ID   PDX1_GINBI              Reviewed;         309 AA.
AC   Q9AT63;
DT   15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2001, sequence version 1.
DT   03-AUG-2022, entry version 67.
DE   RecName: Full=Probable pyridoxal 5'-phosphate synthase subunit PDX1;
DE            Short=PLP synthase subunit PDX1;
DE            EC=4.3.3.6;
DE   AltName: Full=Sor-like protein;
GN   Name=PDX1;
OS   Ginkgo biloba (Ginkgo) (Maidenhair tree).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Ginkgoidae; Ginkgoales; Ginkgoaceae; Ginkgo.
OX   NCBI_TaxID=3311;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RA   Genau A., Drewke C., Leistner E.;
RT   "Cloning and sequencing of a sor-like sequence very likely involved in
RT   vitamin B6 biosynthesis in Ginkgo biloba L.";
RL   Submitted (FEB-2001) to the EMBL/GenBank/DDBJ databases.
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. Also plays an
CC       indirect role in resistance to singlet oxygen-generating
CC       photosensitizers. {ECO:0000250|UniProtKB:O80448}.
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:0000250|UniProtKB:Q03148};
CC   -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC   -!- MISCELLANEOUS: Vitamin B6 is an essential quencher of singlet oxygen in
CC       plants, that can protect cellular membranes from lipid peroxidation.
CC   -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000305}.
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DR   EMBL; AF344827; AAK18310.1; -; mRNA.
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   HAMAP; MF_01824; PdxS; 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   TIGRFAMs; TIGR00343; TIGR00343; 1.
DR   PROSITE; PS01235; PDXS_SNZ_1; 1.
DR   PROSITE; PS51129; PDXS_SNZ_2; 1.
PE   2: Evidence at transcript level;
KW   Lyase; Pyridoxal phosphate; Schiff base.
FT   CHAIN           1..309
FT                   /note="Probable pyridoxal 5'-phosphate synthase subunit
FT                   PDX1"
FT                   /id="PRO_0000109370"
FT   ACT_SITE        97
FT                   /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
FT   BINDING         40
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
FT   BINDING         169
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
FT   BINDING         181
FT                   /ligand="D-glyceraldehyde 3-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:59776"
FT                   /evidence="ECO:0000250|UniProtKB:Q03148"
FT   BINDING         230
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
FT   BINDING         251..252
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
SQ   SEQUENCE   309 AA;  32945 MW;  F4E3FD6698D1D235 CRC64;
     MASDGVVTVY GDGAITDTKV SSYAVKVGLA QMLRGGVIMD VVNAEQARIA EEAGATAVMA
     LERVPADIRA QGGVARMSDP GLIKEIKSAV TIPVMAKARI GHFVEAQILE AIGIDYIDES
     EVLTPADDXH HINKHNFRIP FVCGCRNLGE ALRRIAEGAA MIRTKGEAGT GNVIEAVRHV
     RSVLGDIRKL QSLDDDEVFA FAKQIAAPYE LVRQTKQLGR LPVVNFAAGG VATPADAALM
     MQLGCDGVFV GSGVFKSGDP ARRARAIVQA VTHYNDPHIL AEVSCSLGEA MVGINLKDEK
     VERYAERSE