NDK3_HUMAN
ID NDK3_HUMAN Reviewed; 169 AA.
AC Q13232; Q9BWH4;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 27-MAY-2002, sequence version 2.
DT 03-AUG-2022, entry version 191.
DE RecName: Full=Nucleoside diphosphate kinase 3;
DE Short=NDK 3;
DE Short=NDP kinase 3;
DE EC=2.7.4.6;
DE AltName: Full=DR-nm23;
DE AltName: Full=Nucleoside diphosphate kinase C;
DE Short=NDPKC;
DE AltName: Full=nm23-H3;
GN Name=NME3;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=7638209; DOI=10.1073/pnas.92.16.7435;
RA Venturelli D., Martinez R., Melotti P., Casella I., Peschle C., Cucco C.,
RA Spampinato G., Darzynkiewicz Z., Calabretta B.;
RT "Overexpression of DR-nm23, a protein encoded by a member of the nm23 gene
RT family, inhibits granulocyte differentiation and induces apoptosis in
RT 32Dc13 myeloid cells.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:7435-7439(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=11157797; DOI=10.1093/hmg/10.4.339;
RA Daniels R.J., Peden J.F., Lloyd C., Horsley S.W., Clark K., Tufarelli C.,
RA Kearney L., Buckle V.J., Doggett N.A., Flint J., Higgs D.R.;
RT "Sequence, structure and pathology of the fully annotated terminal 2 Mb of
RT the short arm of human chromosome 16.";
RL Hum. Mol. Genet. 10:339-352(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Eye;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
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. Probably has a role in normal hematopoiesis by inhibition
CC of granulocyte differentiation and induction of apoptosis.
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 -!- INTERACTION:
CC Q13232; Q6ICB0: DESI1; NbExp=6; IntAct=EBI-713684, EBI-2806959;
CC Q13232; P15531: NME1; NbExp=5; IntAct=EBI-713684, EBI-741141;
CC Q13232; O43765: SGTA; NbExp=12; IntAct=EBI-713684, EBI-347996;
CC Q13232; Q96EQ0: SGTB; NbExp=5; IntAct=EBI-713684, EBI-744081;
CC Q13232; Q9UMX0: UBQLN1; NbExp=6; IntAct=EBI-713684, EBI-741480;
CC Q13232; Q9UMX0-2: UBQLN1; NbExp=3; IntAct=EBI-713684, EBI-10173939;
CC Q13232; Q9UHD9: UBQLN2; NbExp=3; IntAct=EBI-713684, EBI-947187;
CC -!- DEVELOPMENTAL STAGE: Preferentially expressed at early stages of
CC myeloid differentiation of highly purified CD34+ cells.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
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DR EMBL; U29656; AAA85097.1; -; mRNA.
DR EMBL; AE006639; AAK61291.1; -; Genomic_DNA.
DR EMBL; BC000250; AAH00250.1; -; mRNA.
DR CCDS; CCDS10443.1; -.
DR PIR; I39074; I39074.
DR RefSeq; NP_002504.2; NM_002513.2.
DR PDB; 1ZS6; X-ray; 2.30 A; A/B/D=1-169.
DR PDBsum; 1ZS6; -.
DR AlphaFoldDB; Q13232; -.
DR SMR; Q13232; -.
DR BioGRID; 110896; 107.
DR DIP; DIP-49960N; -.
DR IntAct; Q13232; 44.
DR MINT; Q13232; -.
DR STRING; 9606.ENSP00000219302; -.
DR iPTMnet; Q13232; -.
DR PhosphoSitePlus; Q13232; -.
DR SwissPalm; Q13232; -.
DR BioMuta; NME3; -.
DR DMDM; 21264477; -.
DR EPD; Q13232; -.
DR jPOST; Q13232; -.
DR MassIVE; Q13232; -.
DR MaxQB; Q13232; -.
DR PaxDb; Q13232; -.
DR PeptideAtlas; Q13232; -.
DR PRIDE; Q13232; -.
DR ProteomicsDB; 59239; -.
DR Antibodypedia; 23225; 209 antibodies from 25 providers.
DR DNASU; 4832; -.
DR Ensembl; ENST00000219302.8; ENSP00000219302.3; ENSG00000103024.8.
DR GeneID; 4832; -.
DR KEGG; hsa:4832; -.
DR MANE-Select; ENST00000219302.8; ENSP00000219302.3; NM_002513.3; NP_002504.2.
DR UCSC; uc002cmm.4; human.
DR CTD; 4832; -.
DR DisGeNET; 4832; -.
DR GeneCards; NME3; -.
DR HGNC; HGNC:7851; NME3.
DR HPA; ENSG00000103024; Low tissue specificity.
DR MIM; 601817; gene.
DR neXtProt; NX_Q13232; -.
DR OpenTargets; ENSG00000103024; -.
DR PharmGKB; PA31656; -.
DR VEuPathDB; HostDB:ENSG00000103024; -.
DR eggNOG; KOG0888; Eukaryota.
DR GeneTree; ENSGT00940000161283; -.
DR InParanoid; Q13232; -.
DR OMA; WFRAEEL; -.
DR OrthoDB; 1334716at2759; -.
DR PhylomeDB; Q13232; -.
DR TreeFam; TF106373; -.
DR BRENDA; 2.7.4.6; 2681.
DR PathwayCommons; Q13232; -.
DR Reactome; R-HSA-499943; Interconversion of nucleotide di- and triphosphates.
DR SignaLink; Q13232; -.
DR BioGRID-ORCS; 4832; 17 hits in 1081 CRISPR screens.
DR ChiTaRS; NME3; human.
DR EvolutionaryTrace; Q13232; -.
DR GeneWiki; NME3; -.
DR GenomeRNAi; 4832; -.
DR Pharos; Q13232; Tbio.
DR PRO; PR:Q13232; -.
DR Proteomes; UP000005640; Chromosome 16.
DR RNAct; Q13232; protein.
DR Bgee; ENSG00000103024; Expressed in adenohypophysis and 175 other tissues.
DR ExpressionAtlas; Q13232; baseline and differential.
DR Genevisible; Q13232; HS.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IBA:GO_Central.
DR GO; GO:0006915; P:apoptotic process; TAS:ProtInc.
DR GO; GO:0006241; P:CTP biosynthetic process; IEA:InterPro.
DR GO; GO:0006183; P:GTP biosynthetic process; IEA:InterPro.
DR GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IEA:InterPro.
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 3D-structure; Apoptosis; ATP-binding; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..169
FT /note="Nucleoside diphosphate kinase 3"
FT /id="PRO_0000137123"
FT ACT_SITE 135
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 29
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 77
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 111
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 122
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 132
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT CONFLICT 60
FT /note="A -> S (in Ref. 1; AAA85097)"
FT /evidence="ECO:0000305"
FT CONFLICT 131
FT /note="Missing (in Ref. 1; AAA85097)"
FT /evidence="ECO:0000305"
FT HELIX 19..21
FT /evidence="ECO:0007829|PDB:1ZS6"
FT STRAND 23..28
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 30..34
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 38..48
FT /evidence="ECO:0007829|PDB:1ZS6"
FT STRAND 51..58
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 62..68
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 70..72
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 78..85
FT /evidence="ECO:0007829|PDB:1ZS6"
FT STRAND 90..97
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 100..108
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 121..125
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:1ZS6"
FT STRAND 133..136
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 140..150
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:1ZS6"
FT HELIX 164..167
FT /evidence="ECO:0007829|PDB:1ZS6"
SQ SEQUENCE 169 AA; 19015 MW; CCA41A122A37202D CRC64;
MICLVLTIFA NLFPAACTGA HERTFLAVKP DGVQRRLVGE IVRRFERKGF KLVALKLVQA
SEELLREHYA ELRERPFYGR LVKYMASGPV VAMVWQGLDV VRTSRALIGA TNPADAPPGT
IRGDFCIEVG KNLIHGSDSV ESARREIALW FRADELLCWE DSAGHWLYE
