NDK_BURTA
ID NDK_BURTA Reviewed; 141 AA.
AC Q2SWE7;
DT 27-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 1.
DT 03-AUG-2022, entry version 94.
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=BTH_I2231;
OS Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 /
OS E264).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; pseudomallei group.
OX NCBI_TaxID=271848;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700388 / DSM 13276 / CIP 106301 / E264;
RX PubMed=16336651; DOI=10.1186/1471-2164-6-174;
RA Kim H.S., Schell M.A., Yu Y., Ulrich R.L., Sarria S.H., Nierman W.C.,
RA DeShazer D.;
RT "Bacterial genome adaptation to niches: divergence of the potential
RT virulence genes in three Burkholderia species of different survival
RT strategies.";
RL BMC Genomics 6:174-174(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. {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; CP000086; ABC37309.1; -; Genomic_DNA.
DR RefSeq; WP_009890817.1; NZ_CP008785.1.
DR PDB; 4DUT; X-ray; 2.50 A; A/B=1-141.
DR PDB; 4EK2; X-ray; 2.00 A; A/B=1-141.
DR PDB; 4HR2; X-ray; 1.95 A; A/B=1-141.
DR PDBsum; 4DUT; -.
DR PDBsum; 4EK2; -.
DR PDBsum; 4HR2; -.
DR AlphaFoldDB; Q2SWE7; -.
DR SMR; Q2SWE7; -.
DR PRIDE; Q2SWE7; -.
DR EnsemblBacteria; ABC37309; ABC37309; BTH_I2231.
DR GeneID; 66547286; -.
DR KEGG; bte:BTH_I2231; -.
DR HOGENOM; CLU_060216_8_1_4; -.
DR OMA; KIVAMKM; -.
DR OrthoDB; 1752581at2; -.
DR BRENDA; 2.7.4.6; 8156.
DR Proteomes; UP000001930; Chromosome I.
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 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; Transferase.
FT CHAIN 1..141
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000242495"
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"
FT STRAND 3..10
FT /evidence="ECO:0007829|PDB:4HR2"
FT HELIX 12..16
FT /evidence="ECO:0007829|PDB:4HR2"
FT HELIX 20..29
FT /evidence="ECO:0007829|PDB:4HR2"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:4HR2"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:4HR2"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:4HR2"
FT HELIX 60..67
FT /evidence="ECO:0007829|PDB:4HR2"
FT STRAND 72..80
FT /evidence="ECO:0007829|PDB:4HR2"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:4HR2"
FT TURN 95..97
FT /evidence="ECO:0007829|PDB:4HR2"
FT HELIX 103..107
FT /evidence="ECO:0007829|PDB:4HR2"
FT STRAND 110..113
FT /evidence="ECO:0007829|PDB:4EK2"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:4HR2"
FT HELIX 122..132
FT /evidence="ECO:0007829|PDB:4HR2"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:4HR2"
SQ SEQUENCE 141 AA; 15618 MW; 30DDF4CDC82EF604 CRC64;
MALERTLSII KPDAVAKNVI GQIYSRFENA GLKIVAARMA HLSRADAEKF YAVHAERPFF
KDLVEFMISG PVMIQVLEGE DAILKNRDLM GATDPKKAEK GTIRADFADS IDANAVHGSD
APETARVEIA FFFPEMNVYS R
