PDXS_BIFLS
ID PDXS_BIFLS Reviewed; 291 AA.
AC B7GUB5; E8MM69;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 10-FEB-2009, sequence version 1.
DT 03-AUG-2022, entry version 73.
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};
GN OrderedLocusNames=Blon_1994, BLIJ_2068;
OS Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM
OS 1222 / NCTC 11817 / S12).
OC Bacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae;
OC Bifidobacterium.
OX NCBI_TaxID=391904;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12;
RX PubMed=19033196; DOI=10.1073/pnas.0809584105;
RA Sela D.A., Chapman J., Adeuya A., Kim J.H., Chen F., Whitehead T.R.,
RA Lapidus A., Rokhsar D.S., Lebrilla C.B., German J.B., Price N.P.,
RA Richardson P.M., Mills D.A.;
RT "The genome sequence of Bifidobacterium longum subsp. infantis reveals
RT adaptations for milk utilization within the infant microbiome.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:18964-18969(2008).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12;
RX PubMed=21270894; DOI=10.1038/nature09646;
RA Fukuda S., Toh H., Hase K., Oshima K., Nakanishi Y., Yoshimura K., Tobe T.,
RA Clarke J.M., Topping D.L., Suzuki T., Taylor T.D., Itoh K., Kikuchi J.,
RA Morita H., Hattori M., Ohno H.;
RT "Bifidobacteria can protect from enteropathogenic infection through
RT production of acetate.";
RL Nature 469:543-547(2011).
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; CP001095; ACJ53061.1; -; Genomic_DNA.
DR EMBL; AP010889; BAJ69646.1; -; Genomic_DNA.
DR RefSeq; WP_007053677.1; NZ_JDTT01000005.1.
DR AlphaFoldDB; B7GUB5; -.
DR SMR; B7GUB5; -.
DR PRIDE; B7GUB5; -.
DR EnsemblBacteria; ACJ53061; ACJ53061; Blon_1994.
DR GeneID; 56564167; -.
DR GeneID; 66504717; -.
DR KEGG; bln:Blon_1994; -.
DR KEGG; blon:BLIJ_2068; -.
DR PATRIC; fig|391904.8.peg.2074; -.
DR HOGENOM; CLU_055352_1_0_11; -.
DR OMA; RYANRGW; -.
DR UniPathway; UPA00245; -.
DR Proteomes; UP000001360; Chromosome.
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..291
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT /id="PRO_1000188215"
FT ACT_SITE 80
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 23
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 152
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 164
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 213
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 234..235
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
SQ SEQUENCE 291 AA; 31106 MW; 92FEE6C9A1FAF2E2 CRC64;
MTQNRAELNR NLAQMLKGGV IMDVTTPEQA KIAQDAGACA VMALERIPAD IRAAGGVSRM
SDPAMIKGIQ EAVSIPVMAK VRIGHIAEAR ILQAIEIDYI DESEVLSPAD DVYHIDKNQF
DVPFVCGAKN LGEALRRIAE GAAMIRTKGE PGTGDVIQAV RHMRTMNKQI RELVGLRDDE
VYEAAKQLAV PYDLAKYVHD NGRLPVVNFA AGGVATPADA ALMMELGAEG VFVGSGIFKS
GDPAKRAAAI VKATANWQDA DLLAKLSENL GEAMVGINED EIQTIMAARG E
