PDXS_THEMA
ID PDXS_THEMA Reviewed; 293 AA.
AC Q9WYU4;
DT 13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 127.
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 Synonyms=yaaD {ECO:0000303|PubMed:17144654}; OrderedLocusNames=TM_0473;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) IN COMPLEX WITH PDXT SUBUNIT;
RP RIBULOSE-5-PHOSPHATE AND PHOSPHATE, SUBUNIT, ACTIVE SITE, AND REACTION
RP MECHANISM.
RX PubMed=17144654; DOI=10.1021/bi061464y;
RA Zein F., Zhang Y., Kang Y.N., Burns K., Begley T.P., Ealick S.E.;
RT "Structural insights into the mechanism of the PLP synthase holoenzyme from
RT Thermotoga maritima.";
RL Biochemistry 45:14609-14620(2006).
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:17144654}.
CC -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000255|HAMAP-
CC Rule:MF_01824}.
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DR EMBL; AE000512; AAD35558.1; -; Genomic_DNA.
DR PIR; A72372; A72372.
DR RefSeq; NP_228283.1; NC_000853.1.
DR RefSeq; WP_004081493.1; NZ_CP011107.1.
DR PDB; 2ISS; X-ray; 2.90 A; A/B/C=1-293.
DR PDBsum; 2ISS; -.
DR AlphaFoldDB; Q9WYU4; -.
DR SMR; Q9WYU4; -.
DR STRING; 243274.THEMA_02325; -.
DR EnsemblBacteria; AAD35558; AAD35558; TM_0473.
DR KEGG; tma:TM0473; -.
DR eggNOG; COG0214; Bacteria.
DR InParanoid; Q9WYU4; -.
DR OMA; RYANRGW; -.
DR OrthoDB; 784095at2; -.
DR UniPathway; UPA00245; -.
DR EvolutionaryTrace; Q9WYU4; -.
DR Proteomes; UP000008183; Chromosome.
DR GO; GO:0016843; F:amine-lyase activity; IBA:GO_Central.
DR GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006520; P:cellular amino acid metabolic process; IBA:GO_Central.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IBA:GO_Central.
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..293
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT /id="PRO_0000109423"
FT ACT_SITE 82
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:17144654"
FT BINDING 25
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:17144654"
FT BINDING 103
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:17144654"
FT BINDING 154
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:17144654"
FT BINDING 166
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 215
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:17144654"
FT BINDING 236..237
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:17144654"
FT STRAND 3..6
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 8..16
FT /evidence="ECO:0007829|PDB:2ISS"
FT TURN 17..20
FT /evidence="ECO:0007829|PDB:2ISS"
FT STRAND 22..28
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 29..38
FT /evidence="ECO:0007829|PDB:2ISS"
FT STRAND 41..45
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 50..56
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 65..74
FT /evidence="ECO:0007829|PDB:2ISS"
FT STRAND 79..84
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 88..97
FT /evidence="ECO:0007829|PDB:2ISS"
FT STRAND 100..105
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 119..121
FT /evidence="ECO:0007829|PDB:2ISS"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 133..141
FT /evidence="ECO:0007829|PDB:2ISS"
FT STRAND 145..149
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 159..175
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 180..190
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 194..203
FT /evidence="ECO:0007829|PDB:2ISS"
FT STRAND 207..214
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 219..227
FT /evidence="ECO:0007829|PDB:2ISS"
FT STRAND 233..236
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 237..240
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 245..257
FT /evidence="ECO:0007829|PDB:2ISS"
FT HELIX 262..269
FT /evidence="ECO:0007829|PDB:2ISS"
SQ SEQUENCE 293 AA; 32127 MW; 83092199901AF356 CRC64;
MEIKKGTWII KKGFAEMFKG GVIMDVTSAE QAKIAEEAGA VAVMALERVP ADIRKEGGVA
RMASIAKIRE IMEAVSIPVM AKVRIGHIAE AKILEELGVD FIDESEVLTP ADDRFHINKH
EFKVPFVCGA RDLGEALRRI AEGAAMIRTK GEAGTGNVVE AVKHMRRVME QIKQVTKMED
EELVAYGKEI GAPVELLREV KRLGRLPVVN FAAGGVATPA DAALMMMLGA DGVFVGSGIF
KSKDPRKMAK AMVLAVTYWD NPRILLKISE DIGEPMRGLD VEELEVRMQE RGW
