ID A0A0Q5P9L9_9SPHN Unreviewed; 243 AA.
AC A0A0Q5P9L9;
DT 20-JAN-2016, integrated into UniProtKB/TrEMBL.
DT 20-JAN-2016, sequence version 1.
DT 24-JAN-2024, entry version 29.
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=ASG07_06850 {ECO:0000313|EMBL:KQR83442.1};
OS Sphingomonas sp. Leaf343.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingomonas.
OX NCBI_TaxID=1736345 {ECO:0000313|EMBL:KQR83442.1, ECO:0000313|Proteomes:UP000051323};
RN [1] {ECO:0000313|EMBL:KQR83442.1, ECO:0000313|Proteomes:UP000051323}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Leaf343 {ECO:0000313|EMBL:KQR83442.1,
RC ECO:0000313|Proteomes:UP000051323};
RA Gilbert D.G.;
RL Submitted (OCT-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:KQR83442.1, ECO:0000313|Proteomes:UP000051323}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Leaf343 {ECO:0000313|EMBL:KQR83442.1,
RC ECO:0000313|Proteomes:UP000051323};
RA Schulze-Lefert P.;
RT "Functional overlap of the Arabidopsis leaf and root microbiotas.";
RL Submitted (NOV-2015) to the EMBL/GenBank/DDBJ databases.
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 -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KQR83442.1}.
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DR EMBL; LMPG01000011; KQR83442.1; -; Genomic_DNA.
DR RefSeq; WP_055844097.1; NZ_LMPG01000011.1.
DR AlphaFoldDB; A0A0Q5P9L9; -.
DR STRING; 1736345.ASG07_06850; -.
DR OrthoDB; 9806590at2; -.
DR UniPathway; UPA00244; UER00313.
DR Proteomes; UP000051323; Unassembled WGS sequence.
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:UP000051323};
KW Transferase {ECO:0000256|HAMAP-Rule:MF_00279}.
FT ACT_SITE 46
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT ACT_SITE 73
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT ACT_SITE 193
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 10
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 12..13
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 21
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 48
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 53
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 103
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 194
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT BINDING 215..216
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
FT SITE 154
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00279"
SQ SEQUENCE 243 AA; 26120 MW; 80D4A068E7D69A6E CRC64;
MTGILRLGVN IDHVATVRNA RGAGYPDPVR AALLAADAGA DGITAHLRED RRHITDDDIA
RLAAELTIPL NLEMAATDEM LAIALRHRPH AACIVPEKRE ERTTEGGLDA AGQHNHLQHL
VSELNGANIR VSLFIEPDAR QIEAAIRLGA PVVELHTGRY AELDGEARTE EVRRLSDAAA
LAAKNGIEVH AGHGLTFDNV GPIAAIPQVR ELNIGHFLVG EALFVGLDEA VRRMRDAMDA
ARG
//
