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    arfB peptidyl-tRNA hydrolase, ribosome rescue factor [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 946046, updated on 17-Dec-2024

    Summary

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    Official Symbol
    arfB
    Official Full Name
    peptidyl-tRNA hydrolase, ribosome rescue factor
    Primary source
    ECOCYC:EG12354
    Locus tag
    b0191
    See related
    ASAP:ABE-0000650
    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
    ECK0191; yaeJ
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    Genomic context

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    Sequence:
    NC_000913.3 (214833..215255)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene tRNA(Ile)-lysidine synthetase Neighboring gene modulator of Rho-dependent transcription termination Neighboring gene PF06786 family protein YaeP Neighboring gene uncharacterized protein YaeQ Neighboring gene sensor lipoprotein NlpE Neighboring gene peptidase C92 family protein YaeF

    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. Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome. Gagnon MG, et al. Science, 2012 Mar 16. PMID 22422986, Free PMC Article
    2. Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways. Chadani Y, et al. Mol Microbiol, 2011 May. PMID 21418110
    3. YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes. Handa Y, et al. Nucleic Acids Res, 2011 Mar. PMID 21051357, Free PMC Article
    4. Overproduction of NlpE, a new outer membrane lipoprotein, suppresses the toxicity of periplasmic LacZ by activation of the Cpx signal transduction pathway. Snyder WB, et al. J Bacteriol, 1995 Aug. PMID 7635808, Free PMC Article
    5. ArfA recruits RF2 into stalled ribosomes. Shimizu Y. J Mol Biol, 2012 Nov 2. PMID 22922063

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. the efficiency of the ArfA-dependent process decreases rapidly with an increase in mRNA length downstream of the A site of the ribosome whereas YaeJ function is maintained on mRNA with sufficient length.
      Title: ArfA recruits RF2 into stalled ribosomes.
    2. 3.2 A crystal structure of YaeJ bound to 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA; structure reveals the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes
      Title: Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.
    3. In this study, the authors identified the E. coli yaeJ gene, encoding a peptide-release factor homologue with GGQ motif, as a multicopy suppressor of the lethal phenotype of ssrA arfA double mutant.
      Title: Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways.
    4. Results suggest that YaeJ functions as a ribosome-attached rescue device for stalled ribosomes.
      Title: YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables aminoacyl-tRNA hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables aminoacyl-tRNA hydrolase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables aminoacyl-tRNA hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ribosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables translation release factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rescue of stalled ribosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within rescue of stalled ribosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in translational termination IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    peptidyl-tRNA hydrolase, ribosome rescue factor
    NP_414733.1

    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
      214833..215255
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_414733.1 peptidyl-tRNA hydrolase, ribosome rescue factor [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_414733.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A376RQK5
      Conserved Domains (1) summary
      PRK09256
      Location:1 → 136
      PRK09256; aminoacyl-tRNA hydrolase
    Nucleotide Protein
    Heading Accession and Version

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