PDXJ_NAUPA
ID PDXJ_NAUPA Reviewed; 259 AA.
AC B9LAE4;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 24-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 84.
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=NAMH_1208;
OS Nautilia profundicola (strain ATCC BAA-1463 / DSM 18972 / AmH).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Nautiliales; Nautiliaceae;
OC Nautilia.
OX NCBI_TaxID=598659;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1463 / DSM 18972 / AmH;
RX PubMed=19197347; DOI=10.1371/journal.pgen.1000362;
RA Campbell B.J., Smith J.L., Hanson T.E., Klotz M.G., Stein L.Y., Lee C.K.,
RA Wu D., Robinson J.M., Khouri H.M., Eisen J.A., Cary S.C.;
RT "Adaptations to submarine hydrothermal environments exemplified by the
RT genome of Nautilia profundicola.";
RL PLoS Genet. 5:E1000362-E1000362(2009).
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; CP001279; ACM92474.1; -; Genomic_DNA.
DR RefSeq; WP_012663845.1; NC_012115.1.
DR AlphaFoldDB; B9LAE4; -.
DR SMR; B9LAE4; -.
DR STRING; 598659.NAMH_1208; -.
DR EnsemblBacteria; ACM92474; ACM92474; NAMH_1208.
DR KEGG; nam:NAMH_1208; -.
DR eggNOG; COG0854; Bacteria.
DR HOGENOM; CLU_074563_0_0_7; -.
DR OMA; SNAGWDT; -.
DR OrthoDB; 1159993at2; -.
DR UniPathway; UPA00244; UER00313.
DR Proteomes; UP000000448; 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..259
FT /note="Pyridoxine 5'-phosphate synthase"
FT /id="PRO_1000132550"
FT ACT_SITE 42
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 69
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 212
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 6
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 8..9
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 17
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 44
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
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 99
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 213
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 234..235
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT SITE 150
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
SQ SEQUENCE 259 AA; 28994 MW; 739D6828B680AD9F CRC64;
MKLGVNIDHI ATIRNARQIN EPDPLMALQI LKEAGADQVT IHLREDRRHI TDFDAGRICQ
NSFLPVNMEC SINPEIIDII CSLKPHRATL VPEKREEVTT EGGLDIIKFE KEIKNAIEKL
HNNDIEVSLF IDPDFEQITK SAEVGAEMIE LHTGKYANLH LALNTNINST PFKVFENMDR
KTLKKELELE LKLLKDATIL GNELGLEVAA GHGLNYQNVK PVADIEGIVE LNIGHSIIAN
SVFLGLKQAI IQMRELING
