NDK_THET8
ID NDK_THET8 Reviewed; 137 AA.
AC Q5SLV5;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 106.
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=TTHA0188;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH ATP.
RX PubMed=14501133; DOI=10.1107/s0907444903017712;
RA Takeishi S., Nakagawa N., Maoka N., Kihara M., Moriguchi M., Masui R.,
RA Kuramitsu S.;
RT "Crystallization and preliminary X-ray diffraction studies of nucleoside
RT diphosphate kinase from Thermus thermophilus HB8.";
RL Acta Crystallogr. D 59:1843-1845(2003).
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; AP008226; BAD70011.1; -; Genomic_DNA.
DR RefSeq; WP_011227764.1; NC_006461.1.
DR RefSeq; YP_143454.1; NC_006461.1.
DR PDB; 1WKJ; X-ray; 2.00 A; A/B=1-137.
DR PDB; 1WKK; X-ray; 2.70 A; A/B=1-137.
DR PDB; 1WKL; X-ray; 2.20 A; A/B=1-137.
DR PDBsum; 1WKJ; -.
DR PDBsum; 1WKK; -.
DR PDBsum; 1WKL; -.
DR AlphaFoldDB; Q5SLV5; -.
DR SMR; Q5SLV5; -.
DR STRING; 300852.55771570; -.
DR EnsemblBacteria; BAD70011; BAD70011; BAD70011.
DR GeneID; 3169489; -.
DR KEGG; ttj:TTHA0188; -.
DR eggNOG; COG0105; Bacteria.
DR HOGENOM; CLU_060216_6_3_0; -.
DR OMA; KIVAMKM; -.
DR PhylomeDB; Q5SLV5; -.
DR EvolutionaryTrace; Q5SLV5; -.
DR Proteomes; UP000000532; 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 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..137
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000137067"
FT ACT_SITE 115
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 9
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000269|PubMed:14501133"
FT BINDING 57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000269|PubMed:14501133"
FT BINDING 85
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000269|PubMed:14501133"
FT BINDING 91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000269|PubMed:14501133"
FT BINDING 102
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000269|PubMed:14501133"
FT BINDING 112
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000269|PubMed:14501133"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:1WKJ"
FT HELIX 10..14
FT /evidence="ECO:0007829|PDB:1WKJ"
FT HELIX 18..28
FT /evidence="ECO:0007829|PDB:1WKJ"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:1WKJ"
FT HELIX 42..48
FT /evidence="ECO:0007829|PDB:1WKJ"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:1WKJ"
FT STRAND 53..57
FT /evidence="ECO:0007829|PDB:1WKJ"
FT HELIX 58..65
FT /evidence="ECO:0007829|PDB:1WKJ"
FT STRAND 70..77
FT /evidence="ECO:0007829|PDB:1WKJ"
FT HELIX 80..88
FT /evidence="ECO:0007829|PDB:1WKJ"
FT TURN 93..95
FT /evidence="ECO:0007829|PDB:1WKJ"
FT HELIX 101..105
FT /evidence="ECO:0007829|PDB:1WKJ"
FT STRAND 113..116
FT /evidence="ECO:0007829|PDB:1WKJ"
FT HELIX 120..130
FT /evidence="ECO:0007829|PDB:1WKJ"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:1WKJ"
SQ SEQUENCE 137 AA; 15344 MW; 750E673CA9C9FE3E CRC64;
MERTFVMIKP DGVRRGLVGE ILARFERKGF RIAALKLMQI SQELAERHYA EHREKPFFPG
LVRFITSGPV VAMVLEGPGV VAEVRKMMGA THPKDALPGT IRGDFATTID ENVIHGSATL
EDAQREIALF FRPEELL
