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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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