ID   PDXS_STAA1              Reviewed;         295 AA.
AC   A7WYT1;
DT   05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT   23-OCT-2007, sequence version 1.
DT   03-AUG-2022, entry version 91.
DE   RecName: Full=Pyridoxal 5'-phosphate synthase subunit PdxS {ECO:0000255|HAMAP-Rule:MF_01824};
DE            Short=PLP synthase subunit PdxS {ECO:0000255|HAMAP-Rule:MF_01824};
DE            EC=4.3.3.6 {ECO:0000255|HAMAP-Rule:MF_01824};
DE   AltName: Full=Pdx1 {ECO:0000255|HAMAP-Rule:MF_01824};
GN   Name=pdxS {ECO:0000255|HAMAP-Rule:MF_01824}; OrderedLocusNames=SAHV_0516;
OS   Staphylococcus aureus (strain Mu3 / ATCC 700698).
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC   Staphylococcus.
OX   NCBI_TaxID=418127;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Mu3 / ATCC 700698;
RX   PubMed=17954695; DOI=10.1128/aac.00534-07;
RA   Neoh H.-M., Cui L., Yuzawa H., Takeuchi F., Matsuo M., Hiramatsu K.;
RT   "Mutated response regulator graR is responsible for phenotypic conversion
RT   of Staphylococcus aureus from heterogeneous vancomycin-intermediate
RT   resistance to vancomycin-intermediate resistance.";
RL   Antimicrob. Agents Chemother. 52:45-53(2008).
CC   -!- FUNCTION: Catalyzes the formation of pyridoxal 5'-phosphate from ribose
CC       5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The
CC       ammonia is provided by the PdxT subunit. Can also use ribulose 5-
CC       phosphate and dihydroxyacetone phosphate as substrates, resulting from
CC       enzyme-catalyzed isomerization of RBP and G3P, respectively.
CC       {ECO:0000255|HAMAP-Rule:MF_01824}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate +
CC         L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-
CC         phosphate; Xref=Rhea:RHEA:31507, ChEBI:CHEBI:15377,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:58273, ChEBI:CHEBI:58359, ChEBI:CHEBI:59776,
CC         ChEBI:CHEBI:597326; EC=4.3.3.6; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_01824};
CC   -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC       {ECO:0000255|HAMAP-Rule:MF_01824}.
CC   -!- SUBUNIT: In the presence of PdxT, forms a dodecamer of heterodimers.
CC       {ECO:0000255|HAMAP-Rule:MF_01824}.
CC   -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000255|HAMAP-
CC       Rule:MF_01824}.
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DR   EMBL; AP009324; BAF77399.1; -; Genomic_DNA.
DR   RefSeq; WP_000034728.1; NZ_CTYB01000013.1.
DR   AlphaFoldDB; A7WYT1; -.
DR   SMR; A7WYT1; -.
DR   GeneID; 66838811; -.
DR   KEGG; saw:SAHV_0516; -.
DR   HOGENOM; CLU_055352_1_0_9; -.
DR   OMA; RYANRGW; -.
DR   UniPathway; UPA00245; -.
DR   GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IEA:UniProtKB-UniRule.
DR   CDD; cd04727; pdxS; 1.
DR   Gene3D; 3.20.20.70; -; 1.
DR   HAMAP; MF_01824; PdxS; 1.
DR   InterPro; IPR013785; Aldolase_TIM.
DR   InterPro; IPR001852; PdxS/SNZ.
DR   InterPro; IPR033755; PdxS/SNZ_N.
DR   InterPro; IPR011060; RibuloseP-bd_barrel.
DR   PANTHER; PTHR31829; PTHR31829; 1.
DR   Pfam; PF01680; SOR_SNZ; 1.
DR   PIRSF; PIRSF029271; Pdx1; 1.
DR   SUPFAM; SSF51366; SSF51366; 1.
DR   TIGRFAMs; TIGR00343; TIGR00343; 1.
DR   PROSITE; PS01235; PDXS_SNZ_1; 1.
DR   PROSITE; PS51129; PDXS_SNZ_2; 1.
PE   3: Inferred from homology;
KW   Lyase; Pyridoxal phosphate; Schiff base.
FT   CHAIN           1..295
FT                   /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT                   /id="PRO_1000070395"
FT   ACT_SITE        82
FT                   /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT   BINDING         25
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT   BINDING         154
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT   BINDING         166
FT                   /ligand="D-glyceraldehyde 3-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:59776"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT   BINDING         215
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT   BINDING         236..237
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
SQ   SEQUENCE   295 AA;  31993 MW;  0C8F0F2BF432A531 CRC64;
     MSKIIGSDRV KRGMAEMQKG GVIMDVVNAE QARIAEEAGA VAVMALERVP SDIRAAGGVA
     RMANPKIVEE VMNAVSIPVM AKARIGHITE ARVLEAMGVD YIDESEVLTP ADEEYHLRKD
     QFTVPFVCGC RNLGEAARRI GEGAAMLRTK GEPGTGNIVE AVRHMRQVNS EVSRLTVMND
     DEIMTFAKDI GAPYEILKQI KDNGRLPVVN FAAGGVATPQ DAALMMELGA DGVFVGSGIF
     KSEDPEKFAK AIVQATTHYQ DYELIGRLAS ELGTAMKGLD INQLSLEERM QERGW