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Entry version 102 (02 Jun 2021)
Sequence version 2 (16 Jun 2009)
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Protein

Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase

Gene

ykfC

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:3 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

Specifically hydrolyzes gamma-D-glutamyl-L-lysine bonds in murein peptides, releasing L-Ala-D-Glu.

1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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

  • The enzyme releases L-Ala-gamma-D-Glu dipeptides from cell wall peptides via cleavage of an L-Ala-gamma-D-Glu-|-L-Lys bond.1 Publication EC:3.4.14.13

<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

kcat is 5.7 sec(-1) with L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala as substrate. kcat is 2.6 sec(-1) with L-Ala-gamma-D-Glu-L-Lys-D-Ala as substrate. kcat is 1.2 sec(-1) with L-Ala-gamma-D-Glu-L-Lys as substrate.1 Publication
  1. KM=310 µM for L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala1 Publication
  2. KM=120 µM for L-Ala-gamma-D-Glu-L-Lys-D-Ala1 Publication
  3. KM=290 µM for L-Ala-gamma-D-Glu-L-Lys1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: peptidoglycan degradation

    This protein is involved in the pathway peptidoglycan degradation, which is part of Cell wall degradation.1 Publication
    View all proteins of this organism that are known to be involved in the pathway peptidoglycan degradation and in Cell wall degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei90SubstrateBy similarity1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> 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 sitei200NucleophilePROSITE-ProRule annotation1
    Active sitei253Proton acceptorPROSITE-ProRule annotation1
    Active sitei265PROSITE-ProRule annotation1

    <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

    <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, Protease, Thiol protease
    Biological processCell wall biogenesis/degradation

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    BSUB:BSU12990-MONOMER

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    3.4.14.13, 658

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    O35010

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

    More...
    UniPathwayi
    UPA00549

    Protein family/group databases

    MEROPS protease database

    More...
    MEROPSi
    C40.009

    <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%5Fand%5Ftaxonomy%5Fsection">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:
    Gamma-D-glutamyl-L-lysine dipeptidyl-peptidaseCurated (EC:3.4.14.131 Publication)
    Alternative name(s):
    Cell wall endopeptidase YkfCCurated
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:ykfC
    Ordered Locus Names:BSU12990
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiBacillus subtilis (strain 168)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri224308 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
    • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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

    <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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003608121 – 296Gamma-D-glutamyl-L-lysine dipeptidyl-peptidaseAdd BLAST296

    Proteomic databases

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

    More...
    PaxDbi
    O35010

    PRoteomics IDEntifications database

    More...
    PRIDEi
    O35010

    <p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

    <p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

    Repressed by AbrB, a transcription factor that negatively controls biofilm formation.1 Publication

    <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

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    224308.BSU12990

    <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

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

    More...
    SMRi
    O35010

    Database of comparative protein structure models

    More...
    ModBasei
    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

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini170 – 295NlpC/P60PROSITE-ProRule annotationAdd BLAST126

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni199 – 201Substrate bindingBy similarity3
    Regioni218 – 219Substrate bindingBy similarity2

    <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 C40 family.PROSITE-ProRule annotationCurated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG0791, Bacteria

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    O35010

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    YEEKLWL

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    O35010

    Family and domain databases

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR000064, NLP_P60_dom
    IPR038765, Papain-like_cys_pep_sf

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00877, NLPC_P60, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF54001, SSF54001, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS51935, NLPC_P60, 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%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

    O35010-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MMHTVISAVA NIWTAPDSPR PSDQFMLQPT VMIRDWLERM TYDERLGLCT
    60 70 80 90 100
    DNVIQTQVLF GEKVLVTAEQ GEWVSVIVPS QPSRKDPRGY PGWMKKYQLE
    110 120 130 140 150
    KTKPIHTQHD VMISKPAAFL YRSNGEKEIE LSFLTVLPLI AKENGYFKVS
    160 170 180 190 200
    TVFGERFVRQ SDAVPVSQQK GTAEDIIQTG AFFLGLPYLW GGISGFGFDC
    210 220 230 240 250
    SGFMYSIFKA NGYSIPRDAG DQAKAGKGVP LDDMKAGDLL FFAYEEGKGA
    260 270 280 290
    IHHVGLYVGG GKMLHSPKTG KSIEILTLTE TIYEKELCAV RRCFSE
    Length:296
    Mass (Da):33,025
    Last modified:June 16, 2009 - v2
    <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:i6B1F0F4480D4FC1E
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti228G → V in CAA05579 (Ref. 1) Curated1

    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
    AJ002571 Genomic DNA Translation: CAA05579.1
    AL009126 Genomic DNA Translation: CAB13156.2

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    A69856

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_389182.2, NC_000964.3
    WP_003245577.1, NZ_JNCM01000035.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CAB13156; CAB13156; BSU_12990

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    937979

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    bsu:BSU12990

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|224308.179.peg.1411

    <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
    AJ002571 Genomic DNA Translation: CAA05579.1
    AL009126 Genomic DNA Translation: CAB13156.2
    PIRiA69856
    RefSeqiNP_389182.2, NC_000964.3
    WP_003245577.1, NZ_JNCM01000035.1

    3D structure databases

    SMRiO35010
    ModBaseiSearch...

    Protein-protein interaction databases

    STRINGi224308.BSU12990

    Protein family/group databases

    MEROPSiC40.009

    Proteomic databases

    PaxDbiO35010
    PRIDEiO35010

    Genome annotation databases

    EnsemblBacteriaiCAB13156; CAB13156; BSU_12990
    GeneIDi937979
    KEGGibsu:BSU12990
    PATRICifig|224308.179.peg.1411

    Phylogenomic databases

    eggNOGiCOG0791, Bacteria
    InParanoidiO35010
    OMAiYEEKLWL
    PhylomeDBiO35010

    Enzyme and pathway databases

    UniPathwayiUPA00549
    BioCyciBSUB:BSU12990-MONOMER
    BRENDAi3.4.14.13, 658
    SABIO-RKiO35010

    Family and domain databases

    InterProiView protein in InterPro
    IPR000064, NLP_P60_dom
    IPR038765, Papain-like_cys_pep_sf
    PfamiView protein in Pfam
    PF00877, NLPC_P60, 1 hit
    SUPFAMiSSF54001, SSF54001, 1 hit
    PROSITEiView protein in PROSITE
    PS51935, NLPC_P60, 1 hit

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    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 nameiYKFC_BACSU
    <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: O35010
    Secondary accession number(s): Q796M4
    <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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 20, 2009
    Last sequence update: June 16, 2009
    Last modified: June 2, 2021
    This is version 102 of the entry and version 2 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

    Reference proteome

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families
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