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Database: UniProt
Entry: M5DN45_9GAMM
LinkDB: M5DN45_9GAMM
Original site: M5DN45_9GAMM 
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}.
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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
//
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