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Protein

L-threonine dehydratase catabolic TdcB

Gene

tdcB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
    Binding sitei88AMPBy similarity1
    Binding sitei314AMPBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi53 – 54AMPBy similarity2
    Nucleotide bindingi119 – 120AMPBy similarity2

    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

    Keywordsi

    Molecular functionAllosteric enzyme, Lyase
    LigandNucleotide-binding, Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciEcoCyc:THREDEHYDCAT-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10990 tdcB

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001855821 – 329L-threonine dehydratase catabolic TdcBAdd BLAST329

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei58N6-(pyridoxal phosphate)lysineBy similarity1

    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, 22 interactors
    DIPiDIP-48063N
    IntActiP0AGF6, 3 interactors
    STRINGi316385.ECDH10B_3291

    Structurei

    3D structure databases

    ProteinModelPortaliP0AGF6
    SMRiP0AGF6
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C7B Bacteria
    COG1171 LUCA
    HOGENOMiHOG000046972
    InParanoidiP0AGF6
    KOiK01754
    OMAiLIHPFDH
    PhylomeDBiP0AGF6

    Family and domain databases

    InterProiView protein in InterPro
    IPR001926 PLP-dep
    IPR000634 Ser/Thr_deHydtase_PyrdxlP-BS
    IPR005789 Thr_deHydtase_catblc
    IPR036052 Trypto_synt_PLP_dependent
    PfamiView protein in Pfam
    PF00291 PALP, 1 hit
    SUPFAMiSSF53686 SSF53686, 1 hit
    TIGRFAMsiTIGR01127 ilvA_1Cterm, 1 hit
    PROSITEiView protein in PROSITE
    PS00165 DEHYDRATASE_SER_THR, 1 hit

    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
    PATRICifig|1411691.4.peg.3613

    Similar proteinsi

    Entry informationi

    Entry nameiTDCB_ECOLI
    AccessioniPrimary (citable) accession number: P0AGF6
    Secondary accession number(s): P05792, Q2M990
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: December 20, 2005
    Last modified: March 28, 2018
    This is version 94 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    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

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