PDXS_METJA
ID PDXS_METJA Reviewed; 330 AA.
AC Q58090;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 123.
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=MJ0677;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS).
RA Manzoku M., Ebihara A., Chen L., Fu Z.-Q., Chrzas J., Wang B.-C.,
RA Yokoyama S., Kuramitsu S.;
RT "Crystal structure of pyridoxine biosynthesis protein from
RT Methanocaldococcus jannaschii.";
RL Submitted (MAY-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}.
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DR EMBL; L77117; AAB98672.1; -; Genomic_DNA.
DR PIR; E64384; E64384.
DR RefSeq; WP_010870182.1; NC_000909.1.
DR PDB; 2YZR; X-ray; 2.30 A; A/B/C=1-330.
DR PDBsum; 2YZR; -.
DR AlphaFoldDB; Q58090; -.
DR SMR; Q58090; -.
DR STRING; 243232.MJ_0677; -.
DR EnsemblBacteria; AAB98672; AAB98672; MJ_0677.
DR GeneID; 1451543; -.
DR KEGG; mja:MJ_0677; -.
DR eggNOG; arCOG04075; Archaea.
DR HOGENOM; CLU_055352_1_0_2; -.
DR InParanoid; Q58090; -.
DR OMA; RYANRGW; -.
DR OrthoDB; 64452at2157; -.
DR PhylomeDB; Q58090; -.
DR UniPathway; UPA00245; -.
DR EvolutionaryTrace; Q58090; -.
DR Proteomes; UP000000805; 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 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; Reference proteome; Schiff base.
FT CHAIN 1..330
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT /id="PRO_0000109435"
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 250
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 271..272
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:2YZR"
FT TURN 15..18
FT /evidence="ECO:0007829|PDB:2YZR"
FT STRAND 19..26
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 27..36
FT /evidence="ECO:0007829|PDB:2YZR"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 48..51
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 63..72
FT /evidence="ECO:0007829|PDB:2YZR"
FT STRAND 77..82
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 86..94
FT /evidence="ECO:0007829|PDB:2YZR"
FT STRAND 98..103
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:2YZR"
FT STRAND 124..127
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 131..140
FT /evidence="ECO:0007829|PDB:2YZR"
FT STRAND 143..147
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 157..173
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 178..189
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 190..193
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 194..202
FT /evidence="ECO:0007829|PDB:2YZR"
FT STRAND 213..216
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 221..238
FT /evidence="ECO:0007829|PDB:2YZR"
FT STRAND 242..247
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 254..262
FT /evidence="ECO:0007829|PDB:2YZR"
FT STRAND 268..271
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 272..275
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 280..292
FT /evidence="ECO:0007829|PDB:2YZR"
FT TURN 293..295
FT /evidence="ECO:0007829|PDB:2YZR"
FT HELIX 297..304
FT /evidence="ECO:0007829|PDB:2YZR"
SQ SEQUENCE 330 AA; 35856 MW; A4FCCE386CEF56AB CRC64;
MKKGTDLLKK GFAKMVKHGV VMDVTNVEQA QIAEEAGAVA VMALERVPAD IRAAGGVARM
SDPALIEEIM DAVSIPVMAK CRIGHTTEAL VLEAIGVDMI DESEVLTQAD PFFHIYKKKF
NVPFVCGARN LGEAVRRIWE GAAMIRTKGE AGTGNIVEAV RHMRLMNEAI AQLQRMTDEE
VYGVAKFYAN RYAELAKTVR EGMGLPATVL ENEPIYEGFT LAEIIDGLYE VLLEVKKLGR
LPVVNFAAGG VATPADAALM MQLGSDGVFV GSGIFKSENP LERARAIVEA TYNYDKPDIV
AEVSKNLGEA MKGIDITQIS EAEKMQYRGD
