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Protein

Pyridoxal 5'-phosphate synthase subunit PdxS

Gene

pdxS

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively.UniRule annotation2 Publications

Catalytic activityi

D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate.UniRule annotation5 Publications

Kineticsi

kcat is 0.040 min(-1) with ribose-5-phosphate as substrate. kcat is 0.042 min(-1) with ribulose-5-phosphate as substrate.1 Publication

  1. KM=68 µM for ribose-5-phosphate1 Publication
  2. KM=53 µM for ribose-5-phosphate1 Publication
  3. KM=3.18 mM for ribulose-5-phosphate1 Publication
  4. KM=77 µM for D-glyceraldehyde-3-phosphate1 Publication

    pH dependencei

    Optimum pH is 6-6.5.1 Publication

    Pathwayi: pyridoxal 5'-phosphate biosynthesis

    This protein is involved in the pathway pyridoxal 5'-phosphate biosynthesis, which is part of Cofactor biosynthesis.UniRule annotation
    View all proteins of this organism that are known to be involved in the pathway pyridoxal 5'-phosphate biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei24 – 241D-ribose 5-phosphateUniRule annotation
    Active sitei81 – 811Schiff-base intermediate with D-ribose 5-phosphateUniRule annotation1 Publication
    Binding sitei153 – 1531D-ribose 5-phosphate; via amide nitrogenUniRule annotation
    Binding sitei165 – 1651Glyceraldehyde 3-phosphateUniRule annotation
    Binding sitei214 – 2141D-ribose 5-phosphate; via amide nitrogenUniRule annotation

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Pyridoxal phosphate, Schiff base

    Enzyme and pathway databases

    BioCyciBSUB:BSU00110-MONOMER.
    MetaCyc:MONOMER-15502.
    BRENDAi4.3.3.6. 658.
    UniPathwayiUPA00245.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxal 5'-phosphate synthase subunit PdxSUniRule annotation (EC:4.3.3.6UniRule annotation5 Publications)
    Short name:
    PLP synthase subunit PdxSUniRule annotation
    Alternative name(s):
    Pdx1UniRule annotation
    Superoxide-inducible protein 7
    Short name:
    SOI7
    Gene namesi
    Name:pdxSUniRule annotation
    Synonyms:yaaD
    Ordered Locus Names:BSU00110
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi18 – 181K → A: Almost no effect on activity. 1 Publication
    Mutagenesisi75 – 751S → A: Almost no effect on activity. 1 Publication
    Mutagenesisi81 – 811K → A or R: No activity, does not form covalent adduct with ribose-5-phosphate. 1 Publication
    Mutagenesisi99 – 991D → A: Results in 20-fold reduction of activity. 1 Publication
    Mutagenesisi149 – 1491K → A: No activity, does not form covalent adduct with ribose-5-phosphate or ribulose 5-phosphate. 2 Publications
    Mutagenesisi149 – 1491K → R: No activity, but can, as the wild-type, form covalent adduct with ribose-5-phosphate. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved2 Publications
    Chaini2 – 294293Pyridoxal 5'-phosphate synthase subunit PdxSPRO_0000109383Add
    BLAST

    Proteomic databases

    PaxDbiP37527.

    Expressioni

    Inductioni

    By superoxide.

    Interactioni

    Subunit structurei

    Homohexamer and homododecamer. In the presence of PdxT, forms a dodecamer of heterodimers.UniRule annotation1 Publication

    Protein-protein interaction databases

    DIPiDIP-61325N.
    IntActiP37527. 1 interaction.
    MINTiMINT-8365858.
    STRINGi224308.Bsubs1_010100000055.

    Structurei

    Secondary structure

    1
    294
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 53Combined sources
    Helixi7 – 159Combined sources
    Turni16 – 194Combined sources
    Beta strandi21 – 277Combined sources
    Helixi28 – 369Combined sources
    Beta strandi40 – 445Combined sources
    Helixi49 – 546Combined sources
    Helixi64 – 7310Combined sources
    Beta strandi78 – 825Combined sources
    Helixi87 – 9610Combined sources
    Beta strandi99 – 1035Combined sources
    Helixi118 – 1203Combined sources
    Beta strandi125 – 1317Combined sources
    Helixi132 – 1409Combined sources
    Beta strandi144 – 1485Combined sources
    Turni152 – 1543Combined sources
    Helixi158 – 17619Combined sources
    Helixi179 – 1813Combined sources
    Helixi182 – 1898Combined sources
    Helixi193 – 20210Combined sources
    Beta strandi209 – 2113Combined sources
    Helixi218 – 2269Combined sources
    Beta strandi232 – 2343Combined sources
    Helixi236 – 2405Combined sources
    Helixi244 – 25613Combined sources
    Turni257 – 2593Combined sources
    Helixi261 – 2677Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2NV1X-ray2.08A/B/C/D/E/F1-294[»]
    2NV2X-ray2.12A/C/E/G/I/K/M/O/Q/S/U/W1-294[»]
    ProteinModelPortaliP37527.
    SMRiP37527. Positions 2-272.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP37527.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni235 – 2362D-ribose 5-phosphate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the PdxS/SNZ family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105CD9. Bacteria.
    COG0214. LUCA.
    HOGENOMiHOG000227586.
    InParanoidiP37527.
    KOiK06215.
    OMAiKVRIGHV.
    OrthoDBiEOG6W9XBJ.
    PhylomeDBiP37527.

    Family and domain databases

    Gene3Di3.20.20.70. 2 hits.
    HAMAPiMF_01824. PdxS.
    InterProiIPR013785. Aldolase_TIM.
    IPR001852. PdxS/SNZ.
    IPR011060. RibuloseP-bd_barrel.
    [Graphical view]
    PfamiPF01680. SOR_SNZ. 1 hit.
    [Graphical view]
    PIRSFiPIRSF029271. Pdx1. 1 hit.
    SUPFAMiSSF51366. SSF51366. 1 hit.
    TIGRFAMsiTIGR00343. TIGR00343. 1 hit.
    PROSITEiPS01235. PDXS_SNZ_1. 1 hit.
    PS51129. PDXS_SNZ_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P37527-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAQTGTERVK RGMAEMQKGG VIMDVINAEQ AKIAEEAGAV AVMALERVPA
    60 70 80 90 100
    DIRAAGGVAR MADPTIVEEV MNAVSIPVMA KARIGHIVEA RVLEAMGVDY
    110 120 130 140 150
    IDESEVLTPA DEEFHLNKNE YTVPFVCGCR DLGEATRRIA EGASMLRTKG
    160 170 180 190 200
    EPGTGNIVEA VRHMRKVNAQ VRKVVAMSED ELMTEAKNLG APYELLLQIK
    210 220 230 240 250
    KDGKLPVVNF AAGGVATPAD AALMMQLGAD GVFVGSGIFK SDNPAKFAKA
    260 270 280 290
    IVEATTHFTD YKLIAELSKE LGTAMKGIEI SNLLPEQRMQ ERGW
    Length:294
    Mass (Da):31,612
    Last modified:January 23, 2007 - v3
    Checksum:i1662DA1925DDA9B1
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti30 – 301Q → D AA sequence (PubMed:9298659).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL009126 Genomic DNA. Translation: CAB11787.1.
    PIRiS66041.
    RefSeqiNP_387892.1. NC_000964.3.
    WP_003247145.1. NZ_JNCM01000024.1.

    Genome annotation databases

    EnsemblBacteriaiCAB11787; CAB11787; BSU00110.
    GeneIDi939988.
    KEGGibsu:BSU00110.
    PATRICi18971481. VBIBacSub10457_0012.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL009126 Genomic DNA. Translation: CAB11787.1.
    PIRiS66041.
    RefSeqiNP_387892.1. NC_000964.3.
    WP_003247145.1. NZ_JNCM01000024.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2NV1X-ray2.08A/B/C/D/E/F1-294[»]
    2NV2X-ray2.12A/C/E/G/I/K/M/O/Q/S/U/W1-294[»]
    ProteinModelPortaliP37527.
    SMRiP37527. Positions 2-272.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-61325N.
    IntActiP37527. 1 interaction.
    MINTiMINT-8365858.
    STRINGi224308.Bsubs1_010100000055.

    Proteomic databases

    PaxDbiP37527.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB11787; CAB11787; BSU00110.
    GeneIDi939988.
    KEGGibsu:BSU00110.
    PATRICi18971481. VBIBacSub10457_0012.

    Phylogenomic databases

    eggNOGiENOG4105CD9. Bacteria.
    COG0214. LUCA.
    HOGENOMiHOG000227586.
    InParanoidiP37527.
    KOiK06215.
    OMAiKVRIGHV.
    OrthoDBiEOG6W9XBJ.
    PhylomeDBiP37527.

    Enzyme and pathway databases

    UniPathwayiUPA00245.
    BioCyciBSUB:BSU00110-MONOMER.
    MetaCyc:MONOMER-15502.
    BRENDAi4.3.3.6. 658.

    Miscellaneous databases

    EvolutionaryTraceiP37527.

    Family and domain databases

    Gene3Di3.20.20.70. 2 hits.
    HAMAPiMF_01824. PdxS.
    InterProiIPR013785. Aldolase_TIM.
    IPR001852. PdxS/SNZ.
    IPR011060. RibuloseP-bd_barrel.
    [Graphical view]
    PfamiPF01680. SOR_SNZ. 1 hit.
    [Graphical view]
    PIRSFiPIRSF029271. Pdx1. 1 hit.
    SUPFAMiSSF51366. SSF51366. 1 hit.
    TIGRFAMsiTIGR00343. TIGR00343. 1 hit.
    PROSITEiPS01235. PDXS_SNZ_1. 1 hit.
    PS51129. PDXS_SNZ_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin."
      Ogasawara N., Nakai S., Yoshikawa H.
      DNA Res. 1:1-14(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    3. "Amino acid sequences of several Bacillus subtilis proteins modified by apparent guanylylation."
      Mitchell C., Morris P.W., Vary J.C.
      Mol. Microbiol. 6:1579-1581(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-16.
      Strain: 168 / DB100.
    4. "First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis."
      Antelmann H., Bernhardt J., Schmid R., Mach H., Voelker U., Hecker M.
      Electrophoresis 18:1451-1463(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-32.
      Strain: 168 / IS58.
    5. "Physical and enzymological interaction of Bacillus subtilis proteins required for de novo pyridoxal 5'-phosphate biosynthesis."
      Belitsky B.R.
      J. Bacteriol. 186:1191-1196(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
      Strain: 168 / SMY.
    6. "Reconstitution and biochemical characterization of a new pyridoxal-5'-phosphate biosynthetic pathway."
      Burns K.E., Xiang Y., Kinsland C.L., McLafferty F.W., Begley T.P.
      J. Am. Chem. Soc. 127:3682-3683(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-149, IDENTIFICATION OF REACTION SUBSTRATES, PH DEPENDENCE.
    7. "On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis."
      Raschle T., Amrhein N., Fitzpatrick T.B.
      J. Biol. Chem. 280:32291-32300(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, IDENTIFICATION OF REACTION PRODUCT.
      Strain: 168.
    8. "Thermodynamic characterization of the protein-protein interaction in the heteromeric Bacillus subtilis pyridoxalphosphate synthase."
      Neuwirth M., Flicker K., Strohmeier M., Tews I., Macheroux P.
      Biochemistry 46:5131-5139(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: COMPLEX FORMATION OF PDXS AND PDXT.
    9. "Reaction mechanism of pyridoxal 5'-phosphate synthase. Detection of an enzyme-bound chromophoric intermediate."
      Raschle T., Arigoni D., Brunisholz R., Rechsteiner H., Amrhein N., Fitzpatrick T.B.
      J. Biol. Chem. 282:6098-6105(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, MUTAGENESIS OF LYS-81 AND LYS-149, ACTIVE SITE, REACTION MECHANISM, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: 168.
    10. "Trapping of a chromophoric intermediate in the Pdx1-catalyzed biosynthesis of pyridoxal 5'-phosphate."
      Hanes J.W., Keresztes I., Begley T.P.
      Angew. Chem. Int. Ed. Engl. 47:2102-2105(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, IDENTIFICATION OF REACTION INTERMEDIATE, REACTION MECHANISM.
    11. "Mechanistic studies on pyridoxal phosphate synthase: the reaction pathway leading to a chromophoric intermediate."
      Hanes J.W., Burns K.E., Hilmey D.G., Chatterjee A., Dorrestein P.C., Begley T.P.
      J. Am. Chem. Soc. 130:3043-3052(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION OF GLYCERALDEHAYDE-3-PHOSPHATE AS SUBSTRATE, CHARACTERIZATION OF REACTION INTERMEDIATE, REACTION MECHANISM.
      Strain: 168.
    12. "13C NMR snapshots of the complex reaction coordinate of pyridoxal phosphate synthase."
      Hanes J.W., Keresztes I., Begley T.P.
      Nat. Chem. Biol. 4:425-430(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, CHARACTERIZATION OF REACTION INTERMEDIATES, REACTION MECHANISM.
    13. "Dissection of contributions from invariant amino acids to complex formation and catalysis in the heteromeric pyridoxal 5-phosphate synthase complex from Bacillus subtilis."
      Wallner S., Neuwirth M., Flicker K., Tews I., Macheroux P.
      Biochemistry 48:1928-1935(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-18; SER-75 AND ASP-99.
    14. "Intersubunit cross-talk in pyridoxal 5'-phosphate synthase, coordinated by the C terminus of the synthase subunit."
      Raschle T., Speziga D., Kress W., Moccand C., Gehrig P., Amrhein N., Weber-Ban E., Fitzpatrick T.B.
      J. Biol. Chem. 284:7706-7718(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FLUORESCENCE SPECTROSCOPY, CROSS LINKING.
    15. Cited for: X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF APOENZYME AND COMPLEX WITH SUBUNIT PDXS, SUBUNIT.

    Entry informationi

    Entry nameiPDXS_BACSU
    AccessioniPrimary (citable) accession number: P37527
    Secondary accession number(s): P27877
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: January 23, 2007
    Last modified: February 17, 2016
    This is version 131 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.