NDKM_DICDI
ID NDKM_DICDI Reviewed; 220 AA.
AC P34093; Q54W33;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 04-DEC-2007, sequence version 2.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Nucleoside diphosphate kinase, mitochondrial;
DE Short=NDK;
DE Short=NDP kinase;
DE EC=2.7.4.6;
DE Flags: Precursor;
GN Name=ndkM; Synonyms=guk, ndkA; ORFNames=DDB_G0279911;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 58-64.
RC STRAIN=AX2;
RX PubMed=8244981; DOI=10.1016/s0021-9258(19)74415-9;
RA Troll H., Winckler T., Lascu I., Mueller N., Saurin W., Veron M.,
RA Mutzel R.;
RT "Separate nuclear genes encode cytosolic and mitochondrial nucleoside
RT diphosphate kinase in Dictyostelium discoideum.";
RL J. Biol. Chem. 268:25469-25475(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
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.
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 -!- SUBCELLULAR LOCATION: Mitochondrion intermembrane space.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
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DR EMBL; L23068; AAA16162.1; -; Genomic_DNA.
DR EMBL; AAFI02000035; EAL67427.1; -; Genomic_DNA.
DR PIR; B49547; B49547.
DR RefSeq; XP_641417.1; XM_636325.1.
DR AlphaFoldDB; P34093; -.
DR SMR; P34093; -.
DR STRING; 44689.DDB0214817; -.
DR PaxDb; P34093; -.
DR EnsemblProtists; EAL67427; EAL67427; DDB_G0279911.
DR GeneID; 8622301; -.
DR KEGG; ddi:DDB_G0279911; -.
DR dictyBase; DDB_G0279911; ndkM.
DR eggNOG; KOG0888; Eukaryota.
DR HOGENOM; CLU_060216_5_0_1; -.
DR InParanoid; P34093; -.
DR OMA; AKHEISM; -.
DR PhylomeDB; P34093; -.
DR Reactome; R-DDI-499943; Interconversion of nucleotide di- and triphosphates.
DR Reactome; R-DDI-6798695; Neutrophil degranulation.
DR Reactome; R-DDI-9748787; Azathioprine ADME.
DR PRO; PR:P34093; -.
DR Proteomes; UP000002195; Chromosome 3.
DR GO; GO:0031012; C:extracellular matrix; HDA:dictyBase.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; IDA:dictyBase.
DR GO; GO:0045335; C:phagocytic vesicle; HDA:dictyBase.
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; ISS:dictyBase.
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:0009142; P:nucleoside triphosphate biosynthetic process; ISS:dictyBase.
DR GO; GO:0009617; P:response to bacterium; HEP:dictyBase.
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; Direct protein sequencing; Kinase; Magnesium; Metal-binding;
KW Mitochondrion; Nucleotide metabolism; Nucleotide-binding; Phosphoprotein;
KW Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..57
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:8244981"
FT CHAIN 58..220
FT /note="Nucleoside diphosphate kinase, mitochondrial"
FT /id="PRO_0000019430"
FT ACT_SITE 186
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 80
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 128
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 156
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 162
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 173
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 183
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT CONFLICT 30
FT /note="A -> G (in Ref. 1; AAA16162)"
FT /evidence="ECO:0000305"
FT CONFLICT 81..82
FT /note="VS -> WN (in Ref. 1; AAA16162)"
FT /evidence="ECO:0000305"
FT CONFLICT 163
FT /note="D -> V (in Ref. 1; AAA16162)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 220 AA; 23998 MW; 42A82CA730CF0FDA CRC64;
MFSRFARAFP KILASGASQR TFATVQKAFA NPTSKKLIVG SSLLIGSAFA TTSFVACENK
SVPLVGLPGT NQERSFIAIK VSSTQRRLIG EIIARFEKKG FKLVGIKILV PTPEHAAKHY
EDLNKKPFFN GLVKFFSSGA VVAMVFEGKD VVRTGRVLIG ATDPSQSAPG TIRFDLCIET
GRNIIHGSDS NESAAHEIAL WFKEDEIANW VSTNPVYEKM
