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    prfB peptide chain release factor RF2 [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947369, updated on 3-Dec-2024

    Summary

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    Official Symbol
    prfB
    Official Full Name
    peptide chain release factor RF2
    Primary source
    ECOCYC:EG10762
    Locus tag
    b2891
    See related
    ASAP:ABE-0009488
    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
    ECK2886; supK
    Summary
    The ribosome changes reading frame after codon 25. [More information is available at EcoGene: EG10762]. Release factor 2 (RF2) is one of two class 1 codon-specific factors in Escherichia coli that facilitate the release of the growing polypeptide chain at stop codons. [More information is available at EcoCyc: EG10762].
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    Genomic context

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    Sequence:
    NC_000913.3 (3035184..3036282, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene isopentenyl-diphosphate Delta-isomerase Neighboring gene lysine--tRNA ligase Neighboring gene ssDNA-specific exonuclease RecJ Neighboring gene protein disulfide isomerase DsbC

    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. Transfer ribonucleic acid methylase deficiency found in UGA supressor strains. Reeves RH, et al. J Bacteriol, 1975 Oct. PMID 1100607, Free PMC Article
    2. Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2. Scarlett DJ, et al. J Biol Chem, 2003 Apr 25. PMID 12458201
    3. A cryo-electron microscopic study of ribosome-bound termination factor RF2. Rawat UB, et al. Nature, 2003 Jan 2. PMID 12511960
    4. Structure of the Escherichia coli ribosomal termination complex with release factor 2. Klaholz BP, et al. Nature, 2003 Jan 2. PMID 12511961
    5. Maintaining the ribosomal reading frame: the influence of the E site during translational regulation of release factor 2. Márquez V, et al. Cell, 2004 Jul 9. PMID 15242643

    See all (80) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide.
      Title: Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide.
    2. Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue.
      Title: Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue.
    3. In translation termination, the catalytic GGQ loop of RF2 is rearranged into a long beta-hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit.
      Title: Extensive ribosome and RF2 rearrangements during translation termination.
    4. Study used time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 A resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.
      Title: The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.
    5. Ribosome termination complexes that carry two factors, RF1-RF3 or RF2-RF3, are dynamic and fluctuate between non-rotated and rotated states, whereas each factor alone has its distinct signature on ribosome dynamics and conformation.
      Title: Dynamics of ribosomes and release factors during translation termination in E. coli.
    6. both RF1 binding and RF2 binding are sufficient to shift the population of posthydrolysis ribosome complexes from primarily the rotated to the nonrotated state only when a cognate stop codon is present in the A-site.
      Title: Operative Binding of Class I Release Factors and YaeJ Stabilizes the Ribosome in the Nonrotated State.
    7. The structures demonstrate how ArfA 'senses' the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled.
      Title: Mechanism of ribosome rescue by ArfA and RF2.
    8. The authors characterized the ArfA pathway of non-productive translation complexe resolution in vitro and identified RF2 as a factor that cooperates with ArfA to hydrolyse peptidyl-tRNAs located in the P-site of the stalled ribosome.
      Title: ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis in Escherichia coli.
    9. RF2 binds to stalled ribosomes only in the presence of ArfA, demonstrating that ArfA recruits RF2 into the A site of the ribosome to facilitate peptidyl-tRNA hydrolysis.
      Title: ArfA recruits RF2 into stalled ribosomes.
    10. Mutations at the two positions on 23S rRNA did not affect aminoacyl-tRNA (aa-tRNA) accommodation, peptide bond formation, or the fidelity of aa-tRNA selection, but impaired RF2-catalyzed peptide release.
      Title: Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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 translation release factor activity, codon specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables translation release factor activity, codon specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within translational termination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in translational termination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in viral translational frameshifting IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    peptide chain release factor RF2

    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
      3035184..3036282 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417367.1 peptide chain release factor RF2 [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417367.1

      Status: PROVISIONAL

      UniProtKB/Swiss-Prot
      A8A432
      UniProtKB/TrEMBL
      A0A418GJ44, A0A7A7FUM9, A0A8S7CIS2
      Conserved Domains (1) summary
      PRK00578
      Location:3 → 365
      prfB; peptide chain release factor 2; Validated
    Nucleotide Protein
    Heading Accession and Version

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