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Protein

Nucleoside diphosphate kinase A

Gene

Nme1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -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. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination. During GZMA-mediated cell death, works in concert with TREX1. NME1 nicks one strand of DNA and TREX1 removes bases from the free 3' end to enhance DNA damage and prevent DNA end reannealing and rapid repair (By similarity).By similarity

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Activity regulationi

Autophosphorylation at His-118 increases serine/threonine protein kinase activity of the enzyme. Interaction with the SET complex inhibits exonuclease activity (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei12ATPBy similarity1
Binding sitei60ATPBy similarity1
Binding sitei88ATPBy similarity1
Binding sitei94ATPBy similarity1
Binding sitei105ATPBy similarity1
Binding sitei115ATPBy similarity1
Active sitei118Pros-phosphohistidine intermediateBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionKinase, Transferase
Biological processDifferentiation, Endocytosis, Neurogenesis, Nucleotide metabolism
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-RNO-499943 Interconversion of nucleotide di- and triphosphates
SABIO-RKiQ05982

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase A (EC:2.7.4.6)
Short name:
NDK A
Short name:
NDP kinase A
Alternative name(s):
Metastasis inhibition factor NM23
Tumor metastatic process-associated protein
Gene namesi
Name:Nme1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 10

Organism-specific databases

RGDi70497 Nme1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

This protein is found in reduced amount in tumor cells of high metastatic potential.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001371161 – 152Nucleoside diphosphate kinase AAdd BLAST152

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki100Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei120PhosphoserineBy similarity1
Modified residuei122PhosphoserineBy similarity1
Modified residuei125PhosphoserineBy similarity1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ05982
PRIDEiQ05982

PTM databases

iPTMnetiQ05982
PhosphoSitePlusiQ05982

Expressioni

Gene expression databases

BgeeiENSRNOG00000002693 Expressed in 10 organ(s), highest expression level in brain
GenevisibleiQ05982 RN

Interactioni

Subunit structurei

Hexamer of two different chains: A and B (A6, A5B, A4B2, A3B3, A2B4, AB5, B6). Interacts with PRUNE1. Component of the SET complex, composed of at least ANP32A, APEX1, HMGB2, NME1, SET and TREX1. Within this complex, interacts directly with SET. Also interacts with TREX1, but only following translocation to the nucleus.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
MEN1O00255-25EBI-1165329,EBI-9869387From a different organism.

GO - Molecular functioni

Protein-protein interaction databases

BioGridi251322, 1 interactor
CORUMiQ05982
IntActiQ05982, 1 interactor
STRINGi10116.ENSRNOP00000003658

Structurei

3D structure databases

ProteinModelPortaliQ05982
SMRiQ05982
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiKOG0888 Eukaryota
COG0105 LUCA
GeneTreeiENSGT00760000119146
HOGENOMiHOG000224564
HOVERGENiHBG000423
InParanoidiQ05982
KOiK00940
OMAiKIVAMKM
OrthoDBiEOG091G0PLD
PhylomeDBiQ05982
TreeFamiTF106373

Family and domain databases

Gene3Di3.30.70.141, 1 hit
HAMAPiMF_00451 NDP_kinase, 1 hit
InterProiView protein in InterPro
IPR034907 NDK-like_dom
IPR036850 NDK-like_dom_sf
IPR001564 Nucleoside_diP_kinase
IPR023005 Nucleoside_diP_kinase_AS
PfamiView protein in Pfam
PF00334 NDK, 1 hit
PRINTSiPR01243 NUCDPKINASE
SMARTiView protein in SMART
SM00562 NDK, 1 hit
SUPFAMiSSF54919 SSF54919, 1 hit
PROSITEiView protein in PROSITE
PS00469 NDP_KINASES, 1 hit

Sequencei

Sequence statusi: Complete.

Q05982-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MANSERTFIA IKPDGVQRGL VGEIIKRFEQ KGFRLVGLKF IQASEDLLKE
60 70 80 90 100
HYIDLKDRPF FSGLVKYMHS GPVVAMVWEG LNVVKTGRVM LGETNPADSK
110 120 130 140 150
PGTIRGDFCI QVGRNIIHGS DSVESAEKEI SLWFQPEELV DYKSCAQNWI

YE
Length:152
Mass (Da):17,193
Last modified:February 1, 1994 - v1
Checksum:i32C49E6271195C3B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13374 mRNA Translation: BAA02635.1
PIRiA45208
RefSeqiNP_612557.1, NM_138548.2
XP_017452467.1, XM_017596978.1
XP_017452468.1, XM_017596979.1
UniGeneiRn.6236

Genome annotation databases

EnsembliENSRNOT00000003658; ENSRNOP00000003658; ENSRNOG00000002693
GeneIDi191575
KEGGirno:191575

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13374 mRNA Translation: BAA02635.1
PIRiA45208
RefSeqiNP_612557.1, NM_138548.2
XP_017452467.1, XM_017596978.1
XP_017452468.1, XM_017596979.1
UniGeneiRn.6236

3D structure databases

ProteinModelPortaliQ05982
SMRiQ05982
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi251322, 1 interactor
CORUMiQ05982
IntActiQ05982, 1 interactor
STRINGi10116.ENSRNOP00000003658

PTM databases

iPTMnetiQ05982
PhosphoSitePlusiQ05982

Proteomic databases

PaxDbiQ05982
PRIDEiQ05982

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000003658; ENSRNOP00000003658; ENSRNOG00000002693
GeneIDi191575
KEGGirno:191575

Organism-specific databases

CTDi4830
RGDi70497 Nme1

Phylogenomic databases

eggNOGiKOG0888 Eukaryota
COG0105 LUCA
GeneTreeiENSGT00760000119146
HOGENOMiHOG000224564
HOVERGENiHBG000423
InParanoidiQ05982
KOiK00940
OMAiKIVAMKM
OrthoDBiEOG091G0PLD
PhylomeDBiQ05982
TreeFamiTF106373

Enzyme and pathway databases

ReactomeiR-RNO-499943 Interconversion of nucleotide di- and triphosphates
SABIO-RKiQ05982

Miscellaneous databases

PROiPR:Q05982

Gene expression databases

BgeeiENSRNOG00000002693 Expressed in 10 organ(s), highest expression level in brain
GenevisibleiQ05982 RN

Family and domain databases

Gene3Di3.30.70.141, 1 hit
HAMAPiMF_00451 NDP_kinase, 1 hit
InterProiView protein in InterPro
IPR034907 NDK-like_dom
IPR036850 NDK-like_dom_sf
IPR001564 Nucleoside_diP_kinase
IPR023005 Nucleoside_diP_kinase_AS
PfamiView protein in Pfam
PF00334 NDK, 1 hit
PRINTSiPR01243 NUCDPKINASE
SMARTiView protein in SMART
SM00562 NDK, 1 hit
SUPFAMiSSF54919 SSF54919, 1 hit
PROSITEiView protein in PROSITE
PS00469 NDP_KINASES, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiNDKA_RAT
AccessioniPrimary (citable) accession number: Q05982
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: September 12, 2018
This is version 155 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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