PDXJ_YERPE
ID PDXJ_YERPE Reviewed; 243 AA.
AC Q8ZCP4; Q0WCX8;
DT 05-MAR-2002, integrated into UniProtKB/Swiss-Prot.
DT 05-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 134.
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=YPO2930, y1300, YP_2525;
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CO-92 / Biovar Orientalis;
RX PubMed=11586360; DOI=10.1038/35097083;
RA Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA Stevens K., Whitehead S., Barrell B.G.;
RT "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL Nature 413:523-527(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(2004).
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; AL590842; CAL21538.1; -; Genomic_DNA.
DR EMBL; AE009952; AAM84874.1; -; Genomic_DNA.
DR EMBL; AE017042; AAS62723.1; -; Genomic_DNA.
DR PIR; AG0356; AG0356.
DR RefSeq; WP_002211569.1; NZ_WUCM01000006.1.
DR RefSeq; YP_002347860.1; NC_003143.1.
DR PDB; 3F4N; X-ray; 2.40 A; A/B/C/D/E/F/G/H=1-243.
DR PDBsum; 3F4N; -.
DR AlphaFoldDB; Q8ZCP4; -.
DR SMR; Q8ZCP4; -.
DR IntAct; Q8ZCP4; 1.
DR STRING; 214092.YPO2930; -.
DR PaxDb; Q8ZCP4; -.
DR DNASU; 1146247; -.
DR EnsemblBacteria; AAM84874; AAM84874; y1300.
DR EnsemblBacteria; AAS62723; AAS62723; YP_2525.
DR GeneID; 57975884; -.
DR KEGG; ype:YPO2930; -.
DR KEGG; ypk:y1300; -.
DR KEGG; ypm:YP_2525; -.
DR PATRIC; fig|214092.21.peg.3381; -.
DR eggNOG; COG0854; Bacteria.
DR HOGENOM; CLU_074563_0_0_6; -.
DR OMA; SNAGWDT; -.
DR UniPathway; UPA00244; UER00313.
DR EvolutionaryTrace; Q8ZCP4; -.
DR Proteomes; UP000000815; Chromosome.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0033856; F:pyridoxine 5'-phosphate synthase activity; IBA:GO_Central.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IBA:GO_Central.
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; Reference proteome;
KW Transferase.
FT CHAIN 1..243
FT /note="Pyridoxine 5'-phosphate synthase"
FT /id="PRO_0000190144"
FT ACT_SITE 45
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 72
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT ACT_SITE 193
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 9
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 11..12
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 20
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 47
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 52
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 102
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 194
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT BINDING 215..216
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT SITE 153
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00279"
FT STRAND 5..9
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 11..18
FT /evidence="ECO:0007829|PDB:3F4N"
FT TURN 19..21
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 27..36
FT /evidence="ECO:0007829|PDB:3F4N"
FT STRAND 40..45
FT /evidence="ECO:0007829|PDB:3F4N"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 55..64
FT /evidence="ECO:0007829|PDB:3F4N"
FT STRAND 69..75
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 77..86
FT /evidence="ECO:0007829|PDB:3F4N"
FT STRAND 89..94
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 98..100
FT /evidence="ECO:0007829|PDB:3F4N"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 110..112
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 113..124
FT /evidence="ECO:0007829|PDB:3F4N"
FT TURN 125..127
FT /evidence="ECO:0007829|PDB:3F4N"
FT STRAND 129..134
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 138..146
FT /evidence="ECO:0007829|PDB:3F4N"
FT STRAND 150..155
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 157..161
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 165..184
FT /evidence="ECO:0007829|PDB:3F4N"
FT STRAND 188..194
FT /evidence="ECO:0007829|PDB:3F4N"
FT TURN 197..199
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 200..205
FT /evidence="ECO:0007829|PDB:3F4N"
FT STRAND 209..214
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 216..225
FT /evidence="ECO:0007829|PDB:3F4N"
FT HELIX 227..241
FT /evidence="ECO:0007829|PDB:3F4N"
SQ SEQUENCE 243 AA; 26297 MW; 0C369688908E0758 CRC64;
MADLLLGVNI DHIATLRNAR GTIYPDPVQA AFIAEQAGAD GITVHLREDR RHITDRDVRI
LRQTIQTRMN LEMAVTDEMV DIACDIKPHF CCLVPEKRQE VTTEGGLDVA GQVDKMTLAV
GRLADVGILV SLFIDADFRQ IDAAVAAGAP YIEIHTGAYA DASTVLERQA ELMRIAKAAT
YAAGKGLKVN AGHGLTYHNV QPIAALPEMH ELNIGHAIIG QAVMTGLAAA VTDMKVLMRE
ARR
