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Entry version 112 (02 Dec 2020)
Sequence version 1 (07 Jun 2005)
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Protein

O-acetyl-ADP-ribose deacetylase

Gene

ymdB

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

Deacetylates O-acetyl-ADP ribose to yield ADP-ribose and free acetate (PubMed:21257746, PubMed:26481419). Down-regulates ribonuclease 3 (RNase III) activity. Acts by interacting directly with the region of the ribonuclease that is required for dimerization/activation (PubMed:19141481). Overexpression inhibits biofilm formation via an RNase III-independent pathway. This inhibition is RpoS-dependent (PubMed:24267348, PubMed:28582517). Overexpression also results in increased susceptibility to apramycin (PubMed:28034758, PubMed:28582517).6 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 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 0.48 sec(-1) (PubMed:21257746). kcat is 1.31 sec(-1) (PubMed:26481419).2 Publications
  1. KM=270 µM for O-acetyl-ADP-ribose1 Publication
  2. KM=430 µM for O-acetyl-ADP-ribose1 Publication

    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 sitei25SubstrateUniRule annotation1 Publication1
    <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 sitei35Proton acceptorUniRule annotation1 Publication1

    <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 processStress response

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    EcoCyc:G6550-MONOMER
    MetaCyc:G6550-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:
    O-acetyl-ADP-ribose deacetylase1 PublicationUniRule annotation (EC:3.1.1.106UniRule annotation2 Publications)
    Alternative name(s):
    Regulator of RNase III activityUniRule annotationCurated
    <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:ymdBUniRule annotation
    Ordered Locus Names:b1045, JW1032
    <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 disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi25N → A: 5-fold decrease in catalytic efficiency. Loss of activity; when associated with A-35. 1 Publication1
    Mutagenesisi35D → A: 41-fold decrease in catalytic efficiency. Loss of activity; when associated with A-25. 1 Publication1
    Mutagenesisi40R → A: Causes a 17-fold increase in the dissociation constant of the YmdB-RNase III interaction. 1 Publication1
    Mutagenesisi124G → E: Abolishes enzyme activity. 1 Publication1
    Mutagenesisi126Y → A: Loss of activity. 1 Publication1
    Mutagenesisi126Y → F: No change in activity. 1 Publication1

    Chemistry databases

    Drug and drug target database

    More...
    DrugBanki
    DB03814, 2-(N-morpholino)ethanesulfonic acid

    <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_00000891911 – 177O-acetyl-ADP-ribose deacetylaseAdd BLAST177

    Proteomic databases

    jPOST - Japan Proteome Standard Repository/Database

    More...
    jPOSTi
    P0A8D6

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

    More...
    PaxDbi
    P0A8D6

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P0A8D6

    <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

    Expression is induced by both entry into stationary phase, via RpoS, and cold-shock stress.2 Publications

    <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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homodimer (PubMed:19141481).

    Interacts with RNase III (PubMed:19141481, PubMed:25546632). Interaction with the ribonuclease decreases homodimer formation (PubMed:19141481).

    2 Publications

    GO - Molecular functioni

    Protein-protein interaction databases

    The Biological General Repository for Interaction Datasets (BioGRID)

    More...
    BioGRIDi
    4260690, 29 interactors

    Database of interacting proteins

    More...
    DIPi
    DIP-48222N

    Protein interaction database and analysis system

    More...
    IntActi
    P0A8D6, 3 interactors

    STRING: functional protein association networks

    More...
    STRINGi
    511145.b1045

    <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

    Secondary structure

    1177
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

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

    More...
    SMRi
    P0A8D6

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    P0A8D6

    <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>Domaini1 – 175MacroUniRule annotationAdd BLAST175

    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>Regioni11 – 12Substrate bindingUniRule annotation1 Publication2
    Regioni33 – 35Substrate bindingUniRule annotation1 Publication3
    Regioni122 – 126Substrate bindingUniRule annotation1 Publication5

    <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 YmdB family.UniRule annotationCurated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG2110, Bacteria

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_046550_5_1_6

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    P0A8D6

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P0A8D6

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.40.220.10, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_01205, YmdB, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR002589, Macro_dom
    IPR043472, Macro_dom-like
    IPR024900, O-Ac-ADP-ribose_deAcase

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF01661, Macro, 1 hit

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM00506, A1pp, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF52949, SSF52949, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS51154, MACRO, 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.

    P0A8D6-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MKTRIHVVQG DITKLAVDVI VNAANPSLMG GGGVDGAIHR AAGPALLDAC
    60 70 80 90 100
    LKVRQQQGDC PTGHAVITLA GDLPAKAVVH TVGPVWRGGE QNEDQLLQDA
    110 120 130 140 150
    YLNSLRLVAA NSYTSVAFPA ISTGVYGYPR AAAAEIAVKT VSEFITRHAL
    160 170
    PEQVYFVCYD EENAHLYERL LTQQGDE
    Length:177
    Mass (Da):18,880
    Last modified:June 7, 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:i6F4E12D5C181CAAF
    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
    U00096 Genomic DNA Translation: AAC74129.1
    AP009048 Genomic DNA Translation: BAA35835.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    B64847

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_415563.1, NC_000913.3
    WP_000857405.1, NZ_SSZK01000058.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAC74129; AAC74129; b1045
    BAA35835; BAA35835; BAA35835

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    49585222
    946987

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ecj:JW1032
    eco:b1045

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|1411691.4.peg.1224

    <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
    U00096 Genomic DNA Translation: AAC74129.1
    AP009048 Genomic DNA Translation: BAA35835.1
    PIRiB64847
    RefSeqiNP_415563.1, NC_000913.3
    WP_000857405.1, NZ_SSZK01000058.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1SPVX-ray2.00A1-176[»]
    5CB3X-ray1.80A1-177[»]
    5CB5X-ray2.80A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R1-177[»]
    5CMSX-ray2.98A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R1-177[»]
    SMRiP0A8D6
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    BioGRIDi4260690, 29 interactors
    DIPiDIP-48222N
    IntActiP0A8D6, 3 interactors
    STRINGi511145.b1045

    Chemistry databases

    DrugBankiDB03814, 2-(N-morpholino)ethanesulfonic acid

    Proteomic databases

    jPOSTiP0A8D6
    PaxDbiP0A8D6
    PRIDEiP0A8D6

    Genome annotation databases

    EnsemblBacteriaiAAC74129; AAC74129; b1045
    BAA35835; BAA35835; BAA35835
    GeneIDi49585222
    946987
    KEGGiecj:JW1032
    eco:b1045
    PATRICifig|1411691.4.peg.1224

    Organism-specific databases

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

    More...
    EchoBASEi
    EB3633

    Phylogenomic databases

    eggNOGiCOG2110, Bacteria
    HOGENOMiCLU_046550_5_1_6
    InParanoidiP0A8D6
    PhylomeDBiP0A8D6

    Enzyme and pathway databases

    BioCyciEcoCyc:G6550-MONOMER
    MetaCyc:G6550-MONOMER

    Miscellaneous databases

    EvolutionaryTraceiP0A8D6

    Protein Ontology

    More...
    PROi
    PR:P0A8D6

    Family and domain databases

    Gene3Di3.40.220.10, 1 hit
    HAMAPiMF_01205, YmdB, 1 hit
    InterProiView protein in InterPro
    IPR002589, Macro_dom
    IPR043472, Macro_dom-like
    IPR024900, O-Ac-ADP-ribose_deAcase
    PfamiView protein in Pfam
    PF01661, Macro, 1 hit
    SMARTiView protein in SMART
    SM00506, A1pp, 1 hit
    SUPFAMiSSF52949, SSF52949, 1 hit
    PROSITEiView protein in PROSITE
    PS51154, MACRO, 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 nameiYMDB_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: P0A8D6
    Secondary accession number(s): P75918
    <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: June 7, 2005
    Last sequence update: June 7, 2005
    Last modified: December 2, 2020
    This is version 112 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

    3D-structure, Reference proteome

    Documents

    1. Uncharacterized protein families (UPF)
      List of uncharacterized protein family (UPF) entries
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
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