ID A0A0K1K5R3_9BURK Unreviewed; 141 AA.
AC A0A0K1K5R3;
DT 11-NOV-2015, integrated into UniProtKB/TrEMBL.
DT 11-NOV-2015, sequence version 1.
DT 27-MAR-2024, entry version 32.
DE RecName: Full=Nucleoside diphosphate kinase {ECO:0000256|HAMAP-Rule:MF_00451};
DE Short=NDK {ECO:0000256|HAMAP-Rule:MF_00451};
DE Short=NDP kinase {ECO:0000256|HAMAP-Rule:MF_00451};
DE EC=2.7.4.6 {ECO:0000256|HAMAP-Rule:MF_00451};
DE AltName: Full=Nucleoside-2-P kinase {ECO:0000256|HAMAP-Rule:MF_00451};
GN Name=ndk {ECO:0000256|HAMAP-Rule:MF_00451};
GN ORFNames=ACZ75_26730 {ECO:0000313|EMBL:AKU24526.1};
OS Massilia sp. NR 4-1.
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Oxalobacteraceae; Telluria group; Massilia.
OX NCBI_TaxID=1678028 {ECO:0000313|EMBL:AKU24526.1, ECO:0000313|Proteomes:UP000056897};
RN [1] {ECO:0000313|EMBL:AKU24526.1, ECO:0000313|Proteomes:UP000056897}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NR 4-1 {ECO:0000313|EMBL:AKU24526.1,
RC ECO:0000313|Proteomes:UP000056897};
RA Sul W.J.;
RT "Massilia sp. NR 4-1 isolated from rhizosphere of Torreya nucifera in
RT national heritage Bijarim forest, volcanic Jeju Island, Korea.";
RL Submitted (JUN-2015) 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:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_00451};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00451};
CC -!- SUBUNIT: Homotetramer. {ECO:0000256|HAMAP-Rule:MF_00451}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00451}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000256|ARBA:ARBA00008142,
CC ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000256|RuleBase:RU004011}.
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DR EMBL; CP012201; AKU24526.1; -; Genomic_DNA.
DR RefSeq; WP_050412223.1; NZ_CP012201.1.
DR AlphaFoldDB; A0A0K1K5R3; -.
DR STRING; 1678028.ACZ75_26730; -.
DR KEGG; mnr:ACZ75_26730; -.
DR PATRIC; fig|1678028.3.peg.5422; -.
DR OrthoDB; 9801161at2; -.
DR Proteomes; UP000056897; 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:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006228; P:UTP biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd04413; NDPk_I; 1.
DR Gene3D; 3.30.70.141; Nucleoside diphosphate kinase-like domain; 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 PANTHER; PTHR46161; NUCLEOSIDE DIPHOSPHATE KINASE; 1.
DR PANTHER; PTHR46161:SF3; NUCLEOSIDE DIPHOSPHATE KINASE DDB_G0292928-RELATED; 1.
DR Pfam; PF00334; NDK; 1.
DR PRINTS; PR01243; NUCDPKINASE.
DR SMART; SM00562; NDK; 1.
DR SUPFAM; SSF54919; Nucleoside diphosphate kinase, NDK; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_00451};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00451};
KW Kinase {ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000313|EMBL:AKU24526.1};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00451};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00451};
KW Nucleotide metabolism {ECO:0000256|HAMAP-Rule:MF_00451};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00451};
KW Phosphoprotein {ECO:0000256|ARBA:ARBA00022553, ECO:0000256|HAMAP-
KW Rule:MF_00451}; Reference proteome {ECO:0000313|Proteomes:UP000056897};
KW Transferase {ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000313|EMBL:AKU24526.1}.
FT DOMAIN 3..140
FT /note="Nucleoside diphosphate kinase-like"
FT /evidence="ECO:0000259|SMART:SM00562"
FT ACT_SITE 117
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 11
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 59
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 87
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 93
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 104
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 114
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
SQ SEQUENCE 141 AA; 15339 MW; 63FAD86B3962A640 CRC64;
MAIERTLSII KPDAVAKNVI GQIYSRFEGA GLKVIAARMA QLSRAEAEGF YAVHRERPFF
KDLVDFMVSG PVMIQVLEGE GAILKNRDLM GATDPKKAEK GTIRADFADS IDANAVHGSD
AAETAAVEIA YYFPALNVYS R
//
