PDX11_ORYSJ
ID PDX11_ORYSJ Reviewed; 318 AA.
AC Q69LA6; B7E5L2;
DT 09-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Probable pyridoxal 5'-phosphate synthase subunit PDX1.1;
DE Short=PLP synthase subunit PDX1.1;
DE EC=4.3.3.6;
GN Name=PDX11; OrderedLocusNames=Os07g0100200, LOC_Os07g01020;
GN ORFNames=B1026C12.3, OSJNOa219C16.3;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16623884; DOI=10.1111/j.1365-313x.2006.02684.x;
RA Mizuno H., Wu J., Kanamori H., Fujisawa M., Namiki N., Saji S.,
RA Katagiri S., Katayose Y., Sasaki T., Matsumoto T.;
RT "Sequencing and characterization of telomere and subtelomere regions on
RT rice chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S.";
RL Plant J. 46:206-217(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AP008222; BAE79758.1; -; Genomic_DNA.
DR EMBL; AP005869; BAD31816.1; -; Genomic_DNA.
DR EMBL; AP008213; BAF20583.1; -; Genomic_DNA.
DR EMBL; AP014963; BAS99667.1; -; Genomic_DNA.
DR EMBL; AK060986; BAG87659.1; -; mRNA.
DR EMBL; AK073305; BAG93387.1; -; mRNA.
DR RefSeq; XP_015646521.1; XM_015791035.1.
DR AlphaFoldDB; Q69LA6; -.
DR SMR; Q69LA6; -.
DR STRING; 4530.OS07T0100200-01; -.
DR PaxDb; Q69LA6; -.
DR PRIDE; Q69LA6; -.
DR EnsemblPlants; Os07t0100200-01; Os07t0100200-01; Os07g0100200.
DR GeneID; 4342162; -.
DR Gramene; Os07t0100200-01; Os07t0100200-01; Os07g0100200.
DR KEGG; osa:4342162; -.
DR eggNOG; KOG1606; Eukaryota.
DR HOGENOM; CLU_055352_1_1_1; -.
DR InParanoid; Q69LA6; -.
DR OMA; EEFHINK; -.
DR OrthoDB; 1090029at2759; -.
DR UniPathway; UPA00245; -.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR Genevisible; Q69LA6; OS.
DR GO; GO:0016843; F:amine-lyase activity; IBA:GO_Central.
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; IBA:GO_Central.
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; Reference proteome; Schiff base.
FT CHAIN 1..318
FT /note="Probable pyridoxal 5'-phosphate synthase subunit
FT PDX1.1"
FT /id="PRO_0000270627"
FT ACT_SITE 106
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 49
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 178
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 190
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250|UniProtKB:Q03148"
FT BINDING 239
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 260..261
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
SQ SEQUENCE 318 AA; 33737 MW; FB8E8E6EABD1DBE6 CRC64;
MATDGTGVVT VYGSGTNGAA LLEPSNHKSA TFSVKVGLAQ MLRGGVIMDV VTPEQARIAE
EAGACAVMAL ERVPADIRAQ GGVARMSDPG LIRDIKRAVT IPVMAKARIG HFVEAQILEA
IGVDYVDESE VLTLADDAHH INKHNFRVPF VCGCRDLGEA LRRIREGAAM IRTKGEAGTG
NVVEAVRHVR SVMGDIRALR NMDDDEVFSY AKRIAAPYDL VMQTKQLGRL PVVQFAAGGV
ATPADAALMM QLGCDGVFVG SGIFKSGDPA RRARAIVQAV THYSDPKILA EVSSGLGEAM
VGINLSDPKV ERFAARSE
