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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

Manual assertion based on experiment ini

  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)DescriptionActionsGraphical viewLength
    Binding sitei24D-ribose 5-phosphateUniRule annotation1
    Active sitei81Schiff-base intermediate with D-ribose 5-phosphateUniRule annotation1 Publication1
    Binding sitei153D-ribose 5-phosphate; via amide nitrogenUniRule annotation1
    Binding sitei165Glyceraldehyde 3-phosphateUniRule annotation1
    Binding sitei214D-ribose 5-phosphate; via amide nitrogenUniRule annotation1

    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)DescriptionActionsGraphical viewLength
    Mutagenesisi18K → A: Almost no effect on activity. 1 Publication1
    Mutagenesisi75S → A: Almost no effect on activity. 1 Publication1
    Mutagenesisi81K → A or R: No activity, does not form covalent adduct with ribose-5-phosphate. 1 Publication1
    Mutagenesisi99D → A: Results in 20-fold reduction of activity. 1 Publication1
    Mutagenesisi149K → A: No activity, does not form covalent adduct with ribose-5-phosphate or ribulose 5-phosphate. 2 Publications1
    Mutagenesisi149K → R: No activity, but can, as the wild-type, form covalent adduct with ribose-5-phosphate. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved2 Publications
    ChainiPRO_00001093832 – 294Pyridoxal 5'-phosphate synthase subunit PdxSAdd BLAST293

    Proteomic databases

    PaxDbiP37527.
    PRIDEiP37527.

    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 interactor.
    MINTiMINT-8365858.
    STRINGi224308.Bsubs1_010100000055.

    Structurei

    Secondary structure

    1294
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 5Combined sources3
    Helixi7 – 15Combined sources9
    Turni16 – 19Combined sources4
    Beta strandi21 – 27Combined sources7
    Helixi28 – 36Combined sources9
    Beta strandi40 – 44Combined sources5
    Helixi49 – 54Combined sources6
    Helixi64 – 73Combined sources10
    Beta strandi78 – 82Combined sources5
    Helixi87 – 96Combined sources10
    Beta strandi99 – 103Combined sources5
    Helixi118 – 120Combined sources3
    Beta strandi125 – 131Combined sources7
    Helixi132 – 140Combined sources9
    Beta strandi144 – 148Combined sources5
    Turni152 – 154Combined sources3
    Helixi158 – 176Combined sources19
    Helixi179 – 181Combined sources3
    Helixi182 – 189Combined sources8
    Helixi193 – 202Combined sources10
    Beta strandi209 – 211Combined sources3
    Helixi218 – 226Combined sources9
    Beta strandi232 – 234Combined sources3
    Helixi236 – 240Combined sources5
    Helixi244 – 256Combined sources13
    Turni257 – 259Combined sources3
    Helixi261 – 267Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP37527.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni235 – 236D-ribose 5-phosphate bindingUniRule annotation2

    Sequence similaritiesi

    Belongs to the PdxS/SNZ family.UniRule annotation

    Phylogenomic databases

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

    Family and domain databases

    CDDicd04727. pdxS. 1 hit.
    Gene3Di3.20.20.70. 2 hits.
    HAMAPiMF_01824. PdxS. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR001852. PdxS/SNZ.
    IPR033755. PdxS/SNZ_N.
    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)DescriptionActionsGraphical viewLength
    Sequence conflicti30Q → D AA sequence (PubMed:9298659).Curated1

    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
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    PaxDbiP37527.
    PRIDEiP37527.

    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.
    PhylomeDBiP37527.

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiP37527.

    Family and domain databases

    CDDicd04727. pdxS. 1 hit.
    Gene3Di3.20.20.70. 2 hits.
    HAMAPiMF_01824. PdxS. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR001852. PdxS/SNZ.
    IPR033755. PdxS/SNZ_N.
    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...

    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: November 30, 2016
    This is version 135 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.