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PDX1_PLAF7
ID   PDX1_PLAF7              Reviewed;         301 AA.
AC   C6KT50;
DT   04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT   01-SEP-2009, sequence version 1.
DT   03-AUG-2022, entry version 78.
DE   RecName: Full=Pyridoxal 5'-phosphate synthase subunit Pdx1;
DE            Short=PLP synthase subunit Pdx1;
DE            EC=4.3.3.6 {ECO:0000269|PubMed:16339145, ECO:0000269|PubMed:22244765};
GN   Name=pdx1; ORFNames=PFF1025c {ECO:0000312|EMBL:CAG25026.1};
OS   Plasmodium falciparum (isolate 3D7).
OC   Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
OC   Plasmodiidae; Plasmodium; Plasmodium (Laverania).
OX   NCBI_TaxID=36329;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=3D7 {ECO:0000312|Proteomes:UP000001450};
RX   PubMed=12368864; DOI=10.1038/nature01097;
RA   Gardner M.J., Hall N., Fung E., White O., Berriman M., Hyman R.W.,
RA   Carlton J.M., Pain A., Nelson K.E., Bowman S., Paulsen I.T., James K.D.,
RA   Eisen J.A., Rutherford K.M., Salzberg S.L., Craig A., Kyes S., Chan M.-S.,
RA   Nene V., Shallom S.J., Suh B., Peterson J., Angiuoli S., Pertea M.,
RA   Allen J., Selengut J., Haft D., Mather M.W., Vaidya A.B., Martin D.M.A.,
RA   Fairlamb A.H., Fraunholz M.J., Roos D.S., Ralph S.A., McFadden G.I.,
RA   Cummings L.M., Subramanian G.M., Mungall C., Venter J.C., Carucci D.J.,
RA   Hoffman S.L., Newbold C., Davis R.W., Fraser C.M., Barrell B.G.;
RT   "Genome sequence of the human malaria parasite Plasmodium falciparum.";
RL   Nature 419:498-511(2002).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=3D7;
RX   PubMed=12368867; DOI=10.1038/nature01095;
RA   Hall N., Pain A., Berriman M., Churcher C.M., Harris B., Harris D.,
RA   Mungall K.L., Bowman S., Atkin R., Baker S., Barron A., Brooks K.,
RA   Buckee C.O., Burrows C., Cherevach I., Chillingworth C., Chillingworth T.,
RA   Christodoulou Z., Clark L., Clark R., Corton C., Cronin A., Davies R.M.,
RA   Davis P., Dear P., Dearden F., Doggett J., Feltwell T., Goble A.,
RA   Goodhead I., Gwilliam R., Hamlin N., Hance Z., Harper D., Hauser H.,
RA   Hornsby T., Holroyd S., Horrocks P., Humphray S., Jagels K., James K.D.,
RA   Johnson D., Kerhornou A., Knights A., Konfortov B., Kyes S., Larke N.,
RA   Lawson D., Lennard N., Line A., Maddison M., Mclean J., Mooney P.,
RA   Moule S., Murphy L., Oliver K., Ormond D., Price C., Quail M.A.,
RA   Rabbinowitsch E., Rajandream M.A., Rutter S., Rutherford K.M., Sanders M.,
RA   Simmonds M., Seeger K., Sharp S., Smith R., Squares R., Squares S.,
RA   Stevens K., Taylor K., Tivey A., Unwin L., Whitehead S., Woodward J.R.,
RA   Sulston J.E., Craig A., Newbold C., Barrell B.G.;
RT   "Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.";
RL   Nature 419:527-531(2002).
RN   [3]
RP   FUNCTION, CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION.
RC   STRAIN=3D7;
RX   PubMed=16339145; DOI=10.1074/jbc.m508696200;
RA   Gengenbacher M., Fitzpatrick T.B., Raschle T., Flicker K., Sinning I.,
RA   Muller S., Macheroux P., Tews I., Kappes B.;
RT   "Vitamin B6 biosynthesis by the malaria parasite Plasmodium falciparum:
RT   biochemical and structural insights.";
RL   J. Biol. Chem. 281:3633-3641(2006).
RN   [4]
RP   MUTAGENESIS OF ASP-26; LYS-83; HIS-88; GLU-91; GLU-107; GLU-136; ARG-139;
RP   ARG-140 AND LYS-151, AND SUBUNIT.
RC   STRAIN=3D7;
RX   PubMed=18350152; DOI=10.1371/journal.pone.0001815;
RA   Mueller I.B., Knoeckel J., Groves M.R., Jordanova R., Ealick S.E.,
RA   Walter R.D., Wrenger C.;
RT   "The assembly of the plasmodial PLP synthase complex follows a defined
RT   course.";
RL   PLoS ONE 3:E1815-E1815(2008).
RN   [5]
RP   CATALYTIC ACTIVITY, AND SUBUNIT.
RC   STRAIN=3D7;
RX   PubMed=22244765; DOI=10.1016/j.str.2011.11.015;
RA   Guedez G., Hipp K., Windeisen V., Derrer B., Gengenbacher M., Bottcher B.,
RA   Sinning I., Kappes B., Tews I.;
RT   "Assembly of the eukaryotic PLP-synthase complex from Plasmodium and
RT   activation of the Pdx1 enzyme.";
RL   Structure 20:172-184(2012).
CC   -!- FUNCTION: Catalyzes the formation of pyridoxal 5'-phosphate from ribose
CC       5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The
CC       ammonia is provided by Pdx2. Can also use ribulose 5-phosphate and
CC       dihydroxyacetone phosphate as substrates, resulting from enzyme-
CC       catalyzed isomerization of RBP and G3P, respectively.
CC       {ECO:0000269|PubMed:16339145}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate +
CC         L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-
CC         phosphate; Xref=Rhea:RHEA:31507, ChEBI:CHEBI:15377,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:58273, ChEBI:CHEBI:58359, ChEBI:CHEBI:59776,
CC         ChEBI:CHEBI:597326; EC=4.3.3.6;
CC         Evidence={ECO:0000269|PubMed:16339145, ECO:0000269|PubMed:22244765};
CC   -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC   -!- SUBUNIT: Homohexamer and homododecamer. In the presence of Pdx2, forms
CC       a dodecamer of heterodimers. {ECO:0000269|PubMed:18350152,
CC       ECO:0000269|PubMed:22244765}.
CC   -!- INTERACTION:
CC       C6KT50; C6KT50: pdx1; NbExp=4; IntAct=EBI-975011, EBI-975011;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16339145}.
CC   -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000305}.
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DR   EMBL; AL844505; CAG25026.1; -; Genomic_DNA.
DR   RefSeq; XP_966196.1; XM_961103.1.
DR   AlphaFoldDB; C6KT50; -.
DR   SMR; C6KT50; -.
DR   IntAct; C6KT50; 1.
DR   MINT; C6KT50; -.
DR   STRING; 5833.PFF1025c; -.
DR   DrugBank; DB11638; Artenimol.
DR   SwissPalm; C6KT50; -.
DR   PRIDE; C6KT50; -.
DR   EnsemblProtists; CAG25026; CAG25026; PF3D7_0621200.
DR   GeneID; 3885888; -.
DR   KEGG; pfa:PF3D7_0621200; -.
DR   VEuPathDB; PlasmoDB:PF3D7_0621200; -.
DR   HOGENOM; CLU_055352_1_0_1; -.
DR   InParanoid; C6KT50; -.
DR   OMA; RYANRGW; -.
DR   PhylomeDB; C6KT50; -.
DR   BRENDA; 4.3.3.6; 4889.
DR   UniPathway; UPA00245; -.
DR   Proteomes; UP000001450; Chromosome 6.
DR   GO; GO:0005829; C:cytosol; TAS:GeneDB.
DR   GO; GO:0016843; F:amine-lyase activity; IBA:GO_Central.
DR   GO; GO:0003824; F:catalytic activity; ISS:GeneDB.
DR   GO; GO:0004359; F:glutaminase activity; IDA:GeneDB.
DR   GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR   GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-EC.
DR   GO; GO:0006520; P:cellular amino acid metabolic process; IBA:GO_Central.
DR   GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR   GO; GO:0008615; P:pyridoxine biosynthetic process; ISS:GeneDB.
DR   GO; GO:0000304; P:response to singlet oxygen; IDA:GeneDB.
DR   GO; GO:0042819; P:vitamin B6 biosynthetic process; IDA:GeneDB.
DR   CDD; cd04727; pdxS; 1.
DR   Gene3D; 3.20.20.70; -; 1.
DR   InterPro; IPR013785; Aldolase_TIM.
DR   InterPro; IPR001852; PdxS/SNZ.
DR   InterPro; IPR033755; PdxS/SNZ_N.
DR   InterPro; IPR011060; RibuloseP-bd_barrel.
DR   PANTHER; PTHR31829; PTHR31829; 1.
DR   Pfam; PF01680; SOR_SNZ; 1.
DR   PIRSF; PIRSF029271; Pdx1; 1.
DR   SUPFAM; SSF51366; SSF51366; 1.
DR   PROSITE; PS01235; PDXS_SNZ_1; 1.
DR   PROSITE; PS51129; PDXS_SNZ_2; 1.
PE   1: Evidence at protein level;
KW   Cytoplasm; Lyase; Pyridoxal phosphate; Reference proteome; Schiff base.
FT   CHAIN           1..301
FT                   /note="Pyridoxal 5'-phosphate synthase subunit Pdx1"
FT                   /id="PRO_0000431838"
FT   ACT_SITE        83
FT                   /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT                   /evidence="ECO:0000250|UniProtKB:P0DMS0"
FT   BINDING         26
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:P0DMS0"
FT   BINDING         155
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:P0DMS0"
FT   BINDING         167
FT                   /ligand="D-glyceraldehyde 3-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:59776"
FT                   /evidence="ECO:0000250|UniProtKB:Q03148"
FT   BINDING         216
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:P0DMS0"
FT   BINDING         237..238
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:P0DMS0"
FT   MUTAGEN         26
FT                   /note="D->A: No activity."
FT                   /evidence="ECO:0000269|PubMed:18350152"
FT   MUTAGEN         83
FT                   /note="K->A: No activity."
FT                   /evidence="ECO:0000269|PubMed:18350152"
FT   MUTAGEN         88
FT                   /note="H->A: No activity. No complexes formed."
FT                   /evidence="ECO:0000269|PubMed:18350152"
FT   MUTAGEN         91
FT                   /note="E->A: No activity. No complexes formed."
FT                   /evidence="ECO:0000269|PubMed:18350152"
FT   MUTAGEN         107
FT                   /note="E->A: No effect."
FT                   /evidence="ECO:0000269|PubMed:18350152"
FT   MUTAGEN         136
FT                   /note="E->A: No effect on dodecamer assembly. No activity;
FT                   when associated with A-139 and A-140."
FT                   /evidence="ECO:0000269|PubMed:18350152"
FT   MUTAGEN         139
FT                   /note="R->A: No activity; when associated with A-136 and A-
FT                   140."
FT                   /evidence="ECO:0000269|PubMed:18350152"
FT   MUTAGEN         140
FT                   /note="R->A: No activity; when associated with A-136 and A-
FT                   139."
FT                   /evidence="ECO:0000269|PubMed:18350152"
FT   MUTAGEN         151
FT                   /note="K->A: No activity. The mutant forms hexamers instead
FT                   of dodecamers."
FT                   /evidence="ECO:0000269|PubMed:18350152"
SQ   SEQUENCE   301 AA;  33013 MW;  87A2886A215ED219 CRC64;
     MENHKDDAVL LKHGWCEMLK GGVIMDVKSV EQAKIAEEAG AIGVMVLENI PSELRNKEGV
     ARSVDPSKVE EIKKCVSINV LAKVRIGHFV EAQILEELKI DMIDESEVLT IADEMHHIDK
     HKFKTPFVCG CTNLGEALRR ISEGASMIRT KGEAGTGNII EAIKHIRTVN NEIKYLCSLS
     DSEVYHFAKK INAPIDLVLL TKKLKRLPVV NFAAGGVATP ADAAMCMQLG MDGVFVGSGI
     FESENPRKMA ASIVSAVSNF NNPKILLDVS MNLGKAMCGS TRVSDKWKNK NEEHTKFLTP
     Q
 
 
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