PDX1_PLABE
ID PDX1_PLABE Reviewed; 297 AA.
AC P0DMS0;
DT 04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT 04-FEB-2015, sequence version 1.
DT 03-AUG-2022, entry version 24.
DE RecName: Full=Pyridoxal 5'-phosphate synthase subunit Pdx1;
DE Short=PLP synthase subunit Pdx1;
DE EC=4.3.3.6 {ECO:0000269|PubMed:22244765};
GN Name=pdx1 {ECO:0000303|PubMed:22244765};
OS Plasmodium berghei.
OC Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
OC Plasmodiidae; Plasmodium; Plasmodium (Vinckeia).
OX NCBI_TaxID=5821;
RN [1]
RP X-RAY CRYSTALLOGRAPHY (2.42 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP D-RIBOSE 5-PHOSPHATE OR SUBUNIT PDX1 FROM P.FALCIPARUM, FUNCTION, CATALYTIC
RP ACTIVITY, SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF MET-19; MET-46; LEU-82;
RP MET-103 AND MET-148.
RC STRAIN=NK65;
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:22244765}.
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: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:22244765}.
CC -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000305}.
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DR PDB; 4ADS; X-ray; 3.61 A; A/B/C/D/E/F=3-282.
DR PDB; 4ADT; X-ray; 2.42 A; A/B=1-297.
DR PDB; 4ADU; X-ray; 2.44 A; A/B=1-297.
DR PDBsum; 4ADS; -.
DR PDBsum; 4ADT; -.
DR PDBsum; 4ADU; -.
DR AlphaFoldDB; P0DMS0; -.
DR SMR; P0DMS0; -.
DR VEuPathDB; PlasmoDB:PBANKA_1120200; -.
DR OMA; RYANRGW; -.
DR UniPathway; UPA00245; -.
DR GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-EC.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IEA:UniProtKB-UniPathway.
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 3D-structure; Lyase; Pyridoxal phosphate; Schiff base.
FT CHAIN 1..297
FT /note="Pyridoxal 5'-phosphate synthase subunit Pdx1"
FT /id="PRO_0000431837"
FT ACT_SITE 84
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000269|PubMed:22244765"
FT BINDING 27
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000269|PubMed:22244765"
FT BINDING 156
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000269|PubMed:22244765"
FT BINDING 168
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250|UniProtKB:Q03148"
FT BINDING 217
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000269|PubMed:22244765"
FT BINDING 238..239
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000269|PubMed:22244765"
FT MUTAGEN 19
FT /note="M->V: 2-fold reduction in glutaminase activity. No
FT effect on overall pyridoxal 5'-phosphate synthase
FT activity."
FT /evidence="ECO:0000269|PubMed:22244765"
FT MUTAGEN 46
FT /note="M->I: 2-fold increase in glutaminase and in overall
FT pyridoxal 5'-phosphate synthase activity."
FT /evidence="ECO:0000269|PubMed:22244765"
FT MUTAGEN 82
FT /note="L->A: No effect on glutaminase activity. 4-fold
FT reduction in overall pyridoxal 5'-phosphate synthase
FT activity."
FT /evidence="ECO:0000269|PubMed:22244765"
FT MUTAGEN 103
FT /note="M->A: No effect on glutaminase activity. 5-fold
FT reduction in overall pyridoxal 5'-phosphate synthase
FT activity."
FT /evidence="ECO:0000269|PubMed:22244765"
FT MUTAGEN 103
FT /note="M->F: No effect on glutaminase activity. Total loss
FT of overall pyridoxal 5'-phosphate synthase activity."
FT /evidence="ECO:0000269|PubMed:22244765"
FT MUTAGEN 148
FT /note="M->L: No effect on glutaminase activity. Changes the
FT affinity of the complex for ammonia."
FT /evidence="ECO:0000269|PubMed:22244765"
SQ SEQUENCE 297 AA; 32689 MW; B7DBDBC4DCC6277E CRC64;
MRDYADNDSI LLKHGWCEML KGGVIMDVKN VEQAKIAEKA GAIGVMILEN IPSELRNTDG
VARSVDPLKI EEIRKCISIN VLAKVRIGHF VEAQILEELK VDMLDESEVL TMADEYNHIN
KHKFKTPFVC GCTNLGEALR RISEGASMIR TKGEAGTGNI IEAIKHIRTV NNEIKYLCSL
DESEVYNFAK KLRAPIDLIL LTRKLKRLPV VNFAAGGIAT PADAAMCMQL GMDGVFVGSG
IFESENPQKM ASSIVMAVSN FNNPKILLNV SLGLGKAMHG NTKVSNKWKN KSEEDNS
