NDKA_RAT
ID NDKA_RAT Reviewed; 152 AA.
AC Q05982;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 173.
DE RecName: Full=Nucleoside diphosphate kinase A;
DE Short=NDK A;
DE Short=NDP kinase A;
DE EC=2.7.4.6;
DE AltName: Full=Metastasis inhibition factor NM23;
DE AltName: Full=Tumor metastatic process-associated protein;
GN Name=Nme1;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=8381409; DOI=10.1016/s0021-9258(18)53814-x;
RA Shimada N., Ishikawa N., Munakata Y., Toda T., Watanabe K., Kimura N.;
RT "A second form (beta isoform) of nucleoside diphosphate kinase from rat.
RT Isolation and characterization of complementary and genomic DNA and
RT expression.";
RL J. Biol. Chem. 268:2583-2589(1993).
RN [2]
RP PROTEIN SEQUENCE OF 7-26; 40-66 AND 89-114, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=Sprague-Dawley; TISSUE=Brain, Hippocampus, and Spinal cord;
RA Lubec G., Afjehi-Sadat L., Chen W.-Q., Kang S.U.;
RL Submitted (JUL-2007) to UniProtKB.
CC -!- FUNCTION: Major role in the synthesis of nucleoside triphosphates other
CC than ATP. The ATP gamma phosphate is transferred to the NDP beta
CC phosphate via a ping-pong mechanism, using a phosphorylated active-site
CC intermediate. Possesses nucleoside-diphosphate kinase,
CC serine/threonine-specific protein kinase, geranyl and farnesyl
CC pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease
CC activities. Involved in cell proliferation, differentiation and
CC development, signal transduction, G protein-coupled receptor
CC endocytosis, and gene expression. Required for neural development
CC including neural patterning and cell fate determination. During GZMA-
CC mediated cell death, works in concert with TREX1. NME1 nicks one strand
CC of DNA and TREX1 removes bases from the free 3' end to enhance DNA
CC damage and prevent DNA end reannealing and rapid repair (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-
CC deoxyribonucleoside 5'-triphosphate + ADP; Xref=Rhea:RHEA:44640,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:61560, ChEBI:CHEBI:73316,
CC ChEBI:CHEBI:456216; EC=2.7.4.6;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-
CC triphosphate + ADP; Xref=Rhea:RHEA:18113, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:61557, ChEBI:CHEBI:456216; EC=2.7.4.6;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- ACTIVITY REGULATION: Autophosphorylation at His-118 increases
CC serine/threonine protein kinase activity of the enzyme. Interaction
CC with the SET complex inhibits exonuclease activity (By similarity).
CC {ECO:0000250}.
CC -!- SUBUNIT: Hexamer of two different chains: A and B (A6, A5B, A4B2, A3B3,
CC A2B4, AB5, B6). Interacts with PRUNE1. Component of the SET complex,
CC composed of at least ANP32A, APEX1, HMGB2, NME1, SET and TREX1. Within
CC this complex, interacts directly with SET. Also interacts with TREX1,
CC but only following translocation to the nucleus.
CC {ECO:0000250|UniProtKB:P15531}.
CC -!- INTERACTION:
CC Q05982; O00255-2: MEN1; Xeno; NbExp=5; IntAct=EBI-1165329, EBI-9869387;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
CC -!- DISEASE: Note=This protein is found in reduced amount in tumor cells of
CC high metastatic potential.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
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DR EMBL; D13374; BAA02635.1; -; mRNA.
DR PIR; A45208; A45208.
DR RefSeq; NP_612557.1; NM_138548.2.
DR RefSeq; XP_017452467.1; XM_017596978.1.
DR RefSeq; XP_017452468.1; XM_017596979.1.
DR AlphaFoldDB; Q05982; -.
DR SMR; Q05982; -.
DR BioGRID; 251322; 2.
DR CORUM; Q05982; -.
DR IntAct; Q05982; 1.
DR STRING; 10116.ENSRNOP00000003658; -.
DR iPTMnet; Q05982; -.
DR PhosphoSitePlus; Q05982; -.
DR jPOST; Q05982; -.
DR PaxDb; Q05982; -.
DR PRIDE; Q05982; -.
DR Ensembl; ENSRNOT00000112785; ENSRNOP00000083790; ENSRNOG00000002693.
DR GeneID; 191575; -.
DR KEGG; rno:191575; -.
DR CTD; 4830; -.
DR RGD; 70497; Nme1.
DR eggNOG; KOG0888; Eukaryota.
DR GeneTree; ENSGT00940000162213; -.
DR HOGENOM; CLU_060216_6_3_1; -.
DR InParanoid; Q05982; -.
DR OMA; KIVAMKM; -.
DR OrthoDB; 1334716at2759; -.
DR PhylomeDB; Q05982; -.
DR TreeFam; TF106373; -.
DR Reactome; R-RNO-499943; Interconversion of nucleotide di- and triphosphates.
DR Reactome; R-RNO-9748787; Azathioprine ADME.
DR SABIO-RK; Q05982; -.
DR PRO; PR:Q05982; -.
DR Proteomes; UP000002494; Chromosome 10.
DR Bgee; ENSRNOG00000002693; Expressed in frontal cortex and 20 other tissues.
DR Genevisible; Q05982; RN.
DR GO; GO:0005813; C:centrosome; IDA:RGD.
DR GO; GO:0005829; C:cytosol; IDA:RGD.
DR GO; GO:0016020; C:membrane; IDA:RGD.
DR GO; GO:0005741; C:mitochondrial outer membrane; IDA:CACAO.
DR GO; GO:0005634; C:nucleus; ISO:RGD.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IDA:RGD.
DR GO; GO:0032587; C:ruffle membrane; ISO:RGD.
DR GO; GO:0005524; F:ATP binding; ISO:RGD.
DR GO; GO:0004536; F:deoxyribonuclease activity; ISO:RGD.
DR GO; GO:0019899; F:enzyme binding; IPI:RGD.
DR GO; GO:0043015; F:gamma-tubulin binding; IDA:RGD.
DR GO; GO:0005525; F:GTP binding; ISO:RGD.
DR GO; GO:0042802; F:identical protein binding; ISO:RGD.
DR GO; GO:0019215; F:intermediate filament binding; IPI:RGD.
DR GO; GO:0000287; F:magnesium ion binding; ISO:RGD.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IDA:RGD.
DR GO; GO:0043024; F:ribosomal small subunit binding; ISO:RGD.
DR GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; IDA:RGD.
DR GO; GO:0003697; F:single-stranded DNA binding; IDA:RGD.
DR GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR GO; GO:0071398; P:cellular response to fatty acid; IEP:RGD.
DR GO; GO:0071333; P:cellular response to glucose stimulus; IEP:RGD.
DR GO; GO:0071466; P:cellular response to xenobiotic stimulus; IEP:RGD.
DR GO; GO:0006241; P:CTP biosynthetic process; IEA:InterPro.
DR GO; GO:0006897; P:endocytosis; IEA:UniProtKB-KW.
DR GO; GO:0006183; P:GTP biosynthetic process; IEA:InterPro.
DR GO; GO:0021766; P:hippocampus development; IEP:RGD.
DR GO; GO:0007595; P:lactation; ISO:RGD.
DR GO; GO:0030879; P:mammary gland development; ISO:RGD.
DR GO; GO:0010629; P:negative regulation of gene expression; IDA:RGD.
DR GO; GO:0002762; P:negative regulation of myeloid leukocyte differentiation; IDA:RGD.
DR GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IDA:RGD.
DR GO; GO:0043388; P:positive regulation of DNA binding; ISO:RGD.
DR GO; GO:0050679; P:positive regulation of epithelial cell proliferation; ISO:RGD.
DR GO; GO:0010976; P:positive regulation of neuron projection development; IMP:RGD.
DR GO; GO:0014075; P:response to amine; IEP:RGD.
DR GO; GO:0051591; P:response to cAMP; IEP:RGD.
DR GO; GO:0033574; P:response to testosterone; IEP:RGD.
DR GO; GO:0009410; P:response to xenobiotic stimulus; IEP:RGD.
DR GO; GO:0006228; P:UTP biosynthetic process; IEA:InterPro.
DR Gene3D; 3.30.70.141; -; 1.
DR HAMAP; MF_00451; NDP_kinase; 1.
DR InterPro; IPR034907; NDK-like_dom.
DR InterPro; IPR036850; NDK-like_dom_sf.
DR InterPro; IPR001564; Nucleoside_diP_kinase.
DR InterPro; IPR023005; Nucleoside_diP_kinase_AS.
DR Pfam; PF00334; NDK; 1.
DR PRINTS; PR01243; NUCDPKINASE.
DR SMART; SM00562; NDK; 1.
DR SUPFAM; SSF54919; SSF54919; 1.
DR PROSITE; PS00469; NDP_KINASES; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Differentiation; Direct protein sequencing;
KW Endocytosis; Isopeptide bond; Kinase; Magnesium; Metal-binding;
KW Neurogenesis; Nucleotide metabolism; Nucleotide-binding; Nucleus;
KW Phosphoprotein; Reference proteome; Transferase; Ubl conjugation.
FT CHAIN 1..152
FT /note="Nucleoside diphosphate kinase A"
FT /id="PRO_0000137116"
FT ACT_SITE 118
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 12
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 60
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 88
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 94
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 105
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 115
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MOD_RES 120
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P15531"
FT MOD_RES 122
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P15531"
FT MOD_RES 125
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P15531"
FT CROSSLNK 100
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:P15531"
SQ SEQUENCE 152 AA; 17193 MW; 32C49E6271195C3B CRC64;
MANSERTFIA IKPDGVQRGL VGEIIKRFEQ KGFRLVGLKF IQASEDLLKE HYIDLKDRPF
FSGLVKYMHS GPVVAMVWEG LNVVKTGRVM LGETNPADSK PGTIRGDFCI QVGRNIIHGS
DSVESAEKEI SLWFQPEELV DYKSCAQNWI YE
