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Protein

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Gene

dapD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O = CoA + N-succinyl-L-2-amino-6-oxoheptanedioate.1 Publication

Enzyme regulationi

Inhibited by N-ethylmaleimide, p-chloromercuriphenyl sulfonate, cobalt and copper ions.1 Publication

Kineticsi

  1. KM=15 µM for succinyl-CoA (at pH 7.4)1 Publication
  2. KM=22 µM for tetrahydrodipicolinate (THDPA) (at pH 7.4)1 Publication

    pH dependencei

    Optimum pH is 8.2.1 Publication

    Pathwayi: L-lysine biosynthesis via DAP pathway

    This protein is involved in step 1 of the subpathway that synthesizes LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route).
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (dapD)
    2. Acetylornithine/succinyldiaminopimelate aminotransferase (argD)
    3. Succinyl-diaminopimelate desuccinylase (dapE)
    This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route), the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei104SubstrateBy similarity1
    Binding sitei141SubstrateBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    • diaminopimelate biosynthetic process Source: EcoCyc
    • lysine biosynthetic process Source: EcoCyc
    • lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
    Complete GO annotation...

    Keywords - Molecular functioni

    Acyltransferase, Transferase

    Keywords - Biological processi

    Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:MONOMER0-2001.
    ECOL316407:JW0161-MONOMER.
    MetaCyc:MONOMER0-2001.
    UniPathwayiUPA00034; UER00019.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC:2.3.1.117)
    Alternative name(s):
    Tetrahydrodipicolinate N-succinyltransferase
    Short name:
    THDP succinyltransferase
    Short name:
    THP succinyltransferase
    Short name:
    Tetrahydropicolinate succinylase
    Gene namesi
    Name:dapD
    Ordered Locus Names:b0166, JW0161
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10207. dapD.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001969331 – 2742,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferaseAdd BLAST274

    Proteomic databases

    EPDiP0A9D8.
    PaxDbiP0A9D8.
    PRIDEiP0A9D8.

    2D gel databases

    SWISS-2DPAGEP0A9D8.

    Interactioni

    Subunit structurei

    Homotrimer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-31866N.
    IntActiP0A9D8. 5 interactors.
    STRINGi511145.b0166.

    Structurei

    3D structure databases

    ProteinModelPortaliP0A9D8.
    SMRiP0A9D8.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiENOG4105DMJ. Bacteria.
    COG2171. LUCA.
    HOGENOMiHOG000003295.
    InParanoidiP0A9D8.
    KOiK00674.
    OMAiWVKKAVV.
    PhylomeDBiP0A9D8.

    Family and domain databases

    Gene3Di1.10.166.10. 1 hit.
    HAMAPiMF_00811. DapD. 1 hit.
    InterProiIPR005664. DapD_Trfase_Hexpep_rpt_fam.
    IPR001451. Hexapep.
    IPR018357. Hexapep_transf_CS.
    IPR023180. THP_succinylTrfase_dom1.
    IPR011004. Trimer_LpxA-like.
    [Graphical view]
    PANTHERiPTHR19136:SF52. PTHR19136:SF52. 1 hit.
    PfamiPF00132. Hexapep. 1 hit.
    PF14602. Hexapep_2. 1 hit.
    PF14805. THDPS_N_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF51161. SSF51161. 1 hit.
    TIGRFAMsiTIGR00965. dapD. 1 hit.
    PROSITEiPS00101. HEXAPEP_TRANSFERASES. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0A9D8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQQLQNIIET AFERRAEITP ANADTVTREA VNQVIALLDS GALRVAEKID
    60 70 80 90 100
    GQWVTHQWLK KAVLLSFRIN DNQVIEGAES RYFDKVPMKF ADYDEARFQK
    110 120 130 140 150
    EGFRVVPPAA VRQGAFIARN TVLMPSYVNI GAYVDEGTMV DTWATVGSCA
    160 170 180 190 200
    QIGKNVHLSG GVGIGGVLEP LQANPTIIED NCFIGARSEV VEGVIVEEGS
    210 220 230 240 250
    VISMGVYIGQ STRIYDRETG EIHYGRVPAG SVVVSGNLPS KDGKYSLYCA
    260 270
    VIVKKVDAKT RGKVGINELL RTID
    Length:274
    Mass (Da):29,892
    Last modified:July 19, 2005 - v1
    Checksum:i42D7A38610DD3AF6
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti31V → D in AAA23667 (PubMed:6094577).Curated1
    Sequence conflicti163G → R in AAA23667 (PubMed:6094577).Curated1
    Sequence conflicti177I → M in AAA23667 (PubMed:6094577).Curated1
    Sequence conflicti190V → L in AAA23667 (PubMed:6094577).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    K02970 Genomic DNA. Translation: AAA23667.1.
    U70214 Genomic DNA. Translation: AAB08595.1.
    U00096 Genomic DNA. Translation: AAC73277.1.
    AP009048 Genomic DNA. Translation: BAB96742.1.
    Z21842 Genomic DNA. Translation: CAA79888.1.
    PIRiF64740. XNECSD.
    RefSeqiNP_414708.1. NC_000913.3.
    WP_001186650.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73277; AAC73277; b0166.
    BAB96742; BAB96742; BAB96742.
    GeneIDi944862.
    KEGGiecj:JW0161.
    eco:b0166.
    PATRICi32115439. VBIEscCol129921_0171.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    K02970 Genomic DNA. Translation: AAA23667.1.
    U70214 Genomic DNA. Translation: AAB08595.1.
    U00096 Genomic DNA. Translation: AAC73277.1.
    AP009048 Genomic DNA. Translation: BAB96742.1.
    Z21842 Genomic DNA. Translation: CAA79888.1.
    PIRiF64740. XNECSD.
    RefSeqiNP_414708.1. NC_000913.3.
    WP_001186650.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP0A9D8.
    SMRiP0A9D8.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-31866N.
    IntActiP0A9D8. 5 interactors.
    STRINGi511145.b0166.

    2D gel databases

    SWISS-2DPAGEP0A9D8.

    Proteomic databases

    EPDiP0A9D8.
    PaxDbiP0A9D8.
    PRIDEiP0A9D8.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73277; AAC73277; b0166.
    BAB96742; BAB96742; BAB96742.
    GeneIDi944862.
    KEGGiecj:JW0161.
    eco:b0166.
    PATRICi32115439. VBIEscCol129921_0171.

    Organism-specific databases

    EchoBASEiEB0203.
    EcoGeneiEG10207. dapD.

    Phylogenomic databases

    eggNOGiENOG4105DMJ. Bacteria.
    COG2171. LUCA.
    HOGENOMiHOG000003295.
    InParanoidiP0A9D8.
    KOiK00674.
    OMAiWVKKAVV.
    PhylomeDBiP0A9D8.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00019.
    BioCyciEcoCyc:MONOMER0-2001.
    ECOL316407:JW0161-MONOMER.
    MetaCyc:MONOMER0-2001.

    Miscellaneous databases

    PROiP0A9D8.

    Family and domain databases

    Gene3Di1.10.166.10. 1 hit.
    HAMAPiMF_00811. DapD. 1 hit.
    InterProiIPR005664. DapD_Trfase_Hexpep_rpt_fam.
    IPR001451. Hexapep.
    IPR018357. Hexapep_transf_CS.
    IPR023180. THP_succinylTrfase_dom1.
    IPR011004. Trimer_LpxA-like.
    [Graphical view]
    PANTHERiPTHR19136:SF52. PTHR19136:SF52. 1 hit.
    PfamiPF00132. Hexapep. 1 hit.
    PF14602. Hexapep_2. 1 hit.
    PF14805. THDPS_N_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF51161. SSF51161. 1 hit.
    TIGRFAMsiTIGR00965. dapD. 1 hit.
    PROSITEiPS00101. HEXAPEP_TRANSFERASES. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDAPD_ECOLI
    AccessioniPrimary (citable) accession number: P0A9D8
    Secondary accession number(s): P03948
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 23, 1986
    Last sequence update: July 19, 2005
    Last modified: November 2, 2016
    This is version 98 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

    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.