{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"P36675","secondaryAccessions":["Q2EET4","Q2M6V6"],"uniProtkbId":"ARFA_ECOLI","entryAudit":{"firstPublicDate":"1994-06-01","lastAnnotationUpdateDate":"2026-09-02","lastSequenceUpdateDate":"1994-06-01","entryVersion":144,"sequenceVersion":1},"annotationScore":5.0,"organism":{"scientificName":"Escherichia coli (strain K12)","taxonId":83333,"lineage":["Bacteria","Pseudomonadati","Pseudomonadota","Gammaproteobacteria","Enterobacterales","Enterobacteriaceae","Escherichia"]},"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"21062370"}],"value":"Alternative ribosome-rescue factor A"}}},"genes":[{"geneName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"21062370"}],"value":"arfA"},"synonyms":[{"value":"yhdL"}],"orderedLocusNames":[{"value":"b4550"},{"value":"JW3253"}]}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21062370"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21435036"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22857598"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22922063"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25355516"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27906160"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27906161"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27934701"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28077875"}],"value":"Rescues ribosomes stalled at the 3' end of non-stop mRNAs (PubMed:21062370, PubMed:21435036). This activity is crucial when the stalled ribosome cannot be rescued by the SsrA(tmRNA)-SmpB quality control system (PubMed:21062370, PubMed:21435036). Binds the 30S subunit, contacting 16S rRNA with the N-terminus near the decoding center and its C-terminus in the mRNA entry channel; contacts change in the presence of release factor 2 (RF2, also named PrfB) (PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Requires RF2/PrfB to hydrolyze stalled peptidyl-tRNA on the ribosome; recruits and probably helps position RF2/PrfB correctly in the ribosomal A site so RF2's GGQ motif can hydrolyze the peptidyl-tRNA bond (PubMed:22857598, PubMed:22922063, PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Does not release ribosomes with a programmed pause caused by regulatory chains such as SecM-mediated pausing (PubMed:22857598). Binds tRNA which may stimulate its ribosome rescue activity (PubMed:22857598)"}],"commentType":"FUNCTION"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21062370"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25355516"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27906160"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27906161"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27934701"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28077875"}],"value":"Interacts with the 50S ribosomal subunit (PubMed:21062370, PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Interacts with RF2/PrfB on the ribosome (PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Contacts ribosomal protein S12 (rpsL) (PubMed:27906160, PubMed:27906161)"}],"commentType":"SUBUNIT"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21062370"}],"value":"Cells lacking this gene are viable, but those lacking both arfA and ssrA are non-viable (PubMed:21062370)"}],"commentType":"DISRUPTION PHENOTYPE"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"21435036"},{"evidenceCode":"ECO:0000305","source":"PubMed","id":"21952205"}],"value":"Active protein is only produced when SsrA(tmRNA)-SmpB-mediated trans translation is limited. ArfA can be synthesized from truncated mRNA, via ribonuclease 3 and the SsrA tagging system. The arfA mRNA is cleaved by ribonuclease 3 within a hairpin structure, probably immediately after the Gly-55 codon, which produces a truncated non-stop transcript and leads to ribosome arrest. In the presence of SsrA, the stalled ribosome is rescued and the incomplete nascent ArfA is tagged for degradation. In the absence of SsrA, truncated ArfA chains are released from the ribosome and are functional. Truncated ArfA could be more active than full-length protein (PubMed:21435036, PubMed:21952205)"}],"commentType":"MISCELLANEOUS"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"Belongs to the alternative ribosome-rescue factor A family"}],"commentType":"SIMILARITY"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27906160"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27906161"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27934701"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28077875"}],"value":"In all 3D-structures with RF2/PrfB and the 70S ribosome this protein is seen to contact 16S rRNA (PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). In most is also seen to contact 23S rRNA (PubMed:27906160, PubMed:27934701, PubMed:28077875). Contact with ribosomal protein S12 is also reported sometimes (PubMed:27906160, PubMed:27906161). These discrepancies may be due to interpretation of results"}],"commentType":"CAUTION"}],"features":[{"type":"Chain","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":72,"modifier":"EXACT"}},"description":"Alternative ribosome-rescue factor A","featureId":"PRO_0000169494"},{"type":"Region","location":{"start":{"value":30,"modifier":"EXACT"},"end":{"value":53,"modifier":"EXACT"}},"description":"Disordered","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Compositional bias","location":{"start":{"value":33,"modifier":"EXACT"},"end":{"value":47,"modifier":"EXACT"}},"description":"Basic residues","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Mutagenesis","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":18,"modifier":"EXACT"}},"description":"90% decrease in kcat for peptidyl-transferase by RF2.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28077875"}],"alternativeSequence":{}},{"type":"Mutagenesis","location":{"start":{"value":8,"modifier":"EXACT"},"end":{"value":8,"modifier":"EXACT"}},"description":"75% decrease in kcat for peptidyl-transferase by RF2.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28077875"}],"alternativeSequence":{"originalSequence":"K","alternativeSequences":["A"]}},{"type":"Mutagenesis","location":{"start":{"value":9,"modifier":"EXACT"},"end":{"value":9,"modifier":"EXACT"}},"description":"75% decrease in kcat for peptidyl-transferase by RF2.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28077875"}],"alternativeSequence":{"originalSequence":"G","alternativeSequences":["V"]}},{"type":"Mutagenesis","location":{"start":{"value":11,"modifier":"EXACT"},"end":{"value":11,"modifier":"EXACT"}},"description":"90% decrease in kcat for peptidyl-transferase by RF2.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28077875"}],"alternativeSequence":{"originalSequence":"I","alternativeSequences":["N"]}},{"type":"Mutagenesis","location":{"start":{"value":18,"modifier":"EXACT"},"end":{"value":18,"modifier":"EXACT"}},"description":"No change in ribosome rescue activity.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25355516"}],"alternativeSequence":{"originalSequence":"A","alternativeSequences":["C"]}},{"type":"Mutagenesis","location":{"start":{"value":18,"modifier":"EXACT"},"end":{"value":18,"modifier":"EXACT"}},"description":"Loss of ribosome rescue activity. 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