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Entry version 150 (12 Aug 2020)
Sequence version 1 (01 Jan 1990)
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Protein

1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD

Gene

ampD

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

Annotation score:4 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

Involved in cell wall peptidoglycan recycling (PubMed:19309146). Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety (PubMed:19309146). Is also involved in beta-lactamase induction (PubMed:2691840, PubMed:2607970).3 Publications

<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

<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

Zn2+By similarityNote: Zn2+ is required for amidase activity.By similarity

<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 0.4 sec(-1).1 Publication
  1. KM=1760 µM for N-acetyl-beta-D-glucosamine-(1-->4)-1,6-anhydro-N-acetyl-beta-D-muramyl-L-Ala-gamma-D-Glu-meso-DAP-D-Ala-D-Ala1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> 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 bindingi34Zinc; catalyticBy 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 sitei116Proton acceptorBy similarity1
    Metal bindingi154Zinc; catalyticBy similarity1
    <p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei162Transition state stabilizerBy similarity1
    Metal bindingi164Zinc; catalyticBy 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

    <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 processCell wall biogenesis/degradation
    LigandMetal-binding, Zinc

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    EcoCyc:EG10041-MONOMER
    ECOL316407:JW0106-MONOMER
    MetaCyc:EG10041-MONOMER

    <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:
    1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpDCurated (EC:3.5.1.281 Publication)
    Alternative name(s):
    N-acetylmuramoyl-L-alanine amidaseCurated
    <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:ampD
    Ordered Locus Names:b0110, JW0106
    <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>OrganismiEscherichia coli (strain K12)
    <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 identifieri83333 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    <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
    • UP000000318 <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
    • UP000000625 Componenti: Chromosome

    <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

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    <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_00001644131 – 1831,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpDAdd BLAST183

    Proteomic databases

    jPOST - Japan Proteome Standard Repository/Database

    More...
    jPOSTi
    P13016

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

    More...
    PaxDbi
    P13016

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P13016

    <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

    Inactivation of AmpD results in AmpR-dependent hyperinduction and AmpD affects beta-lactam susceptibility in the absence of cloned C.freundii amp genes suggesting a linkage between AmpD and peptidoglycan synthesis.

    <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

    The Biological General Repository for Interaction Datasets (BioGRID)

    More...
    BioGRIDi
    4261895, 176 interactors

    STRING: functional protein association networks

    More...
    STRINGi
    511145.b0110

    <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
    P13016

    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>Domaini30 – 167N-acetylmuramoyl-L-alanine amidaseSequence analysisAdd BLAST138

    <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

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG3023, Bacteria

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_049290_1_0_6

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    P13016

    KEGG Orthology (KO)

    More...
    KOi
    K03806

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P13016

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd06583, PGRP, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.40.80.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR036505, Amidase/PGRP_sf
    IPR002502, Amidase_domain

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF01510, Amidase_2, 1 hit

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM00644, Ami_2, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF55846, SSF55846, 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.

    P13016-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MLLEQGWLVG ARRVPSPHYD CRPDDETPTL LVVHNISLPP GEFGGPWIDA
    60 70 80 90 100
    LFTGTIDPQA HPFFAEIAHL RVSAHCLIRR DGEIVQYVPF DKRAWHAGVS
    110 120 130 140 150
    QYQGRERCND FSIGIELEGT DTLAYTDAQY QQLAAVTRAL IDCYPDIAKN
    160 170 180
    MTGHCDIAPD RKTDPGPAFD WARFRVLVSK ETT
    Length:183
    Mass (Da):20,536
    Last modified:January 1, 1990 - 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:iF62910F8F889043D
    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
    X15237 Genomic DNA Translation: CAA33314.1
    U00096 Genomic DNA Translation: AAC73221.1
    AP009048 Genomic DNA Translation: BAB96679.1
    L28105 Genomic DNA Translation: AAC36921.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    S05569

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_414652.1, NC_000913.3
    WP_000923721.1, NZ_STEB01000010.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAC73221; AAC73221; b0110
    BAB96679; BAB96679; BAB96679

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    948877

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ecj:JW0106
    eco:b0110

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|1411691.4.peg.2172

    <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
    X15237 Genomic DNA Translation: CAA33314.1
    U00096 Genomic DNA Translation: AAC73221.1
    AP009048 Genomic DNA Translation: BAB96679.1
    L28105 Genomic DNA Translation: AAC36921.1
    PIRiS05569
    RefSeqiNP_414652.1, NC_000913.3
    WP_000923721.1, NZ_STEB01000010.1

    3D structure databases

    SMRiP13016
    ModBaseiSearch...

    Protein-protein interaction databases

    BioGRIDi4261895, 176 interactors
    STRINGi511145.b0110

    Proteomic databases

    jPOSTiP13016
    PaxDbiP13016
    PRIDEiP13016

    Genome annotation databases

    EnsemblBacteriaiAAC73221; AAC73221; b0110
    BAB96679; BAB96679; BAB96679
    GeneIDi948877
    KEGGiecj:JW0106
    eco:b0110
    PATRICifig|1411691.4.peg.2172

    Organism-specific databases

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

    More...
    EchoBASEi
    EB0039

    Phylogenomic databases

    eggNOGiCOG3023, Bacteria
    HOGENOMiCLU_049290_1_0_6
    InParanoidiP13016
    KOiK03806
    PhylomeDBiP13016

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10041-MONOMER
    ECOL316407:JW0106-MONOMER
    MetaCyc:EG10041-MONOMER

    Miscellaneous databases

    Protein Ontology

    More...
    PROi
    PR:P13016

    Family and domain databases

    CDDicd06583, PGRP, 1 hit
    Gene3Di3.40.80.10, 1 hit
    InterProiView protein in InterPro
    IPR036505, Amidase/PGRP_sf
    IPR002502, Amidase_domain
    PfamiView protein in Pfam
    PF01510, Amidase_2, 1 hit
    SMARTiView protein in SMART
    SM00644, Ami_2, 1 hit
    SUPFAMiSSF55846, SSF55846, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    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 nameiAMPD_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: P13016
    <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 1, 1990
    Last sequence update: January 1, 1990
    Last modified: August 12, 2020
    This is version 150 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

    Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
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