensembl
Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

DisGeNETi4832.
OpenTargetsiENSG00000103024.
PharmGKBiPA31656.

Polymorphism and mutation databases

BioMutaiNME3.
DMDMi21264477.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001371231 – 169Nucleoside diphosphate kinase 3Add BLAST169

Proteomic databases

EPDiQ13232.
MaxQBiQ13232.
PaxDbiQ13232.
PeptideAtlasiQ13232.
PRIDEiQ13232.

PTM databases

iPTMnetiQ13232.
PhosphoSitePlusiQ13232.

Expressioni

Developmental stagei

Preferentially expressed at early stages of myeloid differentiation of highly purified CD34+ cells.

Gene expression databases

BgeeiENSG00000103024.
CleanExiHS_NME3.
ExpressionAtlasiQ13232. baseline and differential.
GenevisibleiQ13232. HS.

Organism-specific databases

HPAiHPA041113.
HPA052733.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
NME1P155314EBI-713684,EBI-741141
SGTAO437656EBI-713684,EBI-347996
UBQLN1Q9UMX05EBI-713684,EBI-741480
UBQLN1Q9UMX0-23EBI-713684,EBI-10173939

Protein-protein interaction databases

BioGridi110896. 21 interactors.
DIPiDIP-49960N.
IntActiQ13232. 13 interactors.
MINTiMINT-1429907.
STRINGi9606.ENSP00000219302.

Structurei

Secondary structure

1169
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi19 – 21Combined sources3
Beta strandi23 – 28Combined sources6
Helixi30 – 34Combined sources5
Helixi38 – 48Combined sources11
Beta strandi51 – 58Combined sources8
Helixi62 – 68Combined sources7
Helixi70 – 72Combined sources3
Helixi78 – 85Combined sources8
Beta strandi90 – 97Combined sources8
Helixi100 – 108Combined sources9
Helixi113 – 115Combined sources3
Helixi121 – 125Combined sources5
Helixi129 – 131Combined sources3
Beta strandi133 – 136Combined sources4
Helixi140 – 150Combined sources11
Helixi153 – 155Combined sources3
Helixi164 – 167Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZS6X-ray2.30A/B/D1-169[»]
ProteinModelPortaliQ13232.
SMRiQ13232.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ13232.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
GeneTreeiENSGT00760000119146.
HOGENOMiHOG000224564.
HOVERGENiHBG000423.
InParanoidiQ13232.
KOiK00940.
OMAiCVEVGRN.
OrthoDBiEOG091G0PLD.
PhylomeDBiQ13232.
TreeFamiTF106373.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
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]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q13232-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MICLVLTIFA NLFPAACTGA HERTFLAVKP DGVQRRLVGE IVRRFERKGF
60 70 80 90 100
KLVALKLVQA SEELLREHYA ELRERPFYGR LVKYMASGPV VAMVWQGLDV
110 120 130 140 150
VRTSRALIGA TNPADAPPGT IRGDFCIEVG KNLIHGSDSV ESARREIALW
160
FRADELLCWE DSAGHWLYE
Length:169
Mass (Da):19,015
Last modified:May 27, 2002 - v2
Checksum:iCCA41A122A37202D
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti60A → S in AAA85097 (PubMed:7638209).Curated1
Sequence conflicti131Missing in AAA85097 (PubMed:7638209).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29656 mRNA. Translation: AAA85097.1.
AE006639 Genomic DNA. Translation: AAK61291.1.
BC000250 mRNA. Translation: AAH00250.1.
CCDSiCCDS10443.1.
PIRiI39074.
RefSeqiNP_002504.2. NM_002513.2.
UniGeneiHs.514065.

Genome annotation databases

EnsembliENST00000219302; ENSP00000219302; ENSG00000103024.
GeneIDi4832.
KEGGihsa:4832.
UCSCiuc002cmm.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29656 mRNA. Translation: AAA85097.1.
AE006639 Genomic DNA. Translation: AAK61291.1.
BC000250 mRNA. Translation: AAH00250.1.
CCDSiCCDS10443.1.
PIRiI39074.
RefSeqiNP_002504.2. NM_002513.2.
UniGeneiHs.514065.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZS6X-ray2.30A/B/D1-169[»]
ProteinModelPortaliQ13232.
SMRiQ13232.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi110896. 21 interactors.
DIPiDIP-49960N.
IntActiQ13232. 13 interactors.
MINTiMINT-1429907.
STRINGi9606.ENSP00000219302.

PTM databases

iPTMnetiQ13232.
PhosphoSitePlusiQ13232.

Polymorphism and mutation databases

BioMutaiNME3.
DMDMi21264477.

Proteomic databases

EPDiQ13232.
MaxQBiQ13232.
PaxDbiQ13232.
PeptideAtlasiQ13232.
PRIDEiQ13232.

Protocols and materials databases

DNASUi4832.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000219302; ENSP00000219302; ENSG00000103024.
GeneIDi4832.
KEGGihsa:4832.
UCSCiuc002cmm.4. human.

Organism-specific databases

CTDi4832.
DisGeNETi4832.
GeneCardsiNME3.
HGNCiHGNC:7851. NME3.
HPAiHPA041113.
HPA052733.
MIMi601817. gene.
neXtProtiNX_Q13232.
OpenTargetsiENSG00000103024.
PharmGKBiPA31656.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
GeneTreeiENSGT00760000119146.
HOGENOMiHOG000224564.
HOVERGENiHBG000423.
InParanoidiQ13232.
KOiK00940.
OMAiCVEVGRN.
OrthoDBiEOG091G0PLD.
PhylomeDBiQ13232.
TreeFamiTF106373.

Enzyme and pathway databases

BioCyciZFISH:HS02442-MONOMER.

Miscellaneous databases

ChiTaRSiNME3. human.
EvolutionaryTraceiQ13232.
GeneWikiiNME3.
GenomeRNAii4832.
PROiQ13232.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000103024.
CleanExiHS_NME3.
ExpressionAtlasiQ13232. baseline and differential.
GenevisibleiQ13232. HS.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
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]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNDK3_HUMAN
AccessioniPrimary (citable) accession number: Q13232
Secondary accession number(s): Q9BWH4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: May 27, 2002
Last modified: November 30, 2016
This is version 156 of the entry and version 2 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, 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.