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Protein

Succinyl-diaminopimelate desuccinylase

Gene

dapE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

Miscellaneous

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

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

    • metal ion binding Source: UniProtKB-KW
    • metallopeptidase activity Source: InterPro
    • succinyl-diaminopimelate desuccinylase activity Source: EcoliWiki

    GO - Biological processi

    Keywordsi

    Molecular functionHydrolase
    Biological processAmino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis
    LigandCobalt, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:MONOMER0-1981
    MetaCyc:MONOMER0-1981
    SABIO-RKiP0AED7
    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

    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

    BioGridi4261716, 4 interactors
    IntActiP0AED7, 6 interactors
    STRINGi316385.ECDH10B_2637

    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
    OMAiLNSHHDT
    PhylomeDBiP0AED7

    Family and domain databases

    CDDicd03891 M20_DapE_proteobac, 1 hit
    HAMAPiMF_01690 DapE, 1 hit
    InterProiView protein in InterPro
    IPR001261 ArgE/DapE_CS
    IPR036264 Bact_exopeptidase_dim_dom
    IPR005941 DapE_proteobac
    IPR002933 Peptidase_M20
    IPR011650 Peptidase_M20_dimer
    PfamiView protein in Pfam
    PF07687 M20_dimer, 1 hit
    PF01546 Peptidase_M20, 1 hit
    SUPFAMiSSF55031 SSF55031, 1 hit
    TIGRFAMsiTIGR01246 dapE_proteo, 1 hit
    PROSITEiView protein in PROSITE
    PS00758 ARGE_DAPE_CPG2_1, 1 hit
    PS00759 ARGE_DAPE_CPG2_2, 1 hit

    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
    PATRICifig|1411691.4.peg.4268

    Similar proteinsi

    Entry informationi

    Entry nameiDAPE_ECOLI
    AccessioniPrimary (citable) accession number: P0AED7
    Secondary accession number(s): P24176
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 6, 2005
    Last sequence update: December 6, 2005
    Last modified: March 28, 2018
    This is version 98 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, Reference proteome
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health