PDXJ_BRADU
ID PDXJ_BRADU Reviewed; 250 AA.
AC O69158;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 28-FEB-2003, sequence version 3.
DT 03-AUG-2022, entry version 119.
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=bll5064;
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium.
OX NCBI_TaxID=224911;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=USDA 110spc4;
RA Mueller P., Stingel D.;
RT "Extended DNA sequencing in the upstream region of sipF in Bradyrhizobium
RT japonicum.";
RL Submitted (JAN-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 67-250.
RC STRAIN=USDA 110spc4;
RX PubMed=9870699; DOI=10.1007/pl00008631;
RA Bairl A., Mueller P.;
RT "A second gene for type I signal peptidase in Bradyrhizobium japonicum,
RT sipF, is located near genes involved in RNA processing and cell division.";
RL Mol. Gen. Genet. 260:346-356(1998).
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}.
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DR EMBL; AF065159; AAD02936.2; -; Genomic_DNA.
DR EMBL; BA000040; BAC50329.1; -; Genomic_DNA.
DR RefSeq; NP_771704.1; NC_004463.1.
DR RefSeq; WP_011087825.1; NZ_CP011360.1.
DR AlphaFoldDB; O69158; -.
DR SMR; O69158; -.
DR STRING; 224911.27353329; -.
DR EnsemblBacteria; BAC50329; BAC50329; BAC50329.
DR GeneID; 64024828; -.
DR KEGG; bja:bll5064; -.
DR PATRIC; fig|224911.44.peg.4932; -.
DR eggNOG; COG0854; Bacteria.
DR HOGENOM; CLU_074563_0_0_5; -.
DR InParanoid; O69158; -.
DR OMA; SNAGWDT; -.
DR PhylomeDB; O69158; -.
DR UniPathway; UPA00244; UER00313.
DR Proteomes; UP000002526; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0033856; F:pyridoxine 5'-phosphate synthase activity; IBA:GO_Central.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IBA:GO_Central.
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..250
FT /note="Pyridoxine 5'-phosphate synthase"
FT /id="PRO_0000190108"
FT ACT_SITE 47
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 74
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 198
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 11
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 13..14
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 22
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 49
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 54
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 104
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 199
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 220..221
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT SITE 155
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT CONFLICT 185..186
FT /note="KL -> NV (in Ref. 1 and 3)"
FT /evidence="ECO:0000305"
FT CONFLICT 238..240
FT /note="SMR -> NA (in Ref. 1 and 3)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 250 AA; 27033 MW; 47DBD839C0FA59CC CRC64;
MPASPLRLGV NVDHVATLRN ARGGRNPDPV RAALLAIEAG ADGITAHLRE DRRHIRDEDM
ARLKAEISKP LNFEMAATDD MMRISLATRP HAVCLVPERR QEVTTEGGLD VVGQHNALAP
YIARLNDAGI RVSLFIAADP AQIEMAARLR APVIEIHTGA WCDAVVDGHT EKADAEWKRI
VAGAKLAKDA GLEVHAGHGL DYATAETIAA LPDIMELNIG YYMIGEALFV GLAETVRSMR
AAMDRGRSRA
