PDXS_PYRHO
ID PDXS_PYRHO Reviewed; 335 AA.
AC O59080;
DT 13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, 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}; OrderedLocusNames=PH1355;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP RIBOSE 5-PHOSPHATE, ACTIVE SITE, AND SUBUNIT.
RX PubMed=23104439; DOI=10.1007/s10059-012-0198-8;
RA Matsuura A., Yoon J.Y., Yoon H.J., Lee H.H., Suh S.W.;
RT "Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus
RT horikoshii.";
RL Mol. Cells 34:407-412(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: Homohexamer. In the presence of PdxT, forms a dodecamer of
CC heterodimers. {ECO:0000255|HAMAP-Rule:MF_01824,
CC ECO:0000269|PubMed:23104439}.
CC -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000255|HAMAP-
CC Rule:MF_01824}.
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DR EMBL; BA000001; BAA30461.1; -; Genomic_DNA.
DR PIR; E71007; E71007.
DR RefSeq; WP_010885443.1; NC_000961.1.
DR PDB; 4FIQ; X-ray; 2.70 A; A/B/C/D/E/F=1-335.
DR PDB; 4FIR; X-ray; 3.10 A; A/B/C/D/E/F=1-335.
DR PDBsum; 4FIQ; -.
DR PDBsum; 4FIR; -.
DR AlphaFoldDB; O59080; -.
DR SMR; O59080; -.
DR IntAct; O59080; 1.
DR MINT; O59080; -.
DR STRING; 70601.3257778; -.
DR EnsemblBacteria; BAA30461; BAA30461; BAA30461.
DR GeneID; 1443680; -.
DR KEGG; pho:PH1355; -.
DR eggNOG; arCOG04075; Archaea.
DR OMA; RYANRGW; -.
DR OrthoDB; 64452at2157; -.
DR BRENDA; 4.3.3.6; 5244.
DR UniPathway; UPA00245; -.
DR Proteomes; UP000000752; 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 InterPro; IPR033983; Thiazole_synthase_ThiG.
DR PANTHER; PTHR31829; PTHR31829; 1.
DR Pfam; PF01680; SOR_SNZ; 1.
DR Pfam; PF05690; ThiG; 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; Schiff base.
FT CHAIN 1..335
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT /id="PRO_0000109445"
FT ACT_SITE 87
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:23104439"
FT BINDING 30
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:23104439"
FT BINDING 159
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:23104439"
FT BINDING 171
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 257
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:23104439"
FT BINDING 278..279
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:23104439"
FT HELIX 3..21
FT /evidence="ECO:0007829|PDB:4FIQ"
FT TURN 22..25
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 26..33
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 34..43
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 46..50
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 55..60
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 70..77
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 84..89
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 93..102
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 105..113
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 131..137
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 138..147
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 150..154
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 164..181
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 185..195
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 197..200
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 201..209
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 228..245
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 249..254
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 261..269
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 273..277
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 279..282
FT /evidence="ECO:0007829|PDB:4FIQ"
FT STRAND 283..285
FT /evidence="ECO:0007829|PDB:4FIQ"
FT HELIX 287..299
FT /evidence="ECO:0007829|PDB:4FIQ"
FT TURN 300..302
FT /evidence="ECO:0007829|PDB:4FIR"
FT HELIX 304..312
FT /evidence="ECO:0007829|PDB:4FIQ"
SQ SEQUENCE 335 AA; 37014 MW; D5E178BB654E5196 CRC64;
MDKLKIIMEK GTERLKRGFA KMVKGGVIMD VTNAEQARIA EEAGAVAVMA LHKVPADIRK
AGGVARMAPV EKIQEIMDAV TIPVMAKCRI GHEAEARILE ALGVDMIDES EVLTPADPFF
HIYKKKFTAP FVCGARNLGE AVRRIWEGAA MIRTKGEAGT GNIIEAVRHV RLVNENIRLI
QRMTDEEIYG VAEKFAEPYL RLAFSVKEIS GLPKRVLENE PIYEGFTYRE IVEDIYKILL
EIKKLGRLPV VNFAAGGVAT PADAALMMAM GMDGVFVGSG IFKSSNPPKM ARAIVEAVNH
WDEPDVLAEI SREIGEPMRG QAIEELQVRM EERGI
