PDX1_PHAVU
ID PDX1_PHAVU Reviewed; 312 AA.
AC Q9FT25;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=Pyridoxal 5'-phosphate synthase subunit PDX1;
DE Short=PLP synthase subunit PDX1;
DE EC=4.3.3.6;
DE AltName: Full=pvPDX1;
GN Name=PDX1;
OS Phaseolus vulgaris (Kidney bean) (French bean).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Phaseolus.
OX NCBI_TaxID=3885;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Taylor's horticultural;
RA Pidgeon C.M., Reid D.M.;
RT "Characterization of a novel gene (pvPDX1) that is regulated by ethylene,
RT methyl jasmonate and light.";
RL Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], AND INDUCTION.
RC STRAIN=cv. Taylor's horticultural;
RX PubMed=15086812; DOI=10.1111/j.0031-9317.2004.00283.x;
RA Graham C.M., Ehrenshaft M., Hausner G., Reid D.M.;
RT "A highly conserved gene for vitamin B biosynthesis may have consequences
RT for stress and hormone responses in plants.";
RL Physiol. Plantarum 121:8-14(2004).
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 -!- INDUCTION: By wounding, gibberelic acid and 1-aminocyclopropane-1-
CC carboxylic acid (ACC), but not after treatment with methyl jasmonate or
CC active oxygen species. {ECO:0000269|PubMed:15086812}.
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; AY007525; AAG17942.1; -; mRNA.
DR RefSeq; XP_007147987.1; XM_007147925.1.
DR AlphaFoldDB; Q9FT25; -.
DR SMR; Q9FT25; -.
DR STRING; 3885.XP_007147987.1; -.
DR EnsemblPlants; ESW19981; ESW19981; PHAVU_006G171100g.
DR GeneID; 18629076; -.
DR Gramene; ESW19981; ESW19981; PHAVU_006G171100g.
DR KEGG; pvu:PHAVU_006G171100g; -.
DR eggNOG; KOG1606; Eukaryota.
DR OMA; RYANRGW; -.
DR OrthoDB; 1090029at2759; -.
DR PhylomeDB; Q9FT25; -.
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..312
FT /note="Pyridoxal 5'-phosphate synthase subunit PDX1"
FT /id="PRO_0000109372"
FT ACT_SITE 100
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 43
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 172
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 184
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250|UniProtKB:Q03148"
FT BINDING 233
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 254..255
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
SQ SEQUENCE 312 AA; 33405 MW; EF614F045AB959C2 CRC64;
MEGEGSRVVA LYDGNGAITE TKKSPFSVKV GLAQMLRGGV IMDVVNADQA RIAEEAGACA
VMALERVPAD IRAQGGVARM SDPQLIKEIK RAVTIPVMAK ARIGHFVEAQ ILEAIGIDYV
DESEVLTLAD DANHINKHNF RIPFVCGCRN LGEALRRIRE GAAMIRTKGE AGTGNIIEAV
RHVRSVMSDI RVLRNMDDDE VFTFAKSIAA PYDLVMQTKQ LGRLPVVHFA AGGVATPADA
ALMMQLGCDG VFVGSGVFKS GDPAKRARAI VQAVTHYSDP EILAEVSCGL GEAMVGINLS
DTNVERFANR SE
