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
