ARFA_ECOLI
ID ARFA_ECOLI Reviewed; 72 AA.
AC P36675; Q2EET4; Q2M6V6;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Alternative ribosome-rescue factor A {ECO:0000303|PubMed:21062370};
GN Name=arfA {ECO:0000303|PubMed:21062370}; Synonyms=yhdL;
GN OrderedLocusNames=b4550, JW3253;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8063098; DOI=10.1016/0378-1119(94)90847-8;
RA Christie G.E., White T.J., Goodwin T.S.;
RT "A merR homologue at 74 minutes on the Escherichia coli genome.";
RL Gene 146:131-132(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP FUNCTION, INTERACTION WITH RIBOSOME, DISRUPTION PHENOTYPE, MUTAGENESIS OF
RP ALA-18, AND GENE NAME.
RC STRAIN=K12 / W3110;
RX PubMed=21062370; DOI=10.1111/j.1365-2958.2010.07375.x;
RA Chadani Y., Ono K., Ozawa S., Takahashi Y., Takai K., Nanamiya H.,
RA Tozawa Y., Kutsukake K., Abo T.;
RT "Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans-
RT translation system.";
RL Mol. Microbiol. 78:796-808(2010).
RN [5]
RP FUNCTION, REGULATION OF SYNTHESIS, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=21435036; DOI=10.1111/j.1365-2958.2011.07638.x;
RA Garza-Sanchez F., Schaub R.E., Janssen B.D., Hayes C.S.;
RT "tmRNA regulates synthesis of the ArfA ribosome rescue factor.";
RL Mol. Microbiol. 80:1204-1219(2011).
RN [6]
RP REGULATION OF SYNTHESIS.
RC STRAIN=K12 / W3110;
RX PubMed=21952205; DOI=10.1266/ggs.86.151;
RA Chadani Y., Matsumoto E., Aso H., Wada T., Kutsukake K., Sutou S., Abo T.;
RT "trans-translation-mediated tight regulation of the expression of the
RT alternative ribosome-rescue factor ArfA in Escherichia coli.";
RL Genes Genet. Syst. 86:151-163(2011).
RN [7]
RP FUNCTION, TRNA-BINDING, AND MUTAGENESIS OF ALA-18.
RX PubMed=22857598; DOI=10.1111/j.1365-2958.2012.08190.x;
RA Chadani Y., Ito K., Kutsukake K., Abo T.;
RT "ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-
RT tRNA hydrolysis in Escherichia coli.";
RL Mol. Microbiol. 86:37-50(2012).
RN [8]
RP FUNCTION, AND MUTAGENESIS OF ALA-18.
RX PubMed=22922063; DOI=10.1016/j.jmb.2012.08.007;
RA Shimizu Y.;
RT "ArfA recruits RF2 into stalled ribosomes.";
RL J. Mol. Biol. 423:624-631(2012).
RN [9]
RP FUNCTION, SUBUNIT, INTERACTION WITH 16S RRNA, AND MUTAGENESIS OF ALA-18 AND
RP LYS-34.
RX PubMed=25355516; DOI=10.1093/nar/gku1069;
RA Kurita D., Chadani Y., Muto A., Abo T., Himeno H.;
RT "ArfA recognizes the lack of mRNA in the mRNA channel after RF2 binding for
RT ribosome rescue.";
RL Nucleic Acids Res. 42:13339-13352(2014).
RN [10]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.0 ANGSTROMS) OF 1-55 IN COMPLEX WITH
RP 70S RIBOSOME AND RF2, FUNCTION, INTERACTION WITH RF2, INTERACTION WITH S12,
RP INTERACTION WITH 16S RRNA, INTERACTION WITH 23S RRNA, AND MUTAGENESIS OF
RP LEU-20; ARG-28; LYS-34; GLY-35; TYR-39 AND ARG-41.
RX PubMed=27906160; DOI=10.1038/nature20822;
RA Ma C., Kurita D., Li N., Chen Y., Himeno H., Gao N.;
RT "Mechanistic insights into the alternative translation termination by ArfA
RT and RF2.";
RL Nature 541:550-553(2017).
RN [11] {ECO:0007744|PDB:5MGP}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.1 ANGSTROMS) OF 2-46 IN COMPLEX WITH
RP 70S RIBOSOME AND RF2, FUNCTION, INTERACTION WITH RF2, INTERACTION WITH S12,
RP AND INTERACTION WITH 16S RRNA.
RX PubMed=27906161; DOI=10.1038/nature20821;
RA Huter P., Mueller C., Beckert B., Arenz S., Berninghausen O., Beckmann R.,
RA Wilson D.N.;
RT "Structural basis for ArfA-RF2-mediated translation termination on mRNAs
RT lacking stop codons.";
RL Nature 541:546-549(2017).
RN [12] {ECO:0007744|PDB:5MDV, ECO:0007744|PDB:5MDW, ECO:0007744|PDB:5MDY}
RP STRUCTURE BY ELECTRON MICROSCOPY (2.97 ANGSTROMS) OF 1-60 IN COMPLEX WITH
RP 70S RIBOSOME AND RF2, FUNCTION, INTERACTION WITH RF2, INTERACTION WITH 16S
RP RRNA, AND INTERACTION WITH 23S RRNA.
RX PubMed=27934701; DOI=10.1126/science.aai9127;
RA James N.R., Brown A., Gordiyenko Y., Ramakrishnan V.;
RT "Translational termination without a stop codon.";
RL Science 354:1437-1440(2016).
RN [13] {ECO:0007744|PDB:5U4I, ECO:0007744|PDB:5U4J}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.52 ANGSTROMS) OF 1-55 IN COMPLEX WITH
RP 70S RIBOSOME AND RF2, FUNCTION, INTERACTION WITH RF2, INTERACTION WITH 16S
RP RRNA, INTERACTION WITH 23S RRNA, AND MUTAGENESIS OF 1-MET--ALA-18; LYS-8;
RP GLY-9; ILE-11; PRO-23; ARG-28; GLU-30; LYS-34; LYS-36 AND ARG-41.
RX PubMed=28077875; DOI=10.1038/nature21053;
RA Zeng F., Chen Y., Remis J., Shekhar M., Phillips J.C., Tajkhorshid E.,
RA Jin H.;
RT "Structural basis of co-translational quality control by ArfA and RF2 bound
RT to ribosome.";
RL Nature 541:554-557(2017).
CC -!- FUNCTION: Rescues ribosomes stalled at the 3' end of non-stop mRNAs
CC (PubMed:21062370, PubMed:21435036). This activity is crucial when the
CC stalled ribosome cannot be rescued by the SsrA(tmRNA)-SmpB quality
CC control system (PubMed:21062370, PubMed:21435036). Binds the 30S
CC subunit, contacting 16S rRNA with the N-terminus near the decoding
CC center and its C-terminus in the mRNA entry channel; contacts change in
CC the presence of release factor 2 (RF2, also named PrfB)
CC (PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701,
CC PubMed:28077875). Requires RF2/PrfB to hydrolyze stalled peptidyl-tRNA
CC on the ribosome; recruits and probably helps position RF2/PrfB
CC correctly in the ribosomal A site so RF2's GGQ motif can hydrolyze the
CC peptidyl-tRNA bond (PubMed:22857598, PubMed:22922063, PubMed:25355516,
CC PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875).
CC Does not release ribosomes with a programmed pause caused by regulatory
CC chains such as SecM-mediated pausing (PubMed:22857598). Binds tRNA
CC which may stimulate its ribosome rescue activity (PubMed:22857598).
CC {ECO:0000269|PubMed:21062370, ECO:0000269|PubMed:21435036,
CC ECO:0000269|PubMed:22857598, ECO:0000269|PubMed:22922063,
CC ECO:0000269|PubMed:25355516, ECO:0000269|PubMed:27906160,
CC ECO:0000269|PubMed:27906161, ECO:0000269|PubMed:27934701,
CC ECO:0000269|PubMed:28077875}.
CC -!- SUBUNIT: Interacts with the 50S ribosomal subunit (PubMed:21062370,
CC PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701,
CC PubMed:28077875). Interacts with RF2/PrfB on the ribosome
CC (PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875).
CC Contacts ribosomal protein S12 (rpsL) (PubMed:27906160,
CC PubMed:27906161). {ECO:0000269|PubMed:21062370,
CC ECO:0000269|PubMed:25355516, ECO:0000269|PubMed:27906160,
CC ECO:0000269|PubMed:27906161, ECO:0000269|PubMed:27934701,
CC ECO:0000269|PubMed:28077875}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are viable, but those
CC lacking both arfA and ssrA are non-viable (PubMed:21062370).
CC {ECO:0000269|PubMed:21062370}.
CC -!- MISCELLANEOUS: Active protein is only produced when SsrA(tmRNA)-SmpB-
CC mediated trans translation is limited. ArfA can be synthesized from
CC truncated mRNA, via ribonuclease 3 and the SsrA tagging system. The
CC arfA mRNA is cleaved by ribonuclease 3 within a hairpin structure,
CC probably immediately after the Gly-55 codon, which produces a truncated
CC non-stop transcript and leads to ribosome arrest. In the presence of
CC SsrA, the stalled ribosome is rescued and the incomplete nascent ArfA
CC is tagged for degradation. In the absence of SsrA, truncated ArfA
CC chains are released from the ribosome and are functional. Truncated
CC ArfA could be more active than full-length protein (PubMed:21435036,
CC PubMed:21952205). {ECO:0000305|PubMed:21435036,
CC ECO:0000305|PubMed:21952205}.
CC -!- SIMILARITY: Belongs to the alternative ribosome-rescue factor A family.
CC {ECO:0000305}.
CC -!- CAUTION: In all 3D-structures with RF2/PrfB and the 70S ribosome this
CC protein is seen to contact 16S rRNA (PubMed:27906160, PubMed:27906161,
CC PubMed:27934701, PubMed:28077875). In most is also seen to contact 23S
CC rRNA (PubMed:27906160, PubMed:27934701, PubMed:28077875). Contact with
CC ribosomal protein S12 is also reported sometimes (PubMed:27906160,
CC PubMed:27906161). These discrepancies may be due to interpretation of
CC results. {ECO:0000269|PubMed:27906160, ECO:0000269|PubMed:27906161,
CC ECO:0000269|PubMed:27934701, ECO:0000269|PubMed:28077875}.
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DR EMBL; L29458; AAA24772.1; -; Genomic_DNA.
DR EMBL; U18997; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U00096; ABD18700.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78000.1; -; Genomic_DNA.
DR PIR; I67891; I67891.
DR RefSeq; WP_000092696.1; NZ_SSZK01000040.1.
DR RefSeq; YP_588467.1; NC_000913.3.
DR PDB; 5H5U; EM; 3.00 A; 3=1-72.
DR PDB; 5MDV; EM; 2.97 A; 6=1-60.
DR PDB; 5MDW; EM; 3.06 A; 6=1-60.
DR PDB; 5MDY; EM; 3.35 A; 6=1-60.
DR PDB; 5MGP; EM; 3.10 A; w=2-46.
DR PDB; 5U4I; EM; 3.50 A; w=1-55.
DR PDB; 5U4J; EM; 3.70 A; w=1-55.
DR PDB; 5U9F; EM; 3.20 A; Y=1-72.
DR PDB; 5U9G; EM; 3.20 A; Y=1-72.
DR PDB; 6C4I; EM; 3.24 A; w=1-55.
DR PDBsum; 5H5U; -.
DR PDBsum; 5MDV; -.
DR PDBsum; 5MDW; -.
DR PDBsum; 5MDY; -.
DR PDBsum; 5MGP; -.
DR PDBsum; 5U4I; -.
DR PDBsum; 5U4J; -.
DR PDBsum; 5U9F; -.
DR PDBsum; 5U9G; -.
DR PDBsum; 6C4I; -.
DR AlphaFoldDB; P36675; -.
DR SMR; P36675; -.
DR BioGRID; 4259344; 8.
DR IntAct; P36675; 53.
DR STRING; 511145.b4550; -.
DR PaxDb; P36675; -.
DR PRIDE; P36675; -.
DR EnsemblBacteria; ABD18700; ABD18700; b4550.
DR EnsemblBacteria; BAE78000; BAE78000; BAE78000.
DR GeneID; 1450289; -.
DR GeneID; 66672815; -.
DR KEGG; ecj:JW3253; -.
DR KEGG; eco:b4550; -.
DR PATRIC; fig|1411691.4.peg.3440; -.
DR EchoBASE; EB1911; -.
DR eggNOG; COG3036; Bacteria.
DR HOGENOM; CLU_170842_3_0_6; -.
DR InParanoid; P36675; -.
DR OMA; HAKGGNW; -.
DR PhylomeDB; P36675; -.
DR BioCyc; EcoCyc:MON0-2687; -.
DR PRO; PR:P36675; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0043023; F:ribosomal large subunit binding; IDA:EcoCyc.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000049; F:tRNA binding; IDA:EcoCyc.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR GO; GO:0072344; P:rescue of stalled ribosome; IDA:EcoCyc.
DR InterPro; IPR005589; ArfA.
DR Pfam; PF03889; ArfA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Reference proteome; RNA-binding; rRNA-binding;
KW Translation regulation; tRNA-binding.
FT CHAIN 1..72
FT /note="Alternative ribosome-rescue factor A"
FT /id="PRO_0000169494"
FT REGION 30..53
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 1..18
FT /note="Missing: 90% decrease in kcat for peptidyl-
FT transferase by RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 8
FT /note="K->A: 75% decrease in kcat for peptidyl-transferase
FT by RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 9
FT /note="G->V: 75% decrease in kcat for peptidyl-transferase
FT by RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 11
FT /note="I->N: 90% decrease in kcat for peptidyl-transferase
FT by RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 18
FT /note="A->C: No change in ribosome rescue activity."
FT /evidence="ECO:0000269|PubMed:25355516"
FT MUTAGEN 18
FT /note="A->T: Loss of ribosome rescue activity. Does not
FT affect binding to the ribosome or to tRNA. Still recruits
FT RF2 to the ribosome."
FT /evidence="ECO:0000269|PubMed:21062370,
FT ECO:0000269|PubMed:22857598, ECO:0000269|PubMed:22922063"
FT MUTAGEN 20
FT /note="L->C: About 50% ribosome rescue activity, initial
FT rate."
FT /evidence="ECO:0000269|PubMed:27906160"
FT MUTAGEN 23
FT /note="P->A: 50% decrease in kcat for peptidyl-transferase
FT by RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 28
FT /note="R->A: No change in kcat for peptidyl-transferase by
FT RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 28
FT /note="R->C: About 50% ribosome rescue activity, initial
FT rate."
FT /evidence="ECO:0000269|PubMed:27906160"
FT MUTAGEN 30
FT /note="E->A: No change in kcat for peptidyl-transferase by
FT RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 34
FT /note="K->A: No change in kcat for peptidyl-transferase by
FT RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 34
FT /note="K->C: About 75% ribosome rescue activity, after 10
FT minutes. About 50% ribosome rescue activity, initial rate."
FT /evidence="ECO:0000269|PubMed:25355516,
FT ECO:0000269|PubMed:27906160"
FT MUTAGEN 35
FT /note="G->C: About 50% ribosome rescue activity, initial
FT rate."
FT /evidence="ECO:0000269|PubMed:27906160"
FT MUTAGEN 36
FT /note="K->A: No change in kcat for peptidyl-transferase by
FT RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 39
FT /note="Y->C: About 25% ribosome rescue activity, initial
FT rate."
FT /evidence="ECO:0000269|PubMed:27906160"
FT MUTAGEN 41
FT /note="R->A: No change in kcat for peptidyl-transferase by
FT RF2."
FT /evidence="ECO:0000269|PubMed:28077875"
FT MUTAGEN 41
FT /note="R->C: About 20% ribosome rescue activity, initial
FT rate."
FT /evidence="ECO:0000269|PubMed:27906160"
SQ SEQUENCE 72 AA; 8171 MW; 2F4025A3650CCA16 CRC64;
MSRYQHTKGQ IKDNAIEALL HDPLFRQRVE KNKKGKGSYM RKGKHGNRGN WEASGKKVNH
FFTTGLLLSG AC
