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prfA [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 949002, updated on 24-Aug-2024

Summary

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Official Symbol
prfA
Primary source
ASAP:ABE-0004066
Locus tag
b1211
See related
ECOCYC:EG10761
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
ECK1199; sueB; uar; ups?
Summary
Overexpression causes filamentous biofilm formation. [More information is available at EcoGene: EG10761]. Release factor 1 (RF1) 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: EG10761].
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Genomic context

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Sequence:
NC_000913.3 (1265012..1266094)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase Neighboring gene outer membrane lipoprotein LolB Neighboring gene glutamyl-tRNA reductase Neighboring gene protein-(glutamine-N(5)) methyltransferase Neighboring gene SirB family protein YchQ Neighboring gene transglutaminase-like/TPR repeat-containing protein

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. Ribosome Induces a Closed to Open Conformational Change in Release Factor 1. Trappl K, et al. J Mol Biol, 2016 Mar 27. PMID 26827724
  2. Cryo-EM visualization of the ribosome in termination complex with apo-RF3 and RF1. Pallesen J, et al. Elife, 2013 Jun 4. PMID 23755360, Free PMC Article
  3. Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. Heinemann IU, et al. FEBS Lett, 2012 Oct 19. PMID 22982858, Free PMC Article
  4. Release factor one is nonessential in Escherichia coli. Johnson DB, et al. ACS Chem Biol, 2012 Aug 17. PMID 22662873, Free PMC Article
  5. Histidine 197 in release factor 1 is essential for a site binding and peptide release. Field A, et al. Biochemistry, 2010 Nov 2. PMID 20873815, Free PMC Article

See all (70) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. Data show that peptide chain release factor RF-3 (RF3) hydrolyzes GTP and dissociates from the ribosome before peptide chain release factor RF-1 (RF1)dissociation.
    Title: Mechanism of Translation Termination: RF1 Dissociation Follows Dissociation of RF3 from the Ribosome.
  5. These results indicate that RF1 undergoes a large conformational change from a closed to an open form upon binding to the ribosome.
    Title: Ribosome Induces a Closed to Open Conformational Change in Release Factor 1.
  6. In a strain lacking RF-1, phosphoserine phosphatase, and where seven UAG codons residing in essential genes were converted to UAA, phosphoserine incorporation into GFP and WNK4 was significantly elevated
    Title: Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion.
  7. Release factor one is nonessential in Escherichia coli
    Title: Release factor one is nonessential in Escherichia coli.
  8. a conformational change within the RF1.ribosome complex that results in a more tightly bound state
    Title: Histidine 197 in release factor 1 is essential for a site binding and peptide release.
  9. Hypomodification of some tRNAs can suppress the Ts phenotype caused by the RF1 mutant.
    Title: Hypomodification of the wobble base in tRNAGlu, tRNALys, and tRNAGln suppresses the temperature-sensitive phenotype caused by mutant release factor 1.
  10. RF1 mutations strongly reduce the specific termination activity of RF1 at UAG codons, and lead to hypersensitivity to Kid and RelE toxins.
    Title: Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE.
Submit: New GeneRIF Correction See all GeneRIFs (12)

General gene information

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Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ribosome binding IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
involved_in translational termination IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within translational termination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 RF1

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
    1265012..1266094
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_415729.1 peptide chain release factor RF1 [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_415729.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A376M8P3, A0A418GSB5, A0A6C9QF94, A0A7A6MJY7
    Conserved Domains (1) summary
    PRK00591
    Location:2 → 358
    prfA; peptide chain release factor 1; Validated
Nucleotide Protein
Heading Accession and Version

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