NDK_HALSA
ID NDK_HALSA Reviewed; 161 AA.
AC P61136; P61137; Q9HQH5;
DT 10-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 10-MAY-2004, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Nucleoside diphosphate kinase {ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000303|PubMed:16293253};
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=VNG_1160G;
OS Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
OS (Halobacterium halobium).
OC Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Halobacteriales;
OC Halobacteriaceae; Halobacterium.
OX NCBI_TaxID=64091;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Ishibashi M., Hiratsuka K., Yonezawa Y., Tokunaga H., Tokunaga M.;
RT "NDK from Halobacterium cutirubrum.";
RL Submitted (DEC-1999) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700922 / JCM 11081 / NRC-1;
RX PubMed=11016950; DOI=10.1073/pnas.190337797;
RA Ng W.V., Kennedy S.P., Mahairas G.G., Berquist B., Pan M., Shukla H.D.,
RA Lasky S.R., Baliga N.S., Thorsson V., Sbrogna J., Swartzell S., Weir D.,
RA Hall J., Dahl T.A., Welti R., Goo Y.A., Leithauser B., Keller K., Cruz R.,
RA Danson M.J., Hough D.W., Maddocks D.G., Jablonski P.E., Krebs M.P.,
RA Angevine C.M., Dale H., Isenbarger T.A., Peck R.F., Pohlschroder M.,
RA Spudich J.L., Jung K.-H., Alam M., Freitas T., Hou S., Daniels C.J.,
RA Dennis P.P., Omer A.D., Ebhardt H., Lowe T.M., Liang P., Riley M., Hood L.,
RA DasSarma S.;
RT "Genome sequence of Halobacterium species NRC-1.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:12176-12181(2000).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH ATP ANALOG.
RX PubMed=16293253; DOI=10.1016/j.febslet.2005.10.052;
RA Besir H., Zeth K., Bracher A., Heider U., Ishibashi M., Tokunaga M.,
RA Oesterhelt D.;
RT "Structure of a halophilic nucleoside diphosphate kinase from Halobacterium
RT salinarum.";
RL FEBS Lett. 579:6595-6600(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 -!- 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; AB036344; BAB17308.1; -; Genomic_DNA.
DR EMBL; AE004437; AAG19540.1; -; Genomic_DNA.
DR PIR; H84271; H84271.
DR RefSeq; WP_010902835.1; NC_002607.1.
DR PDB; 2AZ1; X-ray; 2.35 A; A/B/C/D/E/F=1-161.
DR PDB; 2AZ3; X-ray; 2.20 A; A/B/C/D/E/F/G/H/I=1-161.
DR PDBsum; 2AZ1; -.
DR PDBsum; 2AZ3; -.
DR AlphaFoldDB; P61136; -.
DR SMR; P61136; -.
DR STRING; 64091.VNG_1160G; -.
DR PaxDb; P61136; -.
DR EnsemblBacteria; AAG19540; AAG19540; VNG_1160G.
DR GeneID; 5954227; -.
DR GeneID; 62884525; -.
DR KEGG; hal:VNG_1160G; -.
DR PATRIC; fig|64091.14.peg.887; -.
DR HOGENOM; CLU_060216_6_3_2; -.
DR InParanoid; P61136; -.
DR OMA; KIVAMKM; -.
DR OrthoDB; 106462at2157; -.
DR PhylomeDB; P61136; -.
DR BioCyc; MetaCyc:MON-15776; -.
DR BRENDA; 2.7.4.6; 2552.
DR EvolutionaryTrace; P61136; -.
DR Proteomes; UP000000554; 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: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..161
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000137089"
FT ACT_SITE 119
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 13
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000305|PubMed:16293253"
FT BINDING 61
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000305|PubMed:16293253"
FT BINDING 89
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000305|PubMed:16293253"
FT BINDING 95
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000305|PubMed:16293253"
FT BINDING 106
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000305|PubMed:16293253"
FT BINDING 116
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451,
FT ECO:0000305|PubMed:16293253"
FT STRAND 7..12
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 14..18
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 22..31
FT /evidence="ECO:0007829|PDB:2AZ3"
FT STRAND 35..42
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 46..52
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 54..56
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 62..69
FT /evidence="ECO:0007829|PDB:2AZ3"
FT STRAND 74..81
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 84..92
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 97..99
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 105..109
FT /evidence="ECO:0007829|PDB:2AZ3"
FT STRAND 113..115
FT /evidence="ECO:0007829|PDB:2AZ3"
FT STRAND 117..120
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 128..136
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:2AZ1"
FT HELIX 150..153
FT /evidence="ECO:0007829|PDB:2AZ3"
FT HELIX 155..157
FT /evidence="ECO:0007829|PDB:2AZ1"
SQ SEQUENCE 161 AA; 18065 MW; 8A339F3F4D4C0AF3 CRC64;
MTDHDERTFV MVKPDGVQRG LIGDIVTRLE TKGLKMVGGK FMRIDEELAH EHYAEHEDKP
FFDGLVSFIT SGPVFAMVWE GADATRQVRQ LMGATDAQDA APGTIRGDYG NDLGHNLIHG
SDHEDEGANE REIALFFDDD ELVDWDRDAS AWVYEDLADH D
