NDK_PSEAE
ID NDK_PSEAE Reviewed; 143 AA.
AC Q59636;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 08-DEC-2000, sequence version 2.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Nucleoside diphosphate kinase {ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000303|PubMed:8606147};
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, ECO:0000269|PubMed:8606147, ECO:0000269|PubMed:8955392};
DE AltName: Full=Nucleoside-2-P kinase {ECO:0000255|HAMAP-Rule:MF_00451};
GN Name=ndk {ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000303|PubMed:8606147};
GN OrderedLocusNames=PA3807;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=8822;
RX PubMed=8809750; DOI=10.1111/j.1365-2958.1996.tb02538.x;
RA Sundin G.W., Shankar S., Chugani S.A., Chopade B., Kavanaugh-Black A.,
RA Chakrabarty A.M.;
RT "Nucleoside diphosphate kinase from Pseudomonas aeruginosa:
RT characterization of the gene and its role in cellular growth and
RT exopolysaccharide alginate synthesis.";
RL Mol. Microbiol. 20:965-979(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE,
RP AND PROTEOLYTIC CLEAVAGE.
RC STRAIN=8830;
RX PubMed=8606147; DOI=10.1128/jb.178.7.1777-1781.1996;
RA Shankar S., Kamath S., Chakrabarty A.M.;
RT "Two forms of the nucleoside diphosphate kinase of Pseudomonas aeruginosa
RT 8830: altered specificity of nucleoside triphosphate synthesis by the cell
RT membrane-associated form of the truncated enzyme.";
RL J. Bacteriol. 178:1777-1781(1996).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH PYRUVATE KINASE, AND
RP MUTAGENESIS OF ALA-14; GLY-21; SER-43; GLU-56; SER-69; GLU-80; GLY-91;
RP HIS-117; SER-119; SER-121 AND ALA-125.
RC STRAIN=8830;
RX PubMed=8955392; DOI=10.1128/jb.178.24.7120-7128.1996;
RA Sundin G.W., Shankar S., Chakrabarty A.M.;
RT "Mutational analysis of nucleoside diphosphate kinase from Pseudomonas
RT aeruginosa: characterization of critical amino acid residues involved in
RT exopolysaccharide alginate synthesis.";
RL J. Bacteriol. 178:7120-7128(1996).
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. The 12-kDa membrane-associated form synthesizes GTP in
CC preference to other nucleoside triphosphates. Important for alginate
CC synthesis. {ECO:0000269|PubMed:8606147, ECO:0000269|PubMed:8955392}.
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, ECO:0000269|PubMed:8606147,
CC ECO:0000269|PubMed:8955392};
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 ECO:0000269|PubMed:8606147, ECO:0000269|PubMed:8955392};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00451};
CC -!- SUBUNIT: Homotetramer (By similarity). The 12-kDa form interacts with
CC pyruvate kinase (PubMed:8955392). {ECO:0000255|HAMAP-Rule:MF_00451,
CC ECO:0000269|PubMed:8955392}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00451,
CC ECO:0000269|PubMed:8606147}. Note=Ndk is predominantly cytoplasmic. The
CC 12-kDa form is predominantly membrane-associated.
CC {ECO:0000269|PubMed:8606147}.
CC -!- DEVELOPMENTAL STAGE: The level of the 12-kDa form increases toward the
CC late stationary phase of growth. {ECO:0000269|PubMed:8606147}.
CC -!- PTM: An intracellular protease cleaves Ndk to a truncated 12-kDa form
CC that undergoes autophosphorylation almost as efficiency as Ndk does.
CC {ECO:0000269|PubMed:8606147}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000255|HAMAP-
CC Rule:MF_00451, ECO:0000305}.
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DR EMBL; U41267; AAC44154.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG07194.1; -; Genomic_DNA.
DR PIR; B83172; B83172.
DR PIR; S77589; S77589.
DR RefSeq; NP_252496.1; NC_002516.2.
DR RefSeq; WP_003092811.1; NZ_QZGE01000001.1.
DR AlphaFoldDB; Q59636; -.
DR SMR; Q59636; -.
DR STRING; 287.DR97_4062; -.
DR PaxDb; Q59636; -.
DR PRIDE; Q59636; -.
DR EnsemblBacteria; AAG07194; AAG07194; PA3807.
DR GeneID; 879892; -.
DR KEGG; pae:PA3807; -.
DR PATRIC; fig|208964.12.peg.3986; -.
DR PseudoCAP; PA3807; -.
DR HOGENOM; CLU_060216_8_1_6; -.
DR InParanoid; Q59636; -.
DR OMA; KIVAMKM; -.
DR PhylomeDB; Q59636; -.
DR BioCyc; PAER208964:G1FZ6-3878-MON; -.
DR BRENDA; 2.7.4.6; 5087.
DR PHI-base; PHI:6438; -.
DR Proteomes; UP000002438; 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; IDA:PseudoCAP.
DR GO; GO:0042121; P:alginic acid biosynthetic process; IDA:PseudoCAP.
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:0006163; P:purine nucleotide metabolic process; IDA:PseudoCAP.
DR GO; GO:0006220; P:pyrimidine nucleotide metabolic process; IDA:PseudoCAP.
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 ATP-binding; Cytoplasm; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Phosphoprotein;
KW Reference proteome; Transferase.
FT CHAIN 1..143
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000137024"
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 MUTAGEN 14
FT /note="A->P: Lack of autophosphorylation and of kinase
FT activity. Cleaved to 12-kDa form, but cannot form a complex
FT with pyruvate kinase. Strong decrease in alginate
FT production."
FT MUTAGEN 21
FT /note="G->V: Lack of autophosphorylation and of kinase
FT activity. Cleaved to 12-kDa form, but cannot form a complex
FT with pyruvate kinase. Strong decrease in alginate
FT production."
FT MUTAGEN 43
FT /note="S->A: Decrease in autophosphorylation. Strong
FT decrease in alginate production."
FT MUTAGEN 56
FT /note="E->D: No change in autophosphorylation. Strong
FT decrease in alginate production."
FT MUTAGEN 69
FT /note="S->C: Decrease in autophosphorylation. Strong
FT decrease in alginate production."
FT MUTAGEN 80
FT /note="E->K: Decrease in autophosphorylation. Strong
FT decrease in alginate production."
FT MUTAGEN 91
FT /note="G->V: Decrease in autophosphorylation. Strong
FT decrease in alginate production."
FT MUTAGEN 117
FT /note="H->Q: Lack of autophosphorylation and of kinase
FT activity. Strong decrease in alginate production."
FT MUTAGEN 119
FT /note="S->A: No change in autophosphorylation. Does not
FT affect alginate production."
FT MUTAGEN 121
FT /note="S->A: No change in autophosphorylation. Does not
FT affect alginate production."
FT MUTAGEN 125
FT /note="A->R: Lack of autophosphorylation and of kinase
FT activity. Strong decrease in alginate production."
FT CONFLICT 56
FT /note="E -> A (in Ref. 1; AAC44154)"
FT /evidence="ECO:0000305"
FT CONFLICT 130
FT /note="A -> V (in Ref. 1; AAC44154)"
FT /evidence="ECO:0000305"
FT CONFLICT 135
FT /note="A -> D (in Ref. 1; AAC44154)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 143 AA; 15592 MW; E99FE5CB8556E8B4 CRC64;
MALQRTLSII KPDAVSKNVI GEILTRFEKA GLRVVAAKMV QLSEREAGGF YAEHKERPFF
KDLVSFMTSG PVVVQVLEGE DAIAKNRELM GATDPKKADA GTIRADFAVS IDENAVHGSD
SEASAAREIA YFFAATEVCE RIR
