ID M5DN45_9GAMM Unreviewed; 245 AA.
AC M5DN45;
DT 29-MAY-2013, integrated into UniProtKB/TrEMBL.
DT 29-MAY-2013, sequence version 1.
DT 24-JAN-2024, entry version 45.
DE RecName: Full=Pyridoxine 5'-phosphate synthase {ECO:0000256|HAMAP-Rule:MF_00279};
DE Short=PNP synthase {ECO:0000256|HAMAP-Rule:MF_00279};
DE EC=2.6.99.2 {ECO:0000256|HAMAP-Rule:MF_00279};
GN Name=pdxJ {ECO:0000256|HAMAP-Rule:MF_00279};
GN ORFNames=TOL_0924 {ECO:0000313|EMBL:CCU71360.1};
OS Thalassolituus oleivorans MIL-1.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales;
OC Oceanospirillaceae; Thalassolituus.
OX NCBI_TaxID=1298593 {ECO:0000313|EMBL:CCU71360.1, ECO:0000313|Proteomes:UP000011866};
RN [1] {ECO:0000313|EMBL:CCU71360.1, ECO:0000313|Proteomes:UP000011866}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MIL-1 {ECO:0000313|EMBL:CCU71360.1,
RC ECO:0000313|Proteomes:UP000011866};
RX PubMed=23599290; DOI=10.1128/genomeA.00141-13;
RA Golyshin P.N., Werner J., Chernikova T.N., Tran H., Ferrer M.,
RA Yakimov M.M., Teeling H., Golyshina O.V.;
RT "Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T).";
RL Genome Announc. 1:1-3(2013).
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:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_00279}.
CC -!- SUBUNIT: Homooctamer; tetramer of dimers. {ECO:0000256|HAMAP-
CC Rule:MF_00279}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00279}.
CC -!- SIMILARITY: Belongs to the PNP synthase family. {ECO:0000256|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; HF680312; CCU71360.1; -; Genomic_DNA.
DR RefSeq; WP_015486097.1; NC_020888.1.
DR AlphaFoldDB; M5DN45; -.
DR STRING; 187493.CN03_13570; -.
DR KEGG; tol:TOL_0924; -.
DR PATRIC; fig|1298593.3.peg.892; -.
DR eggNOG; COG0854; Bacteria.
DR HOGENOM; CLU_074563_0_0_6; -.
DR UniPathway; UPA00244; UER00313.
DR Proteomes; UP000011866; 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; Aldolase class I; 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 NCBIfam; TIGR00559; pdxJ; 1.
DR PANTHER; PTHR30456; PYRIDOXINE 5'-PHOSPHATE SYNTHASE; 1.
DR PANTHER; PTHR30456:SF0; PYRIDOXINE 5'-PHOSPHATE SYNTHASE; 1.
DR Pfam; PF03740; PdxJ; 1.
DR SUPFAM; SSF63892; Pyridoxine 5'-phosphate synthase; 1.
PE 3: Inferred from homology;
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00279};
KW Pyridoxine biosynthesis {ECO:0000256|ARBA:ARBA00023096, ECO:0000256|HAMAP-
KW Rule:MF_00279}; Reference proteome {ECO:0000313|Proteomes:UP000011866};
KW Transferase {ECO:0000256|HAMAP-Rule:MF_00279}.
FT ACT_SITE 48
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT ACT_SITE 75
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT ACT_SITE 196
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 12
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000256|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:0000256|HAMAP-Rule:MF_00279"
FT BINDING 23
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 50
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 55
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 105
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 197
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 218..219
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT SITE 156
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
SQ SEQUENCE 245 AA; 26305 MW; 929488A995051240 CRC64;
MSLAKRVLLG VNIDHVATLR QARGTRYPDP VQAAFVAEEA GADGITVHPR EDGRHIQVRD
VRILRDTLAT RMNLEMAVTE KMLQLAEEVC PPCTCLVPEK REELTTEGGL DVAGQEAHIT
AAVARLKAIG SEVSLFIDPD EAQIDATVRT GAPVIELHTG RYADAETNEE RDEELARIIA
AAKYAAGKGL IVNAGHGLNY HNVEAIAAIP EMNELNIGHA IVARAVFVGL AQAVADMRAL
LAAAR
//