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    ymdB 2'-O-acetyl-ADP-ribose deacetylase, regulator of RNase III activity [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 946987, updated on 3-Dec-2024

    Summary

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    Official Symbol
    ymdB
    Official Full Name
    2'-O-acetyl-ADP-ribose deacetylase, regulator of RNase III activity
    Primary source
    ECOCYC:G6550
    Locus tag
    b1045
    See related
    ASAP:ABE-0003549
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    ECK1031
    Summary
    RpoS regulon. [More information is available at EcoGene: EG13874].
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    Genomic context

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    Sequence:
    NC_000913.3 (1105820..1106353)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene curlin chaperone Neighboring gene uncharacterized protein YmdA Neighboring gene cardiolipin synthase C Neighboring gene osmoregulated periplasmic glucans (OPG) biosynthesis protein C

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. YmdB-mediated down-regulation of sucA inhibits biofilm formation and induces apramycin susceptibility in Escherichia coli. Kim M, et al. Biochem Biophys Res Commun, 2017 Jan 29. PMID 28034758
    2. Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator. Kim T, et al. BMC Microbiol, 2013 Nov 24. PMID 24267348, Free PMC Article
    3. The unusual substrate specificity of Escherichia coli cardiolipin synthase C does not require the product of the transcriptionally engaged ymdB gene. Sawasato K, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2024 Jun. PMID 38527666
    4. Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB. Paudyal S, et al. Proteins, 2015 Mar. PMID 25546632, Free PMC Article
    5. 10Sa RNA: processing by and inhibition of RNase III. Makarov EM, et al. Biochem Int, 1992 May. PMID 1378735

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The unusual substrate specificity of Escherichia coli cardiolipin synthase C does not require the product of the transcriptionally engaged ymdB gene.
      Title: The unusual substrate specificity of Escherichia coli cardiolipin synthase C does not require the product of the transcriptionally engaged ymdB gene.
    2. Studied atomic-level features of YmdB-RNase III interaction.
      Title: Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB.
    3. This is the first global profile of target genes modulated by YmdB-induced RNase III inhibition in Escherichia coli, and the data reveal a novel, hitherto unrecognized regulatory role for YmdB in biofilm modulation.
      Title: Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables O-acetyl-ADP-ribose deacetylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables O-acetyl-ADP-ribose deacetylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables O-acetyl-ADP-ribose deacetylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables deacetylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables endoribonuclease inhibitor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables purine nucleoside binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ribonuclease inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in purine nucleoside metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of single-species biofilm formation on inanimate substrate IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to antibiotic IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    2'-O-acetyl-ADP-ribose deacetylase, regulator of RNase III activity
    NP_415563.1

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      1105820..1106353
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_415563.1 2'-O-acetyl-ADP-ribose deacetylase, regulator of RNase III activity [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_415563.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A8T6PQ89
      Conserved Domains (1) summary
      PRK00431
      Location:1 → 177
      PRK00431; ADP-ribose-binding protein
    Nucleotide Protein
    Heading Accession and Version

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