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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>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

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

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

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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
    <p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi66Cobalt or zinc 1By similarity1
    <p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>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

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    • diaminopimelate biosynthetic process Source: UniProtKB-UniRule
    • lysine biosynthetic process via diaminopimelate Source: EcoCyc

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    EcoCyc:MONOMER0-1981
    MetaCyc:MONOMER0-1981

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    P0AED7

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00034;UER00021

    Protein family/group databases

    MEROPS protease database

    More...
    MEROPSi
    M20.010

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:dapE
    Synonyms:msgB
    Ordered Locus Names:b2472, JW2456
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    Escherichia coli strain K12 genome database

    More...
    EcoGenei
    EG10208 dapE

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    GO - Cellular componenti

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001852611 – 375Succinyl-diaminopimelate desuccinylaseAdd BLAST375

    Proteomic databases

    jPOST - Japan Proteome Standard Repository/Database

    More...
    jPOSTi
    P0AED7

    PaxDb, a database of protein abundance averages across all three domains of life

    More...
    PaxDbi
    P0AED7

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P0AED7

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homodimer.1 Publication

    GO - Molecular functioni

    Protein-protein interaction databases

    The Biological General Repository for Interaction Datasets (BioGrid)

    More...
    BioGridi
    4261716, 4 interactors

    Protein interaction database and analysis system

    More...
    IntActi
    P0AED7, 6 interactors

    STRING: functional protein association networks

    More...
    STRINGi
    316385.ECDH10B_2637

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    3D structure databases

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    P0AED7

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    P0AED7

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    <p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the peptidase M20A family. DapE subfamily.Curated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4105C9Y Bacteria
    COG0624 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000243770

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    P0AED7

    KEGG Orthology (KO)

    More...
    KOi
    K01439

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P0AED7

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd03891 M20_DapE_proteobac, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_01690 DapE, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR001261 ArgE/DapE_CS
    IPR036264 Bact_exopeptidase_dim_dom
    IPR005941 DapE_proteobac
    IPR002933 Peptidase_M20
    IPR011650 Peptidase_M20_dimer

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF07687 M20_dimer, 1 hit
    PF01546 Peptidase_M20, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF55031 SSF55031, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR01246 dapE_proteo, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00758 ARGE_DAPE_CPG2_1, 1 hit
    PS00759 ARGE_DAPE_CPG2_2, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i181F43D05E88C20E
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    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

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    A42959

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_416967.1, NC_000913.3
    WP_001277801.1, NZ_LN832404.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAC75525; AAC75525; b2472
    BAA16346; BAA16346; BAA16346

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    948313

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ecj:JW2456
    eco:b2472

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|1411691.4.peg.4268

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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

    BioGridi4261716, 4 interactors
    IntActiP0AED7, 6 interactors
    STRINGi316385.ECDH10B_2637

    Protein family/group databases

    MEROPSiM20.010

    Proteomic databases

    jPOSTiP0AED7
    PaxDbiP0AED7
    PRIDEiP0AED7

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75525; AAC75525; b2472
    BAA16346; BAA16346; BAA16346
    GeneIDi948313
    KEGGiecj:JW2456
    eco:b2472
    PATRICifig|1411691.4.peg.4268

    Organism-specific databases

    EchoBASE - an integrated post-genomic database for E. coli

    More...
    EchoBASEi
    EB0204
    EcoGeneiEG10208 dapE

    Phylogenomic databases

    eggNOGiENOG4105C9Y Bacteria
    COG0624 LUCA
    HOGENOMiHOG000243770
    InParanoidiP0AED7
    KOiK01439
    PhylomeDBiP0AED7

    Enzyme and pathway databases

    UniPathwayi
    UPA00034;UER00021

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

    Miscellaneous databases

    Protein Ontology

    More...
    PROi
    PR:P0AED7

    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

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiDAPE_ECOLI
    <p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0AED7
    Secondary accession number(s): P24176
    <p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 6, 2005
    Last sequence update: December 6, 2005
    Last modified: January 16, 2019
    This is version 103 of the entry and version 1 of the sequence. See complete history.
    <p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    2. SIMILARITY comments
      Index of protein domains and families
    3. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    4. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
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