U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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 19-Feb-2025

Summary

Go to the top of the page Help
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].
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help
Genomic Sequence:
NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Homology

Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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

Go to the top of the page Help
Preferred Names
YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.