PDXS_META3
ID PDXS_META3 Reviewed; 299 AA.
AC A6UWM0;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 21-AUG-2007, sequence version 1.
DT 03-AUG-2022, entry version 81.
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=Maeo_1316;
OS Methanococcus aeolicus (strain ATCC BAA-1280 / DSM 17508 / OCM 812 /
OS Nankai-3).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanococcaceae; Methanococcus.
OX NCBI_TaxID=419665;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1280 / DSM 17508 / OCM 812 / Nankai-3;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A.,
RA Sieprawska-Lupa M., Whitman W.B., Richardson P.;
RT "Complete sequence of Methanococcus aeolicus Nankai-3.";
RL Submitted (JUN-2007) to the EMBL/GenBank/DDBJ databases.
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; CP000743; ABR56892.1; -; Genomic_DNA.
DR RefSeq; WP_011974024.1; NC_009635.1.
DR AlphaFoldDB; A6UWM0; -.
DR SMR; A6UWM0; -.
DR STRING; 419665.Maeo_1316; -.
DR PRIDE; A6UWM0; -.
DR EnsemblBacteria; ABR56892; ABR56892; Maeo_1316.
DR GeneID; 5327242; -.
DR KEGG; mae:Maeo_1316; -.
DR eggNOG; arCOG04075; Archaea.
DR HOGENOM; CLU_055352_1_0_2; -.
DR OMA; RYANRGW; -.
DR OrthoDB; 64452at2157; -.
DR UniPathway; UPA00245; -.
DR Proteomes; UP000001106; 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; Reference proteome; Schiff base.
FT CHAIN 1..299
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT /id="PRO_1000070382"
FT ACT_SITE 81
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 24
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 153
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 165
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 219
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 240..241
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
SQ SEQUENCE 299 AA; 32229 MW; 6401B6BDEFC9F8C0 CRC64;
MKKIGTELLK RGFAKMVKHG VVMDVTNPEQ ARIAEDAGAA AVMALERVPA DIRAEGGVSR
MSDPEMILEI KDEVSIPVMA KARIGHFVEA QALESLGIDM VDESEVLTPA DEIHHIDKNA
FDIPFVCGAR NLGEALRRID EGAAMIRTKG EAGTGDVIEA VKHMRAVNEG IAKVVGYYEM
GCDRELVQMA RNELKVPMDL VYEVAELKRL PVVNFAAGGI ATPADAALMM QLGCDGVFVG
SGIFKSGNPE ERARAIVEAT YNYDKPDVIA EVSKNLGEAM VGINVDAIPE KELLAKRGI
