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Protein

Pyridoxal 5'-phosphate synthase subunit PdxT

Gene

pdxT

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

Functioni

Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS.UniRule annotation1 Publication

Catalytic activityi

D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate.UniRule annotation1 Publication
L-glutamine + H2O = L-glutamate + NH3.UniRule annotation1 Publication

Kineticsi

kcat is 7.60 min(-1) for glutaminase activity.1 Publication

Manual assertion based on experiment ini

  1. KM=0.99 mM for L-glutamine1 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
    Active sitei79NucleophileUniRule annotationCurated1
    Binding sitei106L-glutamineUniRule annotation1 Publication1
    Active sitei170Charge relay systemUniRule annotationCurated1
    Active sitei172Charge relay systemUniRule annotationCurated1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Lyase

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciBSUB:BSU00120-MONOMER.
    MetaCyc:MONOMER-15503.
    BRENDAi4.3.3.6. 658.
    UniPathwayiUPA00245.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxal 5'-phosphate synthase subunit PdxTUniRule annotation (EC:4.3.3.6UniRule annotation1 Publication)
    Alternative name(s):
    Pdx2UniRule annotation
    Pyridoxal 5'-phosphate synthase glutaminase subunitUniRule annotation (EC:3.5.1.2UniRule annotation1 Publication)
    Gene namesi
    Name:pdxTUniRule annotation
    Synonyms:yaaE
    Ordered Locus Names:BSU00120
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi10Q → A: 3-fold reduction in glutaminase activity. 1 Publication1
    Mutagenesisi10Q → E: Almost no activity. 1 Publication1
    Mutagenesisi10Q → N: 10-fold reduction in glutaminase activity. 1 Publication1
    Mutagenesisi15E → A: Almost no effect on glutaminase activity. 1 Publication1
    Mutagenesisi48E → A: No activity, disturbing interaction with PdxS. 1 Publication1
    Mutagenesisi106R → A: No activity, disturbing interaction with PdxS. 1 Publication1
    Mutagenesisi135R → A: No activity, disturbing interaction with PdxS. 1 Publication1
    Mutagenesisi170H → N: No activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001356321 – 196Pyridoxal 5'-phosphate synthase subunit PdxTAdd BLAST196

    Proteomic databases

    PaxDbiP37528.

    Interactioni

    Subunit structurei

    In the presence of PdxS, forms a dodecamer of heterodimers. Only shows activity in the heterodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    DIPiDIP-57719N.
    IntActiP37528. 1 interactor.
    MINTiMINT-7147884.
    STRINGi224308.Bsubs1_010100000060.

    Structurei

    Secondary structure

    1196
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 7Combined sources5
    Beta strandi9 – 11Combined sources3
    Helixi14 – 22Combined sources9
    Beta strandi26 – 30Combined sources5
    Helixi33 – 38Combined sources6
    Beta strandi40 – 44Combined sources5
    Helixi49 – 58Combined sources10
    Helixi62 – 70Combined sources9
    Beta strandi75 – 78Combined sources4
    Helixi80 – 85Combined sources6
    Beta strandi86 – 89Combined sources4
    Beta strandi102 – 105Combined sources4
    Turni106 – 109Combined sources4
    Turni111 – 113Combined sources3
    Beta strandi114 – 120Combined sources7
    Beta strandi129 – 135Combined sources7
    Beta strandi138 – 142Combined sources5
    Beta strandi147 – 152Combined sources6
    Beta strandi155 – 161Combined sources7
    Beta strandi164 – 169Combined sources6
    Beta strandi173 – 175Combined sources3
    Helixi178 – 193Combined sources16

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1R9GX-ray2.50A/B1-196[»]
    2NV0X-ray1.73A/B1-196[»]
    2NV2X-ray2.12B/D/F/H/J/L/N/P/R/T/V/X1-196[»]
    ProteinModelPortaliP37528.
    SMRiP37528.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP37528.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni47 – 49L-glutamine bindingUniRule annotation1 Publication3
    Regioni134 – 135L-glutamine bindingUniRule annotation1 Publication2

    Sequence similaritiesi

    Belongs to the glutaminase PdxT/SNO family.UniRule annotation

    Keywords - Domaini

    Glutamine amidotransferase

    Phylogenomic databases

    eggNOGiENOG4108UHX. Bacteria.
    COG0311. LUCA.
    HOGENOMiHOG000039949.
    InParanoidiP37528.
    KOiK08681.
    OMAiVYGTCAG.
    PhylomeDBiP37528.

    Family and domain databases

    CDDicd01749. GATase1_PB. 1 hit.
    Gene3Di3.40.50.880. 1 hit.
    HAMAPiMF_01615. PdxT. 1 hit.
    InterProiIPR029062. Class_I_gatase-like.
    IPR002161. PdxT/SNO.
    IPR021196. PdxT/SNO_CS.
    [Graphical view]
    PANTHERiPTHR31559:SF0. PTHR31559:SF0. 1 hit.
    PfamiPF01174. SNO. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005639. Glut_amidoT_SNO. 1 hit.
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR03800. PLP_synth_Pdx2. 1 hit.
    PROSITEiPS01236. PDXT_SNO_1. 1 hit.
    PS51130. PDXT_SNO_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P37528-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLTIGVLGLQ GAVREHIHAI EACGAAGLVV KRPEQLNEVD GLILPGGEST
    60 70 80 90 100
    TMRRLIDTYQ FMEPLREFAA QGKPMFGTCA GLIILAKEIA GSDNPHLGLL
    110 120 130 140 150
    NVVVERNSFG RQVDSFEADL TIKGLDEPFT GVFIRAPHIL EAGENVEVLS
    160 170 180 190
    EHNGRIVAAK QGQFLGCSFH PELTEDHRVT QLFVEMVEEY KQKALV
    Length:196
    Mass (Da):21,447
    Last modified:October 1, 1994 - v1
    Checksum:i91111DEF75257882
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D26185 Genomic DNA. Translation: BAA05248.1.
    AL009126 Genomic DNA. Translation: CAB11788.1.
    PIRiS66042.
    RefSeqiNP_387893.1. NC_000964.3.
    WP_003226797.1. NZ_JNCM01000024.1.

    Genome annotation databases

    EnsemblBacteriaiCAB11788; CAB11788; BSU00120.
    GeneIDi939971.
    KEGGibsu:BSU00120.
    PATRICi18971483. VBIBacSub10457_0013.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D26185 Genomic DNA. Translation: BAA05248.1.
    AL009126 Genomic DNA. Translation: CAB11788.1.
    PIRiS66042.
    RefSeqiNP_387893.1. NC_000964.3.
    WP_003226797.1. NZ_JNCM01000024.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1R9GX-ray2.50A/B1-196[»]
    2NV0X-ray1.73A/B1-196[»]
    2NV2X-ray2.12B/D/F/H/J/L/N/P/R/T/V/X1-196[»]
    ProteinModelPortaliP37528.
    SMRiP37528.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-57719N.
    IntActiP37528. 1 interactor.
    MINTiMINT-7147884.
    STRINGi224308.Bsubs1_010100000060.

    Proteomic databases

    PaxDbiP37528.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB11788; CAB11788; BSU00120.
    GeneIDi939971.
    KEGGibsu:BSU00120.
    PATRICi18971483. VBIBacSub10457_0013.

    Phylogenomic databases

    eggNOGiENOG4108UHX. Bacteria.
    COG0311. LUCA.
    HOGENOMiHOG000039949.
    InParanoidiP37528.
    KOiK08681.
    OMAiVYGTCAG.
    PhylomeDBiP37528.

    Enzyme and pathway databases

    UniPathwayiUPA00245.
    BioCyciBSUB:BSU00120-MONOMER.
    MetaCyc:MONOMER-15503.
    BRENDAi4.3.3.6. 658.

    Miscellaneous databases

    EvolutionaryTraceiP37528.

    Family and domain databases

    CDDicd01749. GATase1_PB. 1 hit.
    Gene3Di3.40.50.880. 1 hit.
    HAMAPiMF_01615. PdxT. 1 hit.
    InterProiIPR029062. Class_I_gatase-like.
    IPR002161. PdxT/SNO.
    IPR021196. PdxT/SNO_CS.
    [Graphical view]
    PANTHERiPTHR31559:SF0. PTHR31559:SF0. 1 hit.
    PfamiPF01174. SNO. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005639. Glut_amidoT_SNO. 1 hit.
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR03800. PLP_synth_Pdx2. 1 hit.
    PROSITEiPS01236. PDXT_SNO_1. 1 hit.
    PS51130. PDXT_SNO_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPDXT_BACSU
    AccessioniPrimary (citable) accession number: P37528
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: November 2, 2016
    This is version 117 of the entry and version 1 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
    5. Uncharacterized protein families (UPF)
      List of uncharacterized protein family (UPF) entries

    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.