ID   NDK_VEREI               Reviewed;         141 AA.
AC   A1WE20;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   06-FEB-2007, sequence version 1.
DT   03-AUG-2022, entry version 85.
DE   RecName: Full=Nucleoside diphosphate kinase {ECO:0000255|HAMAP-Rule:MF_00451};
DE            Short=NDK {ECO:0000255|HAMAP-Rule:MF_00451};
DE            Short=NDP kinase {ECO:0000255|HAMAP-Rule:MF_00451};
DE            EC=2.7.4.6 {ECO:0000255|HAMAP-Rule:MF_00451};
DE   AltName: Full=Nucleoside-2-P kinase {ECO:0000255|HAMAP-Rule:MF_00451};
GN   Name=ndk {ECO:0000255|HAMAP-Rule:MF_00451}; OrderedLocusNames=Veis_0084;
OS   Verminephrobacter eiseniae (strain EF01-2).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Comamonadaceae; Verminephrobacter.
OX   NCBI_TaxID=391735;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=EF01-2;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chertkov O., Brettin T.,
RA   Bruce D., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Kyrpides N., Kim E., Stahl D., Richardson P.;
RT   "Complete sequence of chromosome 1 of Verminephrobacter eiseniae EF01-2.";
RL   Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
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. {ECO:0000255|HAMAP-Rule:MF_00451}.
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; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00451};
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         Evidence={ECO:0000255|HAMAP-Rule:MF_00451};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00451};
CC   -!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_00451}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00451}.
CC   -!- SIMILARITY: Belongs to the NDK family. {ECO:0000255|HAMAP-
CC       Rule:MF_00451}.
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DR   EMBL; CP000542; ABM55877.1; -; Genomic_DNA.
DR   RefSeq; WP_011807896.1; NC_008786.1.
DR   AlphaFoldDB; A1WE20; -.
DR   SMR; A1WE20; -.
DR   STRING; 391735.Veis_0084; -.
DR   EnsemblBacteria; ABM55877; ABM55877; Veis_0084.
DR   KEGG; vei:Veis_0084; -.
DR   eggNOG; COG0105; Bacteria.
DR   HOGENOM; CLU_060216_8_1_4; -.
DR   OMA; KIVAMKM; -.
DR   OrthoDB; 1752581at2; -.
DR   Proteomes; UP000000374; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0004550; F:nucleoside diphosphate kinase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0006241; P:CTP biosynthetic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0006183; P:GTP biosynthetic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IEA:InterPro.
DR   GO; GO:0006228; P:UTP biosynthetic process; IEA:UniProtKB-UniRule.
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   Pfam; PF00334; NDK; 1.
DR   PRINTS; PR01243; NUCDPKINASE.
DR   SMART; SM00562; NDK; 1.
DR   SUPFAM; SSF54919; SSF54919; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Cytoplasm; Kinase; Magnesium; Metal-binding;
KW   Nucleotide metabolism; Nucleotide-binding; Phosphoprotein;
KW   Reference proteome; Transferase.
FT   CHAIN           1..141
FT                   /note="Nucleoside diphosphate kinase"
FT                   /id="PRO_1000026309"
FT   ACT_SITE        117
FT                   /note="Pros-phosphohistidine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT   BINDING         11
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT   BINDING         59
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT   BINDING         87
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT   BINDING         93
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT   BINDING         104
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT   BINDING         114
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
SQ   SEQUENCE   141 AA;  15491 MW;  7FAAD119E0CE053E CRC64;
     MAIERTLSII KPDAVAKNVI GQIYARFEAA GLKIVAARMV HLARPEAERF YAVHKERPFF
     KDLVEFMISG PVMVQVLEGE NAVLKNRELM GATDPKKAQT GTIRADFADS IDANAVHGSD
     AAETAQAEVA FFFPGLNIYP R