PDXS_DESHD
ID PDXS_DESHD Reviewed; 291 AA.
AC B8FZR3;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 03-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 72.
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=Dhaf_1077;
OS Desulfitobacterium hafniense (strain DSM 10664 / DCB-2).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Desulfitobacteriaceae;
OC Desulfitobacterium.
OX NCBI_TaxID=272564;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 10664 / DCB-2;
RX PubMed=22316246; DOI=10.1186/1471-2180-12-21;
RA Kim S.H., Harzman C., Davis J.K., Hutcheson R., Broderick J.B., Marsh T.L.,
RA Tiedje J.M.;
RT "Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive
RT anaerobe capable of dehalogenation and metal reduction.";
RL BMC Microbiol. 12:21-21(2012).
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; CP001336; ACL19137.1; -; Genomic_DNA.
DR RefSeq; WP_005813582.1; NC_011830.1.
DR AlphaFoldDB; B8FZR3; -.
DR SMR; B8FZR3; -.
DR EnsemblBacteria; ACL19137; ACL19137; Dhaf_1077.
DR KEGG; dhd:Dhaf_1077; -.
DR HOGENOM; CLU_055352_1_0_9; -.
DR OMA; RYANRGW; -.
DR UniPathway; UPA00245; -.
DR Proteomes; UP000007726; 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; 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_1000188222"
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; 31835 MW; B3F5E2387FC2B37E CRC64;
MDRKRYELNK ELAQMLKGGV IMDVTTPEQA KIAEAAGACA VMALERIPAD IRAVGGVSRM
SDPKMIKGIM EAVSIPVMAK CRIGHFVEAQ ILEAVEIDYI DESEVLSPAD DVYHIDKTRF
KVPFVCGAKD LGEALRRINE GAAMIRTKGE PGTGDIVQAV RHMRMINRQI SRLAGMREDE
LFQEAKELQV PYDLVLYVHE HKRLPVVNFA AGGVATPGDA ALMMQLGAEG VFVGSGIFKS
GDPEKRAQAI VKAVTNYQDP KVLAELSEDL GEAMVGINEQ EIELLMAERG K