PDXS_GEOKA
ID PDXS_GEOKA Reviewed; 294 AA.
AC Q5L3Y2;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 107.
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=GK0011;
OS Geobacillus kaustophilus (strain HTA426).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus;
OC Geobacillus thermoleovorans group.
OX NCBI_TaxID=235909;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HTA426;
RX PubMed=15576355; DOI=10.1093/nar/gkh970;
RA Takami H., Takaki Y., Chee G.-J., Nishi S., Shimamura S., Suzuki H.,
RA Matsui S., Uchiyama I.;
RT "Thermoadaptation trait revealed by the genome sequence of thermophilic
RT Geobacillus kaustophilus.";
RL Nucleic Acids Res. 32:6292-6303(2004).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG,
RP AND SUBUNIT.
RX PubMed=15911615; DOI=10.1074/jbc.m503642200;
RA Zhu J., Burgner J.W., Harms E., Belitsky B.R., Smith J.L.;
RT "A new arrangement of (beta/alpha)8 barrels in the synthase subunit of PLP
RT synthase.";
RL J. Biol. Chem. 280:27914-27923(2005).
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: Homohexamer and homododecamer. In the presence of PdxT, forms
CC a dodecamer of heterodimers. {ECO:0000255|HAMAP-Rule:MF_01824,
CC ECO:0000269|PubMed:15911615}.
CC -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000255|HAMAP-
CC Rule:MF_01824}.
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DR EMBL; BA000043; BAD74296.1; -; Genomic_DNA.
DR RefSeq; WP_011229527.1; NC_006510.1.
DR PDB; 1ZNN; X-ray; 2.20 A; A/B/C/D/E/F=1-294.
DR PDB; 4WXY; X-ray; 2.70 A; A/C/E/G/I/K=1-294.
DR PDB; 4WXZ; X-ray; 2.70 A; A/B/C/D/E/F=1-294.
DR PDB; 4WY0; X-ray; 2.30 A; A/B/C/D/E/F/G/H/I/J/K/L=1-294.
DR PDBsum; 1ZNN; -.
DR PDBsum; 4WXY; -.
DR PDBsum; 4WXZ; -.
DR PDBsum; 4WY0; -.
DR AlphaFoldDB; Q5L3Y2; -.
DR SMR; Q5L3Y2; -.
DR STRING; 235909.GK0011; -.
DR EnsemblBacteria; BAD74296; BAD74296; GK0011.
DR KEGG; gka:GK0011; -.
DR eggNOG; COG0214; Bacteria.
DR HOGENOM; CLU_055352_1_0_9; -.
DR OMA; RYANRGW; -.
DR BRENDA; 4.3.3.6; 8138.
DR UniPathway; UPA00245; -.
DR EvolutionaryTrace; Q5L3Y2; -.
DR Proteomes; UP000001172; 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 1: Evidence at protein level;
KW 3D-structure; Lyase; Pyridoxal phosphate; Reference proteome; Schiff base.
FT CHAIN 1..294
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT /id="PRO_0000109395"
FT ACT_SITE 81
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000305|PubMed:15911615"
FT BINDING 24
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000305|PubMed:15911615"
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 214
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 235..236
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT HELIX 7..14
FT /evidence="ECO:0007829|PDB:4WY0"
FT TURN 16..19
FT /evidence="ECO:0007829|PDB:4WY0"
FT STRAND 20..27
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 28..37
FT /evidence="ECO:0007829|PDB:1ZNN"
FT STRAND 40..44
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 49..55
FT /evidence="ECO:0007829|PDB:4WXY"
FT HELIX 64..73
FT /evidence="ECO:0007829|PDB:1ZNN"
FT STRAND 78..83
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 87..96
FT /evidence="ECO:0007829|PDB:1ZNN"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 118..120
FT /evidence="ECO:0007829|PDB:1ZNN"
FT STRAND 125..131
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 132..140
FT /evidence="ECO:0007829|PDB:1ZNN"
FT STRAND 144..148
FT /evidence="ECO:0007829|PDB:1ZNN"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:4WY0"
FT HELIX 158..176
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 182..189
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 193..202
FT /evidence="ECO:0007829|PDB:1ZNN"
FT STRAND 206..214
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 218..226
FT /evidence="ECO:0007829|PDB:1ZNN"
FT STRAND 230..234
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 236..240
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 244..256
FT /evidence="ECO:0007829|PDB:1ZNN"
FT TURN 257..259
FT /evidence="ECO:0007829|PDB:1ZNN"
FT HELIX 261..267
FT /evidence="ECO:0007829|PDB:1ZNN"
FT TURN 268..270
FT /evidence="ECO:0007829|PDB:1ZNN"
SQ SEQUENCE 294 AA; 31652 MW; 3427A52A7DE63F50 CRC64;
MALTGTDRVK RGMAEMQKGG VIMDVVNAEQ AKIAEAAGAV AVMALERVPA DIRAAGGVAR
MADPTVIEEV MNAVSIPVMA KVRIGHYVEA RVLEALGVDY IDESEVLTPA DEEFHIDKRQ
FTVPFVCGCR DLGEAARRIA EGASMLRTKG EPGTGNIVEA VRHMRKVNAQ IRKVVNMSED
ELVAEAKQLG APVEVLREIK RLGRLPVVNF AAGGVATPAD AALMMHLGAD GVFVGSGIFK
SENPEKYARA IVEATTHYED YELIAHLSKG LGGAMRGIDI ATLLPEHRMQ ERGW
