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    yefM YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 946542, updated on 3-Dec-2024

    Summary

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    Official Symbol
    yefM
    Official Full Name
    YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor
    Primary source
    ECOCYC:EG12844
    Locus tag
    b2017
    See related
    ASAP:ABE-0006705
    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
    ECK2012
    Summary
    Homologous to phage P1 Phd antitoxin and Enterococcus faecium antitoxin, Axe. [More information is available at EcoGene: EG12844]. YoeB and YefM are a toxin-antitoxin pair . [More information is available at EcoCyc: EG12844].
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    Genomic context

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    Sequence:
    NC_000913.3 (2089462..2089713, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene putative DNA-binding transcriptional regulator YeeY Neighboring gene putative epimerase YeeZ Neighboring gene ribosome-dependent mRNA interferase toxin YoeB Neighboring gene his operon leader peptide Neighboring gene ATP phosphoribosyltransferase

    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. Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system. Xue L, et al. Nucleic Acids Res, 2020 Oct 9. PMID 32845304, Free PMC Article
    2. The YefM antitoxin defines a family of natively unfolded proteins: implications as a novel antibacterial target. Cherny I, et al. J Biol Chem, 2004 Feb 27. PMID 14672926
    3. The YoeB toxin is a folded protein that forms a physical complex with the unfolded YefM antitoxin. Implications for a structural-based differential stability of toxin-antitoxin systems. Cherny I, et al. J Biol Chem, 2005 Aug 26. PMID 15980067
    4. Genetic organization of the Francisella plasmid pFNL10. Pomerantsev AP, et al. Plasmid, 2001 Nov. PMID 11735370
    5. The yefM-yoeB toxin-antitoxin systems of Escherichia coli and Streptococcus pneumoniae: functional and structural correlation. Nieto C, et al. J Bacteriol, 2007 Feb. PMID 17071753, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system.
      Title: Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system.
    2. Based on molecular modeling, selected amino acid residues were changed to assess which positions were crucial in the specificity of toxin-antitoxin interaction in the related Axe-Txe and YefM-YoeB complexes.
      Title: Amino acid residues crucial for specificity of toxin-antitoxin interactions in the homologous Axe-Txe and YefM-YoeB complexes.
    3. YefM is an autorepressor that initially recognizes a long palindrome containing the core hexamer, followed by binding to a short repeat.
      Title: Influence of operator site geometry on transcriptional control by the YefM-YoeB toxin-antitoxin complex.
    4. The effect of yefM and yoeB from Streptococcus pneumoniae (S. pneumoniae) on E. coli, and the interaction of the proteins from E. coli with the S. pneumoniae proteins are reported.
      Title: The yefM-yoeB toxin-antitoxin systems of Escherichia coli and Streptococcus pneumoniae: functional and structural correlation.
    5. YefM is the primary transcriptional repressor of the yefM-yoeB cassette.
      Title: Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression.
    6. Interaction of YefM with YoeB in the YefM2/YoeB heterotrimer induces conformational changes in the RNase catalytic site of YoeB, an enzyme that preferentially cleaves at the 3' end of purine ribonucleotides
      Title: Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables toxic substance binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of growth NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within single-species biofilm formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of toxin-antitoxin complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor

    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
      2089462..2089713 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_416521.2 YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_416521.2

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A8S7I337
      Conserved Domains (1) summary
      PRK11409
      Location:1 → 83
      PRK11409; YoeB-YefM toxin-antitoxin system antitoxin YefM
    Nucleotide Protein
    Heading Accession and Version

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