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Protein

L-threonine dehydratase catabolic TdcB

Gene

tdcB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short-lived. The second step is the nonenzymatic hydrolysis of the enamine/imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA. TdcB also dehydrates serine to yield pyruvate via analogous enamine/imine intermediates.3 Publications

Catalytic activityi

L-threonine = 2-oxobutanoate + NH3.
L-serine = pyruvate + NH3.

Cofactori

pyridoxal 5'-phosphate1 Publication

Enzyme regulationi

Each protein molecule can bind up to four molecules of AMP, which act as an allosteric activator to the enzyme. The enzyme is also inhibited by alpha-keto acids and other catabolites.2 Publications

Kineticsi

  1. KM=0.30 µM for L-threonine (at 37 dregrees Celsius and at pH 7.8)1 Publication
  2. KM=0.35 µM for L-serine (at 37 dregrees Celsius and at pH 7.8)1 Publication

    Pathwayi: L-threonine degradation via propanoate pathway

    This protein is involved in step 1 of the subpathway that synthesizes propanoate from L-threonine.
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. L-threonine dehydratase catabolic TdcB (tdcB)
    2. PFL-like enzyme TdcE (tdcE)
    3. no protein annotated in this organism
    4. Propionate kinase (tdcD)
    This subpathway is part of the pathway L-threonine degradation via propanoate pathway, which is itself part of Amino-acid degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes propanoate from L-threonine, the pathway L-threonine degradation via propanoate pathway and in Amino-acid degradation.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei88 – 881AMPBy similarity
    Binding sitei314 – 3141AMPBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi53 – 542AMPBy similarity
    Nucleotide bindingi119 – 1202AMPBy similarity

    GO - Molecular functioni

    • amino acid binding Source: EcoliWiki
    • L-serine ammonia-lyase activity Source: EcoCyc
    • L-threonine ammonia-lyase activity Source: EcoCyc
    • nucleotide binding Source: UniProtKB-KW
    • pyridoxal phosphate binding Source: EcoliWiki
    • threonine aldolase activity Source: EcoliWiki

    GO - Biological processi

    • L-serine catabolic process Source: EcoCyc
    • L-threonine catabolic process to propionate Source: UniProtKB-UniPathway
    • threonine catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Nucleotide-binding, Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciEcoCyc:THREDEHYDCAT-MONOMER.
    ECOL316407:JW3088-MONOMER.
    MetaCyc:THREDEHYDCAT-MONOMER.
    UniPathwayiUPA00052; UER00507.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    L-threonine dehydratase catabolic TdcB (EC:4.3.1.19)
    Alternative name(s):
    L-serine dehydratase (EC:4.3.1.17)
    Threonine deaminase
    Gene namesi
    Name:tdcB
    Ordered Locus Names:b3117, JW3088
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10990. tdcB.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 329329L-threonine dehydratase catabolic TdcBPRO_0000185582Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei58 – 581N6-(pyridoxal phosphate)lysineBy similarity

    Proteomic databases

    PaxDbiP0AGF6.
    PRIDEiP0AGF6.

    Expressioni

    Inductioni

    In the absence of glucose and oxygen,.1 Publication

    Interactioni

    Subunit structurei

    In the native structure, TdcB is in a dimeric form, whereas in the TdcB-AMP complex, it exists in a tetrameric form (dimer of dimers).By similarity

    Protein-protein interaction databases

    BioGridi4262419. 9 interactions.
    DIPiDIP-48063N.
    IntActiP0AGF6. 3 interactions.
    STRINGi511145.b3117.

    Structurei

    3D structure databases

    ProteinModelPortaliP0AGF6.
    SMRiP0AGF6. Positions 2-325.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C7B. Bacteria.
    COG1171. LUCA.
    HOGENOMiHOG000046972.
    InParanoidiP0AGF6.
    KOiK01754.
    OMAiNPTINII.
    PhylomeDBiP0AGF6.

    Family and domain databases

    InterProiIPR000634. Ser/Thr_deHydtase_PyrdxlP-BS.
    IPR005789. Thr_deHydtase_catblc.
    IPR001926. TrpB-like_PLP-dep.
    [Graphical view]
    PfamiPF00291. PALP. 1 hit.
    [Graphical view]
    SUPFAMiSSF53686. SSF53686. 1 hit.
    TIGRFAMsiTIGR01127. ilvA_1Cterm. 1 hit.
    PROSITEiPS00165. DEHYDRATASE_SER_THR. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0AGF6-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MHITYDLPVA IDDIIEAKQR LAGRIYKTGM PRSNYFSERC KGEIFLKFEN
    60 70 80 90 100
    MQRTGSFKIR GAFNKLSSLT DAEKRKGVVA CSAGNHAQGV SLSCAMLGID
    110 120 130 140 150
    GKVVMPKGAP KSKVAATCDY SAEVVLHGDN FNDTIAKVSE IVEMEGRIFI
    160 170 180 190 200
    PPYDDPKVIA GQGTIGLEIM EDLYDVDNVI VPIGGGGLIA GIAVAIKSIN
    210 220 230 240 250
    PTIRVIGVQS ENVHGMAASF HSGEITTHRT TGTLADGCDV SRPGNLTYEI
    260 270 280 290 300
    VRELVDDIVL VSEDEIRNSM IALIQRNKVV TEGAGALACA ALLSGKLDQY
    310 320
    IQNRKTVSII SGGNIDLSRV SQITGFVDA
    Length:329
    Mass (Da):35,232
    Last modified:December 20, 2005 - v1
    Checksum:iE7DF018FCCF743B1
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M21312 Genomic DNA. Translation: AAA24660.1.
    X14430 Genomic DNA. Translation: CAA32593.1.
    U18997 Genomic DNA. Translation: AAA57921.1.
    U00096 Genomic DNA. Translation: AAC76152.1.
    AP009048 Genomic DNA. Translation: BAE77166.1.
    M23638 Genomic DNA. Translation: AAA24661.1.
    PIRiA26367. DWECTD.
    RefSeqiNP_417587.1. NC_000913.3.
    WP_000548347.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76152; AAC76152; b3117.
    BAE77166; BAE77166; BAE77166.
    GeneIDi947633.
    KEGGiecj:JW3088.
    eco:b3117.
    PATRICi32121650. VBIEscCol129921_3211.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M21312 Genomic DNA. Translation: AAA24660.1.
    X14430 Genomic DNA. Translation: CAA32593.1.
    U18997 Genomic DNA. Translation: AAA57921.1.
    U00096 Genomic DNA. Translation: AAC76152.1.
    AP009048 Genomic DNA. Translation: BAE77166.1.
    M23638 Genomic DNA. Translation: AAA24661.1.
    PIRiA26367. DWECTD.
    RefSeqiNP_417587.1. NC_000913.3.
    WP_000548347.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP0AGF6.
    SMRiP0AGF6. Positions 2-325.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4262419. 9 interactions.
    DIPiDIP-48063N.
    IntActiP0AGF6. 3 interactions.
    STRINGi511145.b3117.

    Proteomic databases

    PaxDbiP0AGF6.
    PRIDEiP0AGF6.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76152; AAC76152; b3117.
    BAE77166; BAE77166; BAE77166.
    GeneIDi947633.
    KEGGiecj:JW3088.
    eco:b3117.
    PATRICi32121650. VBIEscCol129921_3211.

    Organism-specific databases

    EchoBASEiEB0983.
    EcoGeneiEG10990. tdcB.

    Phylogenomic databases

    eggNOGiENOG4105C7B. Bacteria.
    COG1171. LUCA.
    HOGENOMiHOG000046972.
    InParanoidiP0AGF6.
    KOiK01754.
    OMAiNPTINII.
    PhylomeDBiP0AGF6.

    Enzyme and pathway databases

    UniPathwayiUPA00052; UER00507.
    BioCyciEcoCyc:THREDEHYDCAT-MONOMER.
    ECOL316407:JW3088-MONOMER.
    MetaCyc:THREDEHYDCAT-MONOMER.

    Miscellaneous databases

    PROiP0AGF6.

    Family and domain databases

    InterProiIPR000634. Ser/Thr_deHydtase_PyrdxlP-BS.
    IPR005789. Thr_deHydtase_catblc.
    IPR001926. TrpB-like_PLP-dep.
    [Graphical view]
    PfamiPF00291. PALP. 1 hit.
    [Graphical view]
    SUPFAMiSSF53686. SSF53686. 1 hit.
    TIGRFAMsiTIGR01127. ilvA_1Cterm. 1 hit.
    PROSITEiPS00165. DEHYDRATASE_SER_THR. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiTDCB_ECOLI
    AccessioniPrimary (citable) accession number: P0AGF6
    Secondary accession number(s): P05792, Q2M990
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: December 20, 2005
    Last modified: September 7, 2016
    This is version 84 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

    Allosteric enzyme, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. 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.