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Protein

L-threonine dehydratase catabolic TdcB

Gene

tdcB

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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.1 Publication

Catalytic activityi

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

Cofactori

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 inhibited by alpha-keto acids and other catabolites.

Kineticsi

  1. KM=16 mM for L-threonine (in the presence of 5 mM of AMP at 25 dregrees Celsius and at pH 8)1 Publication
  2. KM=32 mM for L-threonine (in the presence of 5 mM of CMP at 25 dregrees Celsius and at pH 8)1 Publication
  3. KM=123 mM for L-threonine (at 25 dregrees Celsius and at pH 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. no protein annotated in this organism
    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 – 881AMP
    Binding sitei314 – 3141AMP

    Regions

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

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Nucleotide-binding, Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciSENT99287:GCTI-3264-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:STM3244
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 329329L-threonine dehydratase catabolic TdcBPRO_0000185585Add
    BLAST

    Amino acid modifications

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

    Proteomic databases

    PaxDbiP11954.
    PRIDEiP11954.

    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).1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM3244.

    Structurei

    Secondary structure

    1
    329
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi2 – 65Combined sources
    Beta strandi7 – 93Combined sources
    Helixi11 – 2111Combined sources
    Turni22 – 243Combined sources
    Helixi34 – 407Combined sources
    Beta strandi42 – 487Combined sources
    Helixi49 – 513Combined sources
    Helixi53 – 553Combined sources
    Helixi58 – 6811Combined sources
    Helixi71 – 755Combined sources
    Beta strandi78 – 814Combined sources
    Helixi85 – 9713Combined sources
    Beta strandi101 – 1055Combined sources
    Helixi111 – 12010Combined sources
    Beta strandi123 – 1264Combined sources
    Helixi131 – 14515Combined sources
    Beta strandi152 – 1554Combined sources
    Helixi156 – 17217Combined sources
    Beta strandi178 – 1825Combined sources
    Beta strandi184 – 1863Combined sources
    Helixi187 – 19913Combined sources
    Beta strandi203 – 2108Combined sources
    Helixi215 – 2228Combined sources
    Helixi236 – 2383Combined sources
    Helixi245 – 25410Combined sources
    Beta strandi257 – 2615Combined sources
    Helixi263 – 27715Combined sources
    Helixi284 – 2863Combined sources
    Helixi287 – 2937Combined sources
    Turni294 – 2974Combined sources
    Helixi298 – 3014Combined sources
    Beta strandi304 – 3107Combined sources
    Helixi317 – 3248Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GN0X-ray1.70A/B/C/D2-329[»]
    2GN1X-ray2.20A/B2-329[»]
    2GN2X-ray2.50A2-329[»]
    ProteinModelPortaliP11954.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP11954.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C7B. Bacteria.
    COG1171. LUCA.
    HOGENOMiHOG000046972.
    KOiK01754.
    OMAiDTPCVES.
    OrthoDBiEOG6ZSP7D.
    PhylomeDBiP11954.

    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.

    P11954-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MHITYDLPVA IEDILEAKKR LAGKIYKTGM PRSNYFSERC KGEIFLKFEN
    60 70 80 90 100
    MQRTGSFKIR GAFNKLSSLT EAEKRKGVVA CSAGNHAQGV SLSCAMLGID
    110 120 130 140 150
    GKVVMPKGAP KSKVAATCDY SAEVVLHGDN FNDTIAKVSE IVETEGRIFI
    160 170 180 190 200
    PPYDDPKVIA GQGTIGLEIM EDLYDVDNVI VPIGGGGLIA GIAIAIKSIN
    210 220 230 240 250
    PTIKVIGVQA ENVHGMAASY YTGEITTHRT TGTLADGCDV SRPGNLTYEI
    260 270 280 290 300
    VRELVDDIVL VSEDEIRNSM IALIQRNKVI TEGAGALACA ALLSGKLDSH
    310 320
    IQNRKTVSII SGGNIDLSRV SQITGLVDA
    Length:329
    Mass (Da):35,141
    Last modified:December 13, 2001 - v2
    Checksum:iC1C619B021DE817C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti24 – 241K → I AA sequence (PubMed:6751404).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE006468 Genomic DNA. Translation: AAL22117.1.
    RefSeqiNP_462158.1. NC_003197.1.
    WP_000548370.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL22117; AAL22117; STM3244.
    GeneIDi1254767.
    KEGGistm:STM3244.
    PATRICi32385269. VBISalEnt20916_3440.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE006468 Genomic DNA. Translation: AAL22117.1.
    RefSeqiNP_462158.1. NC_003197.1.
    WP_000548370.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GN0X-ray1.70A/B/C/D2-329[»]
    2GN1X-ray2.20A/B2-329[»]
    2GN2X-ray2.50A2-329[»]
    ProteinModelPortaliP11954.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM3244.

    Proteomic databases

    PaxDbiP11954.
    PRIDEiP11954.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL22117; AAL22117; STM3244.
    GeneIDi1254767.
    KEGGistm:STM3244.
    PATRICi32385269. VBISalEnt20916_3440.

    Phylogenomic databases

    eggNOGiENOG4105C7B. Bacteria.
    COG1171. LUCA.
    HOGENOMiHOG000046972.
    KOiK01754.
    OMAiDTPCVES.
    OrthoDBiEOG6ZSP7D.
    PhylomeDBiP11954.

    Enzyme and pathway databases

    UniPathwayiUPA00052; UER00507.
    BioCyciSENT99287:GCTI-3264-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP11954.

    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...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.
    2. "Chemical characterization of biodegradative threonine dehydratases from two enteric bacteria."
      Kim S.S., Datta P.
      Biochim. Biophys. Acta 706:27-35(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-24.
    3. "Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate."
      Simanshu D.K., Chittori S., Savithri H.S., Murthy M.R.
      J. Biosci. 32:1195-1206(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    4. "Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation."
      Simanshu D.K., Savithri H.S., Murthy M.R.
      J. Biol. Chem. 281:39630-39641(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 2-329 IN COMPLEX WITH CMP AND PYRIDOXAL PHOSPHATE, FUNCTION AS A THREONINE DEHYDRATASE, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.

    Entry informationi

    Entry nameiTDCB_SALTY
    AccessioniPrimary (citable) accession number: P11954
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: December 13, 2001
    Last modified: February 17, 2016
    This is version 116 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

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

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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.