PDXJ_BURP1
ID PDXJ_BURP1 Reviewed; 257 AA.
AC Q3JQ80;
DT 04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 93.
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};
GN OrderedLocusNames=BURPS1710b_2892;
OS Burkholderia pseudomallei (strain 1710b).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; pseudomallei group.
OX NCBI_TaxID=320372;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1710b;
RX PubMed=20333227; DOI=10.1093/gbe/evq003;
RA Losada L., Ronning C.M., DeShazer D., Woods D., Fedorova N., Kim H.S.,
RA Shabalina S.A., Pearson T.R., Brinkac L., Tan P., Nandi T., Crabtree J.,
RA Badger J., Beckstrom-Sternberg S., Saqib M., Schutzer S.E., Keim P.,
RA Nierman W.C.;
RT "Continuing evolution of Burkholderia mallei through genome reduction and
RT large-scale rearrangements.";
RL Genome Biol. Evol. 2:102-116(2010).
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; CP000124; ABA48208.1; -; Genomic_DNA.
DR RefSeq; WP_004524619.1; NC_007434.1.
DR PDB; 3GK0; X-ray; 2.28 A; A/B/C/D/E/F/G/H=1-257.
DR PDBsum; 3GK0; -.
DR AlphaFoldDB; Q3JQ80; -.
DR SMR; Q3JQ80; -.
DR EnsemblBacteria; ABA48208; ABA48208; BURPS1710b_2892.
DR GeneID; 56528758; -.
DR KEGG; bpm:BURPS1710b_2892; -.
DR HOGENOM; CLU_074563_0_0_4; -.
DR OMA; SNAGWDT; -.
DR OrthoDB; 1159993at2; -.
DR UniPathway; UPA00244; UER00313.
DR EvolutionaryTrace; Q3JQ80; -.
DR Proteomes; UP000002700; Chromosome I.
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 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Pyridoxine biosynthesis; Transferase.
FT CHAIN 1..257
FT /note="Pyridoxine 5'-phosphate synthase"
FT /id="PRO_0000231794"
FT ACT_SITE 52
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 79
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 200
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 16
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 18..19
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 27
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
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 59
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 109
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 201
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 222..223
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT SITE 160
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT HELIX 8..10
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 11..16
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 18..27
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 28..30
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 34..43
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 47..52
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 62..71
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 76..80
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 84..93
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 96..100
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 110..114
FT /evidence="ECO:0007829|PDB:3GK0"
FT TURN 116..119
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 120..132
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 136..141
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 145..154
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 157..161
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 164..167
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 172..191
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 195..198
FT /evidence="ECO:0007829|PDB:3GK0"
FT TURN 204..206
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 207..211
FT /evidence="ECO:0007829|PDB:3GK0"
FT STRAND 216..221
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 223..232
FT /evidence="ECO:0007829|PDB:3GK0"
FT HELIX 234..253
FT /evidence="ECO:0007829|PDB:3GK0"
SQ SEQUENCE 257 AA; 27509 MW; A4BD148BDA418247 CRC64;
MSFFLTTPAA IDLGVNIDHV ATLRNARGTA YPDPVRAALA AEDAGADAIT LHLREDRRHI
VDADVRTLRP RVKTRMNLEC AVTPEMLDIA CEIRPHDACL VPEKRSELTT EGGLDVVGHF
DAVRAACKQL ADAGVRVSLF IDPDEAQIRA AHETGAPVIE LHTGRYADAH DAAEQQREFE
RIATGVDAGI ALGLKVNAGH GLHYTNVQAI AALPGIAELN IGHAIVAHAV FVGWDNAVRE
MKAIMVAARV AALHGGR
