PDXS_THET8
ID PDXS_THET8 Reviewed; 293 AA.
AC Q5SKD9;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2005, sequence version 2.
DT 03-AUG-2022, entry version 114.
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=TTHA0704;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).
RA Manzoku M., Ebihara A., Fujimoto Y., Yokoyama S., Kuramitsu S.;
RT "Crystal structure of pyridoxine biosynthesis protein from Thermus
RT thermophilus HB8.";
RL Submitted (OCT-2007) to the PDB data bank.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAD70527.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AP008226; BAD70527.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_024119184.1; NC_006461.1.
DR RefSeq; YP_143970.1; NC_006461.1.
DR PDB; 2ZBT; X-ray; 1.65 A; A/B/C/D=1-293.
DR PDBsum; 2ZBT; -.
DR AlphaFoldDB; Q5SKD9; -.
DR SMR; Q5SKD9; -.
DR STRING; 300852.55772086; -.
DR EnsemblBacteria; BAD70527; BAD70527; BAD70527.
DR GeneID; 3169908; -.
DR KEGG; ttj:TTHA0704; -.
DR PATRIC; fig|300852.9.peg.698; -.
DR eggNOG; COG0214; Bacteria.
DR HOGENOM; CLU_055352_1_0_0; -.
DR OMA; RYANRGW; -.
DR UniPathway; UPA00245; -.
DR EvolutionaryTrace; Q5SKD9; -.
DR Proteomes; UP000000532; 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..293
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT /id="PRO_0000109425"
FT ACT_SITE 80
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 23
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 152
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 164
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 213
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 234..235
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT STRAND 1..8
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 11..13
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 14..16
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 19..26
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 27..36
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 48..53
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 63..70
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 77..82
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 86..94
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 98..103
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 124..130
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 131..139
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 143..147
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 151..153
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 157..175
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 178..180
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 181..188
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 192..201
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 217..225
FT /evidence="ECO:0007829|PDB:2ZBT"
FT STRAND 229..233
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 235..239
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 243..255
FT /evidence="ECO:0007829|PDB:2ZBT"
FT TURN 256..258
FT /evidence="ECO:0007829|PDB:2ZBT"
FT HELIX 260..267
FT /evidence="ECO:0007829|PDB:2ZBT"
SQ SEQUENCE 293 AA; 32026 MW; 50693B1FFEDB777F CRC64;
MEKGTFQIKT GFAEMFKGGV IMDVTTPEQA VIAEEAGAVA VMALERVPAD IRAQGGVARM
SDPKIIKEIM AAVSIPVMAK VRIGHFVEAM ILEAIGVDFI DESEVLTPAD EEHHIDKWKF
KVPFVCGARN LGEALRRIAE GAAMIRTKGE AGTGNVVEAV RHARTMWKEI RYVQSLREDE
LMAYAKEIGA PFELVKWVHD HGRLPVVNFA AGGIATPADA ALMMHLGMDG VFVGSGIFKS
GDPRKRARAI VRAVAHYNDP EVLAEVSEDL GEPMVGINLD QLKEEERLAK RGW
