NDK_AQUAE
ID NDK_AQUAE Reviewed; 142 AA.
AC O67528;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 122.
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=aq_1590;
OS Aquifex aeolicus (strain VF5).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex.
OX NCBI_TaxID=224324;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VF5;
RX PubMed=9537320; DOI=10.1038/32831;
RA Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.,
RA Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R.,
RA Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.;
RT "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.";
RL Nature 392:353-358(1998).
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, ECO:0000305}.
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DR EMBL; AE000657; AAC07481.1; -; Genomic_DNA.
DR PIR; F70437; F70437.
DR RefSeq; NP_214093.1; NC_000918.1.
DR RefSeq; WP_010881031.1; NC_000918.1.
DR PDB; 3ZTO; X-ray; 1.47 A; A=1-142.
DR PDB; 3ZTP; X-ray; 1.37 A; A/C=1-142.
DR PDB; 3ZTQ; X-ray; 2.10 A; A/B/C/D/E/F/G/H=1-142.
DR PDB; 3ZTR; X-ray; 2.30 A; A/B/C/D/E/F/G/H/I/J/K/L=1-142.
DR PDB; 3ZTS; X-ray; 2.30 A; A/B/C/D/E/F/G/H/I/J/K/L=1-142.
DR PDBsum; 3ZTO; -.
DR PDBsum; 3ZTP; -.
DR PDBsum; 3ZTQ; -.
DR PDBsum; 3ZTR; -.
DR PDBsum; 3ZTS; -.
DR AlphaFoldDB; O67528; -.
DR SMR; O67528; -.
DR STRING; 224324.aq_1590; -.
DR EnsemblBacteria; AAC07481; AAC07481; aq_1590.
DR KEGG; aae:aq_1590; -.
DR PATRIC; fig|224324.8.peg.1227; -.
DR eggNOG; COG0105; Bacteria.
DR HOGENOM; CLU_060216_8_1_0; -.
DR InParanoid; O67528; -.
DR OMA; KIVAMKM; -.
DR OrthoDB; 1752581at2; -.
DR Proteomes; UP000000798; 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; IBA:GO_Central.
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:0006163; P:purine nucleotide metabolic process; IBA:GO_Central.
DR GO; GO:0006220; P:pyrimidine nucleotide metabolic process; IBA:GO_Central.
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 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; ATP-binding; Cytoplasm; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Phosphoprotein;
KW Reference proteome; Transferase.
FT CHAIN 1..142
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000136936"
FT ACT_SITE 120
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 107
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 117
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT STRAND 3..10
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 12..17
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 20..29
FT /evidence="ECO:0007829|PDB:3ZTP"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 60..67
FT /evidence="ECO:0007829|PDB:3ZTP"
FT STRAND 72..80
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 95..101
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 106..110
FT /evidence="ECO:0007829|PDB:3ZTP"
FT STRAND 113..116
FT /evidence="ECO:0007829|PDB:3ZTP"
FT STRAND 118..121
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 125..135
FT /evidence="ECO:0007829|PDB:3ZTP"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:3ZTP"
SQ SEQUENCE 142 AA; 15942 MW; 189B5DFA0317E998 CRC64;
MAVERTLIIV KPDAMEKGAL GKILDRFIQE GFQIKALKMF RFTPEKAGEF YYVHRERPFF
QELVEFMSSG PVVAAVLEGE DAIKRVREII GPTDSEEARK VAPNSIRAQF GTDKGKNAIH
ASDSPESAQY EICFIFSGLE IV
