PDXS_BACSU
ID PDXS_BACSU Reviewed; 294 AA.
AC P37527; P27877;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 162.
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, ECO:0000269|PubMed:16030023, ECO:0000269|PubMed:17189272, ECO:0000269|PubMed:18260082, ECO:0000269|PubMed:18271580, ECO:0000269|PubMed:18516049};
DE AltName: Full=Pdx1 {ECO:0000255|HAMAP-Rule:MF_01824};
DE AltName: Full=Superoxide-inducible protein 7;
DE Short=SOI7;
GN Name=pdxS {ECO:0000255|HAMAP-Rule:MF_01824}; Synonyms=yaaD;
GN OrderedLocusNames=BSU00110;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=7584024; DOI=10.1093/dnares/1.1.1;
RA Ogasawara N., Nakai S., Yoshikawa H.;
RT "Systematic sequencing of the 180 kilobase region of the Bacillus subtilis
RT chromosome containing the replication origin.";
RL DNA Res. 1:1-14(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP PROTEIN SEQUENCE OF 2-16.
RC STRAIN=168 / DB100;
RX PubMed=1495386; DOI=10.1111/j.1365-2958.1992.tb00882.x;
RA Mitchell C., Morris P.W., Vary J.C.;
RT "Amino acid sequences of several Bacillus subtilis proteins modified by
RT apparent guanylylation.";
RL Mol. Microbiol. 6:1579-1581(1992).
RN [4]
RP PROTEIN SEQUENCE OF 2-32.
RC STRAIN=168 / IS58;
RX PubMed=9298659; DOI=10.1002/elps.1150180820;
RA Antelmann H., Bernhardt J., Schmid R., Mach H., Voelker U., Hecker M.;
RT "First steps from a two-dimensional protein index towards a response-
RT regulation map for Bacillus subtilis.";
RL Electrophoresis 18:1451-1463(1997).
RN [5]
RP CHARACTERIZATION.
RC STRAIN=168 / SMY;
RX PubMed=14762015; DOI=10.1128/jb.186.4.1191-1196.2004;
RA Belitsky B.R.;
RT "Physical and enzymological interaction of Bacillus subtilis proteins
RT required for de novo pyridoxal 5'-phosphate biosynthesis.";
RL J. Bacteriol. 186:1191-1196(2004).
RN [6]
RP MUTAGENESIS OF LYS-149, IDENTIFICATION OF REACTION SUBSTRATES, AND PH
RP DEPENDENCE.
RX PubMed=15771487; DOI=10.1021/ja042792t;
RA Burns K.E., Xiang Y., Kinsland C.L., McLafferty F.W., Begley T.P.;
RT "Reconstitution and biochemical characterization of a new pyridoxal-5'-
RT phosphate biosynthetic pathway.";
RL J. Am. Chem. Soc. 127:3682-3683(2005).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP IDENTIFICATION OF REACTION PRODUCT.
RC STRAIN=168;
RX PubMed=16030023; DOI=10.1074/jbc.m501356200;
RA Raschle T., Amrhein N., Fitzpatrick T.B.;
RT "On the two components of pyridoxal 5'-phosphate synthase from Bacillus
RT subtilis.";
RL J. Biol. Chem. 280:32291-32300(2005).
RN [8]
RP COMPLEX FORMATION OF PDXS AND PDXT.
RX PubMed=17408246; DOI=10.1021/bi602602x;
RA Neuwirth M., Flicker K., Strohmeier M., Tews I., Macheroux P.;
RT "Thermodynamic characterization of the protein-protein interaction in the
RT heteromeric Bacillus subtilis pyridoxalphosphate synthase.";
RL Biochemistry 46:5131-5139(2007).
RN [9]
RP CATALYTIC ACTIVITY, MUTAGENESIS OF LYS-81 AND LYS-149, ACTIVE SITE,
RP REACTION MECHANISM, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=168;
RX PubMed=17189272; DOI=10.1074/jbc.m610614200;
RA Raschle T., Arigoni D., Brunisholz R., Rechsteiner H., Amrhein N.,
RA Fitzpatrick T.B.;
RT "Reaction mechanism of pyridoxal 5'-phosphate synthase. Detection of an
RT enzyme-bound chromophoric intermediate.";
RL J. Biol. Chem. 282:6098-6105(2007).
RN [10]
RP CATALYTIC ACTIVITY, IDENTIFICATION OF REACTION INTERMEDIATE, AND REACTION
RP MECHANISM.
RX PubMed=18260082; DOI=10.1002/anie.200704390;
RA Hanes J.W., Keresztes I., Begley T.P.;
RT "Trapping of a chromophoric intermediate in the Pdx1-catalyzed biosynthesis
RT of pyridoxal 5'-phosphate.";
RL Angew. Chem. Int. Ed. Engl. 47:2102-2105(2008).
RN [11]
RP FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION OF GLYCERALDEHAYDE-3-PHOSPHATE
RP AS SUBSTRATE, CHARACTERIZATION OF REACTION INTERMEDIATE, AND REACTION
RP MECHANISM.
RC STRAIN=168;
RX PubMed=18271580; DOI=10.1021/ja076604l;
RA Hanes J.W., Burns K.E., Hilmey D.G., Chatterjee A., Dorrestein P.C.,
RA Begley T.P.;
RT "Mechanistic studies on pyridoxal phosphate synthase: the reaction pathway
RT leading to a chromophoric intermediate.";
RL J. Am. Chem. Soc. 130:3043-3052(2008).
RN [12]
RP CATALYTIC ACTIVITY, CHARACTERIZATION OF REACTION INTERMEDIATES, AND
RP REACTION MECHANISM.
RX PubMed=18516049; DOI=10.1038/nchembio.93;
RA Hanes J.W., Keresztes I., Begley T.P.;
RT "13C NMR snapshots of the complex reaction coordinate of pyridoxal
RT phosphate synthase.";
RL Nat. Chem. Biol. 4:425-430(2008).
RN [13]
RP MUTAGENESIS OF LYS-18; SER-75 AND ASP-99.
RX PubMed=19152323; DOI=10.1021/bi801887r;
RA Wallner S., Neuwirth M., Flicker K., Tews I., Macheroux P.;
RT "Dissection of contributions from invariant amino acids to complex
RT formation and catalysis in the heteromeric pyridoxal 5-phosphate synthase
RT complex from Bacillus subtilis.";
RL Biochemistry 48:1928-1935(2009).
RN [14]
RP FLUORESCENCE SPECTROSCOPY, AND CROSS LINKING.
RX PubMed=19074821; DOI=10.1074/jbc.m804728200;
RA Raschle T., Speziga D., Kress W., Moccand C., Gehrig P., Amrhein N.,
RA Weber-Ban E., Fitzpatrick T.B.;
RT "Intersubunit cross-talk in pyridoxal 5'-phosphate synthase, coordinated by
RT the C terminus of the synthase subunit.";
RL J. Biol. Chem. 284:7706-7718(2009).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF APOENZYME AND COMPLEX WITH
RP SUBUNIT PDXS, AND SUBUNIT.
RX PubMed=17159152; DOI=10.1073/pnas.0604950103;
RA Strohmeier M., Raschle T., Mazurkiewicz J., Rippe K., Sinning I.,
RA Fitzpatrick T.B., Tews I.;
RT "Structure of a bacterial pyridoxal 5'-phosphate synthase complex.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:19284-19289(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, ECO:0000269|PubMed:16030023,
CC ECO:0000269|PubMed:18271580}.
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, ECO:0000269|PubMed:16030023,
CC ECO:0000269|PubMed:17189272, ECO:0000269|PubMed:18260082,
CC ECO:0000269|PubMed:18271580, ECO:0000269|PubMed:18516049};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=68 uM for ribose-5-phosphate {ECO:0000269|PubMed:16030023};
CC KM=53 uM for ribose-5-phosphate {ECO:0000269|PubMed:17189272};
CC KM=3.18 mM for ribulose-5-phosphate {ECO:0000269|PubMed:17189272};
CC KM=77 uM for D-glyceraldehyde-3-phosphate
CC {ECO:0000269|PubMed:16030023};
CC Note=kcat is 0.040 min(-1) with ribose-5-phosphate as substrate. kcat
CC is 0.042 min(-1) with ribulose-5-phosphate as substrate.
CC {ECO:0000269|PubMed:17189272};
CC pH dependence:
CC Optimum pH is 6-6.5. {ECO:0000269|PubMed:15771487};
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:17159152}.
CC -!- INTERACTION:
CC P37527; P37527: pdxS; NbExp=2; IntAct=EBI-7828661, EBI-7828661;
CC P37527; P37528: pdxT; NbExp=5; IntAct=EBI-7828661, EBI-7051766;
CC -!- INDUCTION: By superoxide.
CC -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000255|HAMAP-
CC Rule:MF_01824}.
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DR EMBL; AL009126; CAB11787.1; -; Genomic_DNA.
DR PIR; S66041; S66041.
DR RefSeq; NP_387892.1; NC_000964.3.
DR RefSeq; WP_003247145.1; NZ_JNCM01000024.1.
DR PDB; 2NV1; X-ray; 2.08 A; A/B/C/D/E/F=1-294.
DR PDB; 2NV2; X-ray; 2.12 A; A/C/E/G/I/K/M/O/Q/S/U/W=1-294.
DR PDBsum; 2NV1; -.
DR PDBsum; 2NV2; -.
DR AlphaFoldDB; P37527; -.
DR SMR; P37527; -.
DR DIP; DIP-61325N; -.
DR IntAct; P37527; 2.
DR MINT; P37527; -.
DR STRING; 224308.BSU00110; -.
DR jPOST; P37527; -.
DR PaxDb; P37527; -.
DR PRIDE; P37527; -.
DR EnsemblBacteria; CAB11787; CAB11787; BSU_00110.
DR GeneID; 939988; -.
DR KEGG; bsu:BSU00110; -.
DR PATRIC; fig|224308.179.peg.11; -.
DR eggNOG; COG0214; Bacteria.
DR InParanoid; P37527; -.
DR OMA; RYANRGW; -.
DR PhylomeDB; P37527; -.
DR BioCyc; BSUB:BSU00110-MON; -.
DR BioCyc; MetaCyc:MON-15502; -.
DR BRENDA; 4.3.3.6; 658.
DR SABIO-RK; P37527; -.
DR UniPathway; UPA00245; -.
DR EvolutionaryTrace; P37527; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0016843; F:amine-lyase activity; IBA:GO_Central.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
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; Direct protein sequencing; Lyase; Pyridoxal phosphate;
KW Reference proteome; Schiff base.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:1495386,
FT ECO:0000269|PubMed:9298659"
FT CHAIN 2..294
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT /id="PRO_0000109383"
FT ACT_SITE 81
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824,
FT ECO:0000269|PubMed:17189272"
FT BINDING 24
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
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 MUTAGEN 18
FT /note="K->A: Almost no effect on activity."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 75
FT /note="S->A: Almost no effect on activity."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 81
FT /note="K->A,R: No activity, does not form covalent adduct
FT with ribose-5-phosphate."
FT /evidence="ECO:0000269|PubMed:17189272"
FT MUTAGEN 99
FT /note="D->A: Results in 20-fold reduction of activity."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 149
FT /note="K->A: No activity, does not form covalent adduct
FT with ribose-5-phosphate or ribulose 5-phosphate."
FT /evidence="ECO:0000269|PubMed:15771487,
FT ECO:0000269|PubMed:17189272"
FT MUTAGEN 149
FT /note="K->R: No activity, but can, as the wild-type, form
FT covalent adduct with ribose-5-phosphate."
FT /evidence="ECO:0000269|PubMed:17189272"
FT CONFLICT 30
FT /note="Q -> D (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:2NV2"
FT HELIX 7..15
FT /evidence="ECO:0007829|PDB:2NV1"
FT TURN 16..19
FT /evidence="ECO:0007829|PDB:2NV1"
FT STRAND 21..27
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 28..36
FT /evidence="ECO:0007829|PDB:2NV1"
FT STRAND 40..44
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 49..54
FT /evidence="ECO:0007829|PDB:2NV2"
FT HELIX 64..73
FT /evidence="ECO:0007829|PDB:2NV1"
FT STRAND 78..82
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 87..96
FT /evidence="ECO:0007829|PDB:2NV1"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 118..120
FT /evidence="ECO:0007829|PDB:2NV1"
FT STRAND 125..131
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 132..140
FT /evidence="ECO:0007829|PDB:2NV1"
FT STRAND 144..148
FT /evidence="ECO:0007829|PDB:2NV1"
FT TURN 152..154
FT /evidence="ECO:0007829|PDB:2NV2"
FT HELIX 158..176
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 182..189
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 193..202
FT /evidence="ECO:0007829|PDB:2NV1"
FT STRAND 209..211
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 218..226
FT /evidence="ECO:0007829|PDB:2NV1"
FT STRAND 232..234
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 236..240
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 244..256
FT /evidence="ECO:0007829|PDB:2NV1"
FT TURN 257..259
FT /evidence="ECO:0007829|PDB:2NV1"
FT HELIX 261..267
FT /evidence="ECO:0007829|PDB:2NV1"
SQ SEQUENCE 294 AA; 31612 MW; 1662DA1925DDA9B1 CRC64;
MAQTGTERVK RGMAEMQKGG VIMDVINAEQ AKIAEEAGAV AVMALERVPA DIRAAGGVAR
MADPTIVEEV MNAVSIPVMA KARIGHIVEA RVLEAMGVDY IDESEVLTPA DEEFHLNKNE
YTVPFVCGCR DLGEATRRIA EGASMLRTKG EPGTGNIVEA VRHMRKVNAQ VRKVVAMSED
ELMTEAKNLG APYELLLQIK KDGKLPVVNF AAGGVATPAD AALMMQLGAD GVFVGSGIFK
SDNPAKFAKA IVEATTHFTD YKLIAELSKE LGTAMKGIEI SNLLPEQRMQ ERGW
