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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-Experimental evidence at protein leveli

Functioni

Deacetylates O-acetyl-ADP ribose. Down-regulates ribonuclease 3 (RNase III) activity. Acts by interacting directly with the region of the ribonuclease that is required for dimerization/activation.UniRule annotation2 Publications

Kineticsi

  1. KM=270 µM for O-acetyl-ADP-ribose1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei35 – 351Proton acceptorUniRule annotation

    GO - Molecular functioni

    • enzyme binding Source: EcoCyc
    • O-acetyl-ADP-ribose deacetylase activity Source: EcoCyc
    • purine nucleoside binding Source: UniProtKB-HAMAP
    • ribonuclease inhibitor activity Source: EcoCyc

    GO - Biological processi

    • negative regulation of nuclease activity Source: EcoCyc
    • negative regulation of ribonuclease activity Source: UniProtKB-HAMAP
    • purine nucleoside metabolic process Source: UniProtKB-HAMAP
    • regulation of single-species biofilm formation on inanimate substrate Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Stress response

    Enzyme and pathway databases

    BioCyciEcoCyc:G6550-MONOMER.
    ECOL316407:JW1032-MONOMER.
    MetaCyc:G6550-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    O-acetyl-ADP-ribose deacetylaseUniRule annotation (EC:3.5.1.-UniRule annotation)
    Alternative name(s):
    Regulator of RNase III activityUniRule annotation
    Gene namesi
    Name:ymdBUniRule annotation
    Ordered Locus Names:b1045, JW1032
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13874. ymdB.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi124 – 1241G → E: Abolishes enzyme activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 177177O-acetyl-ADP-ribose deacetylasePRO_0000089191Add
    BLAST

    Proteomic databases

    PaxDbiP0A8D6.
    PRIDEiP0A8D6.

    Expressioni

    Inductioni

    Expression is induced by both entry into stationary phase, via RpoS, and cold-shock stress.1 Publication

    Interactioni

    Subunit structurei

    Homodimer. Interaction with the ribonuclease decreases homodimer formation.UniRule annotation1 Publication

    GO - Molecular functioni

    • enzyme binding Source: EcoCyc

    Protein-protein interaction databases

    BioGridi4260690. 11 interactions.
    DIPiDIP-48222N.
    IntActiP0A8D6. 3 interactions.
    STRINGi511145.b1045.

    Structurei

    Secondary structure

    1
    177
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 106Combined sources
    Helixi12 – 143Combined sources
    Beta strandi18 – 236Combined sources
    Helixi34 – 429Combined sources
    Helixi44 – 5714Combined sources
    Beta strandi65 – 695Combined sources
    Beta strandi73 – 819Combined sources
    Beta strandi87 – 926Combined sources
    Helixi93 – 11018Combined sources
    Beta strandi115 – 1184Combined sources
    Helixi130 – 14718Combined sources
    Beta strandi149 – 16012Combined sources
    Helixi161 – 17111Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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[»]
    ProteinModelPortaliP0A8D6.
    SMRiP0A8D6. Positions 3-174.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A8D6.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 175175MacroUniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni121 – 1277Substrate bindingCurated

    Sequence similaritiesi

    Belongs to the YmdB family.Curated
    Contains 1 Macro domain.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4108UVJ. Bacteria.
    COG2110. LUCA.
    HOGENOMiHOG000086960.
    InParanoidiP0A8D6.
    OMAiLLANCYW.
    PhylomeDBiP0A8D6.

    Family and domain databases

    HAMAPiMF_01205. YmdB. 1 hit.
    InterProiIPR002589. Macro_dom.
    IPR024900. O-Ac-ADP-ribose_deAcase.
    [Graphical view]
    PfamiPF01661. Macro. 1 hit.
    [Graphical view]
    SMARTiSM00506. A1pp. 1 hit.
    [Graphical view]
    PROSITEiPS51154. MACRO. 1 hit.
    [Graphical view]

    Sequencei

    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
    Checksum:i6F4E12D5C181CAAF
    GO

    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_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74129; AAC74129; b1045.
    BAA35835; BAA35835; BAA35835.
    GeneIDi946987.
    KEGGiecj:JW1032.
    eco:b1045.
    PATRICi32117327. VBIEscCol129921_1086.

    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_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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[»]
    ProteinModelPortaliP0A8D6.
    SMRiP0A8D6. Positions 3-174.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260690. 11 interactions.
    DIPiDIP-48222N.
    IntActiP0A8D6. 3 interactions.
    STRINGi511145.b1045.

    Proteomic databases

    PaxDbiP0A8D6.
    PRIDEiP0A8D6.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74129; AAC74129; b1045.
    BAA35835; BAA35835; BAA35835.
    GeneIDi946987.
    KEGGiecj:JW1032.
    eco:b1045.
    PATRICi32117327. VBIEscCol129921_1086.

    Organism-specific databases

    EchoBASEiEB3633.
    EcoGeneiEG13874. ymdB.

    Phylogenomic databases

    eggNOGiENOG4108UVJ. Bacteria.
    COG2110. LUCA.
    HOGENOMiHOG000086960.
    InParanoidiP0A8D6.
    OMAiLLANCYW.
    PhylomeDBiP0A8D6.

    Enzyme and pathway databases

    BioCyciEcoCyc:G6550-MONOMER.
    ECOL316407:JW1032-MONOMER.
    MetaCyc:G6550-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP0A8D6.
    PROiP0A8D6.

    Family and domain databases

    HAMAPiMF_01205. YmdB. 1 hit.
    InterProiIPR002589. Macro_dom.
    IPR024900. O-Ac-ADP-ribose_deAcase.
    [Graphical view]
    PfamiPF01661. Macro. 1 hit.
    [Graphical view]
    SMARTiSM00506. A1pp. 1 hit.
    [Graphical view]
    PROSITEiPS51154. MACRO. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiYMDB_ECOLI
    AccessioniPrimary (citable) accession number: P0A8D6
    Secondary accession number(s): P75918
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 7, 2005
    Last sequence update: June 7, 2005
    Last modified: September 7, 2016
    This is version 87 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Uncharacterized protein families (UPF)
      List of uncharacterized protein family (UPF) entries

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.