PDXJ_BRASO
ID PDXJ_BRASO Reviewed; 256 AA.
AC A4YWD1;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 29-MAY-2007, sequence version 1.
DT 03-AUG-2022, entry version 76.
DE RecName: Full=Pyridoxine 5'-phosphate synthase {ECO:0000255|HAMAP-Rule:MF_00279};
DE Short=PNP synthase {ECO:0000255|HAMAP-Rule:MF_00279};
DE EC=2.6.99.2 {ECO:0000255|HAMAP-Rule:MF_00279};
GN Name=pdxJ {ECO:0000255|HAMAP-Rule:MF_00279}; OrderedLocusNames=BRADO4467;
OS Bradyrhizobium sp. (strain ORS 278).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium; unclassified Bradyrhizobium.
OX NCBI_TaxID=114615;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ORS 278;
RX PubMed=17540897; DOI=10.1126/science.1139548;
RA Giraud E., Moulin L., Vallenet D., Barbe V., Cytryn E., Avarre J.-C.,
RA Jaubert M., Simon D., Cartieaux F., Prin Y., Bena G., Hannibal L.,
RA Fardoux J., Kojadinovic M., Vuillet L., Lajus A., Cruveiller S., Rouy Z.,
RA Mangenot S., Segurens B., Dossat C., Franck W.L., Chang W.-S., Saunders E.,
RA Bruce D., Richardson P., Normand P., Dreyfus B., Pignol D., Stacey G.,
RA Emerich D., Vermeglio A., Medigue C., Sadowsky M.;
RT "Legumes symbioses: absence of nod genes in photosynthetic bradyrhizobia.";
RL Science 316:1307-1312(2007).
CC -!- FUNCTION: Catalyzes the complicated ring closure reaction between the
CC two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-
CC 2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form
CC pyridoxine 5'-phosphate (PNP) and inorganic phosphate.
CC {ECO:0000255|HAMAP-Rule:MF_00279}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
CC = H(+) + 2 H2O + phosphate + pyridoxine 5'-phosphate;
CC Xref=Rhea:RHEA:15265, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57279, ChEBI:CHEBI:57792,
CC ChEBI:CHEBI:58589; EC=2.6.99.2; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00279};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis;
CC pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5.
CC {ECO:0000255|HAMAP-Rule:MF_00279}.
CC -!- SUBUNIT: Homooctamer; tetramer of dimers. {ECO:0000255|HAMAP-
CC Rule:MF_00279}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00279}.
CC -!- SIMILARITY: Belongs to the PNP synthase family. {ECO:0000255|HAMAP-
CC Rule:MF_00279}.
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; CU234118; CAL78207.1; -; Genomic_DNA.
DR RefSeq; WP_011927321.1; NC_009445.1.
DR AlphaFoldDB; A4YWD1; -.
DR SMR; A4YWD1; -.
DR STRING; 114615.BRADO4467; -.
DR EnsemblBacteria; CAL78207; CAL78207; BRADO4467.
DR KEGG; bra:BRADO4467; -.
DR eggNOG; COG0854; Bacteria.
DR HOGENOM; CLU_074563_0_0_5; -.
DR OMA; SNAGWDT; -.
DR OrthoDB; 1159993at2; -.
DR BioCyc; BSP114615:BRADO_RS20815-MON; -.
DR UniPathway; UPA00244; UER00313.
DR Proteomes; UP000001994; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0033856; F:pyridoxine 5'-phosphate synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd00003; PNPsynthase; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00279; PdxJ; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR004569; PyrdxlP_synth_PdxJ.
DR InterPro; IPR036130; Pyridoxine-5'_phos_synth.
DR PANTHER; PTHR30456; PTHR30456; 1.
DR Pfam; PF03740; PdxJ; 1.
DR SUPFAM; SSF63892; SSF63892; 1.
DR TIGRFAMs; TIGR00559; pdxJ; 1.
PE 3: Inferred from homology;
KW Cytoplasm; Pyridoxine biosynthesis; Reference proteome; Transferase.
FT CHAIN 1..256
FT /note="Pyridoxine 5'-phosphate synthase"
FT /id="PRO_1000022363"
FT ACT_SITE 48
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 75
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 199
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 12
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 14..15
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 23
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 50
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 55
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 105
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 200
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 221..222
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT SITE 156
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
SQ SEQUENCE 256 AA; 27615 MW; EAAAF62464865093 CRC64;
MSHPPKLRLG VNVDHIATLR NARGGRAPDP VRAALLAIEA GADGITAHLR EDRRHIRDDD
MARLKAQISR PLNFEMAATE EMVRIALATK PHACCLVPER REELTTEGGL DVVGQHNALA
PAIARLSEAG IRVSLFIAAD PAQIEMAARL RAPVIEIHTG GWCDAITDGH HDKADAEWQR
IVAGARQAYA AGLEVHAGHG LDYATAEQIA ALPEIRELNI GYFIMGEALF VGLAESVRTM
RAAMDRGRDR ATGATA
