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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
 
 
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