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Protein

Succinyl-diaminopimelate desuccinylase

Gene

dapE

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

Functioni

Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls.1 Publication

Catalytic activityi

N-succinyl-LL-2,6-diaminoheptanedioate + H2O = succinate + LL-2,6-diaminoheptanedioate.

Cofactori

Protein has several cofactor binding sites:
  • Zn2+1 PublicationNote: Binds 1 Zn2+ ion per subunit.1 Publication
  • Co2+1 PublicationNote: Binds 1 Co2+ ion per subunit.1 Publication

Kineticsi

  1. KM=0.41 mM for L,L-SDAP (in the presence of Zn2+ at pH 7.0)1 Publication

    Pathwayi: L-lysine biosynthesis via DAP pathway

    This protein is involved in step 3 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
    Metal bindingi66Cobalt or zinc 1By similarity1
    Active sitei68By similarity1
    Metal bindingi99Cobalt or zinc 1By similarity1
    Metal bindingi99Cobalt or zinc 2By similarity1
    Active sitei133Proton acceptorBy similarity1
    Metal bindingi134Cobalt or zinc 2By similarity1
    Metal bindingi162Cobalt or zinc 1By similarity1
    Metal bindingi348Cobalt or zinc 2By similarity1

    GO - Molecular functioni

    • cobalt ion binding Source: UniProtKB-HAMAP
    • metallopeptidase activity Source: InterPro
    • succinyl-diaminopimelate desuccinylase activity Source: EcoliWiki
    • zinc ion binding Source: GO_Central

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    Cobalt, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:MONOMER0-1981.
    ECOL316407:JW2456-MONOMER.
    MetaCyc:MONOMER0-1981.
    SABIO-RKP0AED7.
    UniPathwayiUPA00034; UER00021.

    Protein family/group databases

    MEROPSiM20.010.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Succinyl-diaminopimelate desuccinylase (EC:3.5.1.18)
    Short name:
    SDAP desuccinylase
    Alternative name(s):
    N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase
    Gene namesi
    Name:dapE
    Synonyms:msgB
    Ordered Locus Names:b2472, JW2456
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10208. dapE.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001852611 – 375Succinyl-diaminopimelate desuccinylaseAdd BLAST375

    Proteomic databases

    PaxDbiP0AED7.
    PRIDEiP0AED7.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    IntActiP0AED7. 6 interactors.
    STRINGi511145.b2472.

    Structurei

    3D structure databases

    ProteinModelPortaliP0AED7.
    SMRiP0AED7.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase M20A family. DapE subfamily.Curated

    Phylogenomic databases

    eggNOGiENOG4105C9Y. Bacteria.
    COG0624. LUCA.
    HOGENOMiHOG000243770.
    InParanoidiP0AED7.
    KOiK01439.
    OMAiITANLYI.
    PhylomeDBiP0AED7.

    Family and domain databases

    CDDicd03891. M20_DapE_proteobac. 1 hit.
    Gene3Di3.30.70.360. 1 hit.
    HAMAPiMF_01690. DapE. 1 hit.
    InterProiIPR001261. ArgE/DapE_CS.
    IPR005941. DapE_proteobac.
    IPR002933. Peptidase_M20.
    IPR011650. Peptidase_M20_dimer.
    [Graphical view]
    PfamiPF07687. M20_dimer. 1 hit.
    PF01546. Peptidase_M20. 1 hit.
    [Graphical view]
    SUPFAMiSSF55031. SSF55031. 1 hit.
    TIGRFAMsiTIGR01246. dapE_proteo. 1 hit.
    PROSITEiPS00758. ARGE_DAPE_CPG2_1. 1 hit.
    PS00759. ARGE_DAPE_CPG2_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0AED7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSCPVIELTQ QLIRRPSLSP DDAGCQALLI ERLQAIGFTV ERMDFADTQN
    60 70 80 90 100
    FWAWRGQGET LAFAGHTDVV PPGDADRWIN PPFEPTIRDG MLFGRGAADM
    110 120 130 140 150
    KGSLAAMVVA AERFVAQHPN HTGRLAFLIT SDEEASAHNG TVKVVEALMA
    160 170 180 190 200
    RNERLDYCLV GEPSSIEVVG DVVKNGRRGS LTCNLTIHGV QGHVAYPHLA
    210 220 230 240 250
    DNPVHRAAPF LNELVAIEWD QGNEFFPATS MQIANIQAGT GSNNVIPGEL
    260 270 280 290 300
    FVQFNFRFST ELTDEMIKAQ VLALLEKHQL RYTVDWWLSG QPFLTARGKL
    310 320 330 340 350
    VDAVVNAVEH YNEIKPQLLT TGGTSDGRFI ARMGAQVVEL GPVNATIHKI
    360 370
    NECVNAADLQ LLARMYQRIM EQLVA
    Length:375
    Mass (Da):41,269
    Last modified:December 6, 2005 - v1
    Checksum:i181F43D05E88C20E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    S41760 Genomic DNA. Translation: AAB22798.1.
    X57403 Genomic DNA. Translation: CAA40665.1.
    U00096 Genomic DNA. Translation: AAC75525.1.
    AP009048 Genomic DNA. Translation: BAA16346.1.
    PIRiA42959.
    RefSeqiNP_416967.1. NC_000913.3.
    WP_001277801.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75525; AAC75525; b2472.
    BAA16346; BAA16346; BAA16346.
    GeneIDi948313.
    KEGGiecj:JW2456.
    eco:b2472.
    PATRICi32120327. VBIEscCol129921_2566.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    S41760 Genomic DNA. Translation: AAB22798.1.
    X57403 Genomic DNA. Translation: CAA40665.1.
    U00096 Genomic DNA. Translation: AAC75525.1.
    AP009048 Genomic DNA. Translation: BAA16346.1.
    PIRiA42959.
    RefSeqiNP_416967.1. NC_000913.3.
    WP_001277801.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP0AED7.
    SMRiP0AED7.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP0AED7. 6 interactors.
    STRINGi511145.b2472.

    Protein family/group databases

    MEROPSiM20.010.

    Proteomic databases

    PaxDbiP0AED7.
    PRIDEiP0AED7.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75525; AAC75525; b2472.
    BAA16346; BAA16346; BAA16346.
    GeneIDi948313.
    KEGGiecj:JW2456.
    eco:b2472.
    PATRICi32120327. VBIEscCol129921_2566.

    Organism-specific databases

    EchoBASEiEB0204.
    EcoGeneiEG10208. dapE.

    Phylogenomic databases

    eggNOGiENOG4105C9Y. Bacteria.
    COG0624. LUCA.
    HOGENOMiHOG000243770.
    InParanoidiP0AED7.
    KOiK01439.
    OMAiITANLYI.
    PhylomeDBiP0AED7.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00021.
    BioCyciEcoCyc:MONOMER0-1981.
    ECOL316407:JW2456-MONOMER.
    MetaCyc:MONOMER0-1981.
    SABIO-RKP0AED7.

    Miscellaneous databases

    PROiP0AED7.

    Family and domain databases

    CDDicd03891. M20_DapE_proteobac. 1 hit.
    Gene3Di3.30.70.360. 1 hit.
    HAMAPiMF_01690. DapE. 1 hit.
    InterProiIPR001261. ArgE/DapE_CS.
    IPR005941. DapE_proteobac.
    IPR002933. Peptidase_M20.
    IPR011650. Peptidase_M20_dimer.
    [Graphical view]
    PfamiPF07687. M20_dimer. 1 hit.
    PF01546. Peptidase_M20. 1 hit.
    [Graphical view]
    SUPFAMiSSF55031. SSF55031. 1 hit.
    TIGRFAMsiTIGR01246. dapE_proteo. 1 hit.
    PROSITEiPS00758. ARGE_DAPE_CPG2_1. 1 hit.
    PS00759. ARGE_DAPE_CPG2_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDAPE_ECOLI
    AccessioniPrimary (citable) accession number: P0AED7
    Secondary accession number(s): P24176
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 6, 2005
    Last sequence update: December 6, 2005
    Last modified: November 2, 2016
    This is version 90 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    DapE/msgB is a multicopy suppressor of a temperature-sensitive allele of the heat shock gene grpE.

    Keywords - Technical termi

    Complete proteome, 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. Peptidase families
      Classification of peptidase families and list of entries
    4. 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.