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 27-MAR-2024, entry version 113. 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; Bacillota; 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 KEGG; gka:GK0011; -. DR eggNOG; COG0214; Bacteria. DR HOGENOM; CLU_055352_1_0_9; -. 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; Aldolase class I; 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 NCBIfam; TIGR00343; pyridoxal 5'-phosphate synthase lyase subunit PdxS; 1. DR PANTHER; PTHR31829; PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT SNZ1-RELATED; 1. DR PANTHER; PTHR31829:SF0; PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT SNZ1-RELATED; 1. DR Pfam; PF01680; SOR_SNZ; 1. DR PIRSF; PIRSF029271; Pdx1; 1. DR SUPFAM; SSF51366; Ribulose-phoshate binding barrel; 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 //