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Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6) (Nucleoside-2-P kinase)

 NDK_STRCO               Reviewed;         137 AA.
P50589; O06853;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
01-OCT-1996, sequence version 1.
08-MAY-2019, entry version 127.
RecName: Full=Nucleoside diphosphate kinase {ECO:0000255|HAMAP-Rule:MF_00451};
Short=NDK {ECO:0000255|HAMAP-Rule:MF_00451};
Short=NDP kinase {ECO:0000255|HAMAP-Rule:MF_00451};
EC=2.7.4.6 {ECO:0000255|HAMAP-Rule:MF_00451};
AltName: Full=Nucleoside-2-P kinase {ECO:0000255|HAMAP-Rule:MF_00451};
Name=ndk {ECO:0000255|HAMAP-Rule:MF_00451}; OrderedLocusNames=SCO2612;
ORFNames=SCC88.23c;
Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145).
Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
Streptomyces; Streptomyces albidoflavus group.
NCBI_TaxID=100226;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=A3(2) / MT1110;
PubMed=8706710; DOI=10.1111/j.1432-1033.1996.0208u.x;
Brodbeck M., Rohling A., Wohlleben W., Thompson C.J., Suesstrunk U.;
"Nucleoside-diphosphate kinase from Streptomyces coelicolor.";
Eur. J. Biochem. 239:208-213(1996).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=9503623; DOI=10.1111/j.1574-6968.1998.tb12873.x;
Burger A., Brandt B., Suesstrunk U., Thompson C.J., Wohlleben W.;
"Analysis of a Streptomyces coelicolor A3(2) locus containing the
nucleoside diphosphate kinase (ndk) and folylpolyglutamate synthetase
(folC) genes.";
FEMS Microbiol. Lett. 159:283-291(1998).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=12000953; DOI=10.1038/417141a;
Bentley S.D., Chater K.F., Cerdeno-Tarraga A.-M., Challis G.L.,
Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H.,
Harper D., Bateman A., Brown S., Chandra G., Chen C.W., Collins M.,
Cronin A., Fraser A., Goble A., Hidalgo J., Hornsby T., Howarth S.,
Huang C.-H., Kieser T., Larke L., Murphy L.D., Oliver K., O'Neil S.,
Rabbinowitsch E., Rajandream M.A., Rutherford K.M., Rutter S.,
Seeger K., Saunders D., Sharp S., Squares R., Squares S., Taylor K.,
Warren T., Wietzorrek A., Woodward J.R., Barrell B.G., Parkhill J.,
Hopwood D.A.;
"Complete genome sequence of the model actinomycete Streptomyces
coelicolor A3(2).";
Nature 417:141-147(2002).
-!- FUNCTION: Major role in the synthesis of nucleoside triphosphates
other than ATP. The ATP gamma phosphate is transferred to the NDP
beta phosphate via a ping-pong mechanism, using a phosphorylated
active-site intermediate. {ECO:0000255|HAMAP-Rule:MF_00451}.
-!- CATALYTIC ACTIVITY:
Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-
deoxyribonucleoside 5'-triphosphate + ADP; Xref=Rhea:RHEA:44640,
ChEBI:CHEBI:30616, ChEBI:CHEBI:61560, ChEBI:CHEBI:73316,
ChEBI:CHEBI:456216; EC=2.7.4.6; Evidence={ECO:0000255|HAMAP-
Rule:MF_00451};
-!- CATALYTIC ACTIVITY:
Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside
5'-triphosphate + ADP; Xref=Rhea:RHEA:18113, ChEBI:CHEBI:30616,
ChEBI:CHEBI:57930, ChEBI:CHEBI:61557, ChEBI:CHEBI:456216;
EC=2.7.4.6; Evidence={ECO:0000255|HAMAP-Rule:MF_00451};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000255|HAMAP-Rule:MF_00451};
-!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_00451}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00451}.
-!- SIMILARITY: Belongs to the NDK family. {ECO:0000255|HAMAP-
Rule:MF_00451, ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X95643; CAA64899.1; -; Genomic_DNA.
EMBL; Y13070; CAA73513.1; -; Genomic_DNA.
EMBL; AL939113; CAB75393.1; -; Genomic_DNA.
PIR; S68956; S68956.
RefSeq; NP_626849.1; NC_003888.3.
RefSeq; WP_003976187.1; NC_003888.3.
SMR; P50589; -.
STRING; 100226.SCO2612; -.
PRIDE; P50589; -.
EnsemblBacteria; CAB75393; CAB75393; CAB75393.
GeneID; 1098046; -.
KEGG; sco:SCO2612; -.
PATRIC; fig|100226.15.peg.2658; -.
eggNOG; ENOG4108UGX; Bacteria.
eggNOG; COG0105; LUCA.
HOGENOM; HOG000224565; -.
InParanoid; P50589; -.
KO; K00940; -.
OMA; KIVAMKM; -.
PhylomeDB; P50589; -.
Proteomes; UP000001973; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004550; F:nucleoside diphosphate kinase activity; IBA:GO_Central.
GO; GO:0006241; P:CTP biosynthetic process; IEA:UniProtKB-UniRule.
GO; GO:0006183; P:GTP biosynthetic process; IEA:UniProtKB-UniRule.
GO; GO:0006163; P:purine nucleotide metabolic process; IBA:GO_Central.
GO; GO:0006220; P:pyrimidine nucleotide metabolic process; IBA:GO_Central.
GO; GO:0006228; P:UTP biosynthetic process; IEA:UniProtKB-UniRule.
Gene3D; 3.30.70.141; -; 1.
HAMAP; MF_00451; NDP_kinase; 1.
InterPro; IPR034907; NDK-like_dom.
InterPro; IPR036850; NDK-like_dom_sf.
InterPro; IPR001564; Nucleoside_diP_kinase.
InterPro; IPR023005; Nucleoside_diP_kinase_AS.
Pfam; PF00334; NDK; 1.
PRINTS; PR01243; NUCDPKINASE.
SMART; SM00562; NDK; 1.
SUPFAM; SSF54919; SSF54919; 1.
PROSITE; PS00469; NDP_KINASES; 1.
3: Inferred from homology;
ATP-binding; Complete proteome; Cytoplasm; Kinase; Magnesium;
Metal-binding; Nucleotide metabolism; Nucleotide-binding;
Phosphoprotein; Reference proteome; Transferase.
CHAIN 1 137 Nucleoside diphosphate kinase.
/FTId=PRO_0000137055.
ACT_SITE 117 117 Pros-phosphohistidine intermediate.
{ECO:0000255|HAMAP-Rule:MF_00451}.
BINDING 10 10 ATP. {ECO:0000255|HAMAP-Rule:MF_00451}.
BINDING 59 59 ATP. {ECO:0000255|HAMAP-Rule:MF_00451}.
BINDING 87 87 ATP. {ECO:0000255|HAMAP-Rule:MF_00451}.
BINDING 93 93 ATP. {ECO:0000255|HAMAP-Rule:MF_00451}.
BINDING 104 104 ATP. {ECO:0000255|HAMAP-Rule:MF_00451}.
BINDING 114 114 ATP. {ECO:0000255|HAMAP-Rule:MF_00451}.
CONFLICT 12 12 D -> E (in Ref. 2; CAA73513).
{ECO:0000305}.
SEQUENCE 137 AA; 15110 MW; 31FC0BE6006C1018 CRC64;
MTQRSLVLLK PDAVRRGLTG EIISRIERKA GWQITALELR TLDTETLEQH YGEHKGKPFY
EPLVEFMASG PVVAMVVEGE RVIEGVRALA GPTDPIAAAP GSIRGDYGVI VRENLIHASD
SEESAERELK IFFPGRV


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Pathways :
WP253: Glycolysis
WP1619: Amino sugar and nucleotide sugar metabolism
WP1946: Cori Cycle
WP2341: vitamin B1 (thiamin) biosynthesis and salvage pathway
WP1567: Glycolysis and Gluconeogenesis
WP1681: Pantothenate and CoA biosynthesis
WP1703: Streptomycin biosynthesis
WP1844: MAP kinase cascade
WP2340: Thiamine (vitamin B1) biosynthesis and salvage
WP1493: Carbon assimilation C4 pathway
WP32: Translation Factors
WP1653: Galactose metabolism
WP1701: Starch and sucrose metabolism
WP1694: Pyrimidine metabolism
WP1708: Terpenoid backbone biosynthesis
WP677: Momilactone biosynthesis
WP174: Hexaprenyl Diphosphate Biosynthesis
WP2211: Geranylgeranyldiphosphate biosynthesis II (plastidic)

Related Genes :
[Nme2] Nucleoside diphosphate kinase B (NDK B) (NDP kinase B) (EC 2.7.4.6) (Histidine protein kinase NDKB) (EC 2.7.13.3) (P18) (nm23-M2)
[Nme2] Nucleoside diphosphate kinase B (NDK B) (NDP kinase B) (EC 2.7.4.6) (Histidine protein kinase NDKB) (EC 2.7.13.3) (P18)
[NME2 NM23B] Nucleoside diphosphate kinase B (NDK B) (NDP kinase B) (EC 2.7.4.6) (C-myc purine-binding transcription factor PUF) (Histidine protein kinase NDKB) (EC 2.7.13.3) (nm23-H2)
[NME2] Nucleoside diphosphate kinase B (NDK B) (NDP kinase B) (EC 2.7.4.6) (Histidine protein kinase NDKB) (EC 2.7.13.3)
[NME1 NDPKA NM23] Nucleoside diphosphate kinase A (NDK A) (NDP kinase A) (EC 2.7.4.6) (Granzyme A-activated DNase) (GAAD) (Metastasis inhibition factor nm23) (NM23-H1) (Tumor metastatic process-associated protein)
[YNK1 NDK1 YNK YKL067W YKL333] Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6)
[NME2] Nucleoside diphosphate kinase B (NDK B) (NDP kinase B) (EC 2.7.4.6) (Histidine protein kinase NDKB) (EC 2.7.13.3)
[awd K-pn CG2210] Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6) (Abnormal wing disks protein) (Killer of prune protein)
[ndpk1 ZEAMMB73_Zm00001d029968] Nucleoside diphosphate kinase 1 (EC 2.7.4.6) (Nucleoside diphosphate kinase I) (NDK I) (NDP kinase I) (NDPK I) (ZmNDPK1)
[NME2 NM23B] Nucleoside diphosphate kinase B (NDK B) (NDP kinase B) (EC 2.7.4.6) (Histidine protein kinase NDKB) (EC 2.7.13.3) (nm23-C2)
[NME2] Nucleoside diphosphate kinase B (NDK B) (NDP kinase B) (EC 2.7.4.6) (Histidine protein kinase NDKB) (EC 2.7.13.3)
[CMPK2] UMP-CMP kinase 2, mitochondrial (EC 2.7.4.14) (Nucleoside-diphosphate kinase) (EC 2.7.4.6)
[ndk MSMEG_4627 MSMEI_4510] Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6) (Nucleoside-2-P kinase)
[gag-pol] Gag-Pol polyprotein (Pr160Gag-Pol) [Cleaved into: Matrix protein p17 (MA); Capsid protein p24 (CA); Spacer peptide 1 (SP1) (p2); Nucleocapsid protein p7 (NC); Transframe peptide (TF); p6-pol (p6*); Protease (EC 3.4.23.16) (PR) (Retropepsin); Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2) (p66 RT); p51 RT; p15; Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]
[Pik3cd] Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (PI3-kinase subunit delta) (PI3K-delta) (PI3Kdelta) (PtdIns-3-kinase subunit delta) (EC 2.7.1.153) (Phosphatidylinositol 4,5-bisphosphate 3-kinase 110 kDa catalytic subunit delta) (PtdIns-3-kinase subunit p110-delta) (p110delta)
[UL97] Serine/threonine protein kinase UL97 (EC 2.7.1.-) (Ganciclovir kinase) (HSRF3 protein)
[Ta0880] Nucleoside kinase (NK) (Adenosine kinase) (EC 2.7.1.20) (Broad specificity nucleoside kinase) (Cytidine kinase) (EC 2.7.1.213) (Guanosine kinase) (EC 2.7.1.-) (Inosine kinase) (EC 2.7.1.73)
[ndk-1 21D9.020 NCU04202] Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6)
[] Genome polyprotein [Cleaved into: Core protein p21 (Capsid protein C) (p21); Core protein p19; Envelope glycoprotein E1 (gp32) (gp35); Envelope glycoprotein E2 (NS1) (gp68) (gp70); p7; Protease NS2-3 (p23) (EC 3.4.22.-); Serine protease NS3 (EC 3.4.21.98) (EC 3.6.1.15) (EC 3.6.4.13) (Hepacivirin) (NS3P) (p70); Non-structural protein 4A (NS4A) (p8); Non-structural protein 4B (NS4B) (p27); Non-structural protein 5A (NS5A) (p56); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5B) (p68)]
[] Genome polyprotein [Cleaved into: Core protein p21 (Capsid protein C) (p21); Core protein p19; Envelope glycoprotein E1 (gp32) (gp35); Envelope glycoprotein E2 (NS1) (gp68) (gp70); p7; Protease NS2-3 (p23) (EC 3.4.22.-); Serine protease NS3 (EC 3.4.21.98) (EC 3.6.1.15) (EC 3.6.4.13) (Hepacivirin) (NS3P) (p70); Non-structural protein 4A (NS4A) (p8); Non-structural protein 4B (NS4B) (p27); Non-structural protein 5A (NS5A) (p56); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5B) (p68)]
[Eif2ak2 Pkr Prkr Tik] Interferon-induced, double-stranded RNA-activated protein kinase (EC 2.7.11.1) (Eukaryotic translation initiation factor 2-alpha kinase 2) (eIF-2A protein kinase 2) (Interferon-inducible RNA-dependent protein kinase) (P1/eIF-2A protein kinase) (Protein kinase RNA-activated) (PKR) (Protein kinase R) (Serine/threonine-protein kinase TIK) (Tyrosine-protein kinase EIF2AK2) (EC 2.7.10.2) (p68 kinase)
[Cdkn2a P16ink4a] Cyclin-dependent kinase inhibitor 2A (Cyclin-dependent kinase 4 inhibitor A) (CDK4I) (p16-INK4a) (p16-INK4)
[ndk OR16_10349] Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6) (Nucleoside-2-P kinase)
[] Genome polyprotein [Cleaved into: Core protein p21 (Capsid protein C) (p21); Core protein p19; Envelope glycoprotein E1 (gp32) (gp35); Envelope glycoprotein E2 (NS1) (gp68) (gp70); p7; Protease NS2-3 (p23) (EC 3.4.22.-); Serine protease NS3 (EC 3.4.21.98) (EC 3.6.1.15) (EC 3.6.4.13) (Hepacivirin) (NS3P) (p70); Non-structural protein 4A (NS4A) (p8); Non-structural protein 4B (NS4B) (p27); Non-structural protein 5A (NS5A) (p56); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5B) (p68)]
[ndk C2I27_28315 C2I28_03210 C3744_08500 CIB87_19995 CN367_27720 CN383_23285 CN890_24655 CN918_18725 CN955_10050 CN973_21260 CN978_05975 CN981_26505 COA18_20680 COC52_20785 COC53_25040 COC61_05415 COC62_09265 COD13_03675 COD15_18345 COE08_11190 COE55_24010 COE67_27575 COI68_13840 COI84_11105 COJ00_11480 COJ19_12010 COJ21_19810 COJ23_27995 COJ36_14750 COJ70_12815 COJ90_15430 COJ92_08070 COK01_12310 COK03_11095 COK68_14175 COK90_14655 COL08_09125 NCTC6005_04676 SAMN04487776_101672] Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6) (Nucleoside-2-P kinase)
[AK9 AKD1 AKD2 C6orf199 C6orf224] Adenylate kinase 9 (AK 9) (EC 2.7.4.4) (EC 2.7.4.6) (Adenylate kinase domain-containing protein 1) (Adenylate kinase domain-containing protein 2)
[AHK4 CRE1 RAW1 WOL At2g01830 T23K3.2] Histidine kinase 4 (EC 2.7.13.3) (Arabidopsis histidine kinase 4) (AtHK4) (Cytokinin receptor CYTOKININ RESPONSE 1) (AtCRE1) (Cytokinin receptor CRE1) (Phosphoprotein phosphatase AHK4) (EC 3.1.3.16) (Protein AUTHENTIC HIS-KINASE 4) (Protein ROOT AS IN WOL 1) (Protein WOODEN LEG)
[Rps6ka2 Mapkapk1c Rsk3] Ribosomal protein S6 kinase alpha-2 (S6K-alpha-2) (EC 2.7.11.1) (90 kDa ribosomal protein S6 kinase 2) (p90-RSK 2) (p90RSK2) (MAP kinase-activated protein kinase 1c) (MAPK-activated protein kinase 1c) (MAPKAP kinase 1c) (MAPKAPK-1c) (Protein-tyrosine kinase Mpk-9) (Ribosomal S6 kinase 3) (RSK-3) (pp90RSK3)
[ndk OR1_00218] Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6) (Nucleoside-2-P kinase)
[ndk OR37_00089] Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6) (Nucleoside-2-P kinase)

Bibliography :
[29870023] Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties.
[28551817] Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization.
[27268980] Vanadium-Binding Ability of Nucleoside Diphosphate Kinase from the Vanadium-Rich Fan Worm, Pseudopotamilla occelata.
[26630542] NDK Interacts with FtsZ and Converts GDP to GTP to Trigger FtsZ Polymerisation--A Novel Role for NDK.
[26548994] Biophysical Characterization of the Nucleoside Diphosphate Kinase of Leishmania major and Effect of the P95S Mutation.
[18621712] The relationship between dNTP pool levels and mutagenesis in an Escherichia coli NDP kinase mutant.
[17355283] The role of Ureaplasma nucleoside monophosphate kinases in the synthesis of nucleoside triphosphates.
[16957984] Molecular interactions involving Escherichia coli nucleoside diphosphate kinase.
[15169771] Escherichia coli nucleoside diphosphate kinase interactions with T4 phage proteins of deoxyribonucleotide synthesis and possible regulatory functions.
[12925801] Purification, crystallization and preliminary X-ray crystallographic analysis of nucleoside diphosphate kinase from rice.