ARFB_ECOLI
ID ARFB_ECOLI Reviewed; 140 AA.
AC P40711;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 2.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Peptidyl-tRNA hydrolase ArfB;
DE Short=PTH;
DE EC=3.1.1.29;
DE AltName: Full=Alternative ribosome-rescue factor B;
GN Name=arfB; Synonyms=yaeJ; OrderedLocusNames=b0191, JW0187;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=7635807; DOI=10.1128/jb.177.15.4207-4215.1995;
RA Gupta S.D., Lee B.T.O., Camakaris J., Wu H.C.;
RT "Identification of cutC and cutF (nlpE) genes involved in copper tolerance
RT in Escherichia coli.";
RL J. Bacteriol. 177:4207-4215(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Yamamoto Y.;
RL Submitted (DEC-1995) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T.,
RA Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S.,
RA Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0
RT - 6.0 min (189,987 - 281,416bp) region.";
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION TO 36.
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 [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 17-140.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=7635808; DOI=10.1128/jb.177.15.4216-4223.1995;
RA Snyder W.B., Davis L.J., Danese P.N., Cosma C.L., Silhavy T.J.;
RT "Overproduction of NlpE, a new outer membrane lipoprotein, suppresses the
RT toxicity of periplasmic LacZ by activation of the Cpx signal transduction
RT pathway.";
RL J. Bacteriol. 177:4216-4223(1995).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, GENE NAME, INTERACTION WITH RIBOSOMES,
RP DOMAIN, AND MUTAGENESIS OF GLY-27.
RC STRAIN=K12;
RX PubMed=21418110; DOI=10.1111/j.1365-2958.2011.07607.x;
RA Chadani Y., Ono K., Kutsukake K., Abo T.;
RT "Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway
RT distinct from SsrA- and ArfA-mediated pathways.";
RL Mol. Microbiol. 80:772-785(2011).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH RIBOSOMES, DOMAIN, AND
RP MUTAGENESIS OF 26-GLY-GLY-27; 27-GLY-GLN-28; GLY-27 AND GLN-28.
RC STRAIN=K12;
RX PubMed=21051357; DOI=10.1093/nar/gkq1097;
RA Handa Y., Inaho N., Nameki N.;
RT "YaeJ is a novel ribosome-associated protein in Escherichia coli that can
RT hydrolyze peptidyl-tRNA on stalled ribosomes.";
RL Nucleic Acids Res. 39:1739-1748(2011).
RN [10]
RP FUNCTION.
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 [11]
RP X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) IN COMPLEX WITH THERMUS THERMOPHILUS
RP 70S RIBOSOME, FUNCTION, DOMAIN, AND REACTION MECHANISM.
RC STRAIN=K12;
RX PubMed=22422986; DOI=10.1126/science.1217443;
RA Gagnon M.G., Seetharaman S.V., Bulkley D., Steitz T.A.;
RT "Structural basis for the rescue of stalled ribosomes: structure of YaeJ
RT bound to the ribosome.";
RL Science 335:1370-1372(2012).
CC -!- FUNCTION: Rescues stalled ribosomes (PubMed:21418110, PubMed:21051357,
CC PubMed:22922063). Can hydrolyze peptidyl-tRNA on ribosomes stalled by
CC both non-stop mRNAs and mRNAs that contain rare codon clusters
CC (PubMed:21051357) or ribosomes stalled in the middle of mRNA
CC (PubMed:22922063). First identified as a complementary ribosome rescue
CC system when the stalled ribosome cannot be rescued by the SsrA(tmRNA)-
CC SmpB quality control system or the alternative ribosome-rescue factor A
CC (arfA) (PubMed:21418110). {ECO:0000269|PubMed:21051357,
CC ECO:0000269|PubMed:21418110, ECO:0000269|PubMed:22422986,
CC ECO:0000269|PubMed:22922063}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-
CC amino acid + H(+); Xref=Rhea:RHEA:54448, Rhea:RHEA-COMP:10123,
CC Rhea:RHEA-COMP:13883, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:59874, ChEBI:CHEBI:78442, ChEBI:CHEBI:138191;
CC EC=3.1.1.29; Evidence={ECO:0000269|PubMed:21051357,
CC ECO:0000269|PubMed:21418110};
CC -!- SUBUNIT: Associated with 70S ribosomes and polysomes.
CC {ECO:0000269|PubMed:22422986}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DOMAIN: The unstructured C-terminal region is required for ribosome
CC binding and peptidyl-tRNA hydrolase activity. The C-terminal tail
CC functions as a sensor to discriminate between stalled and actively
CC translating ribosomes by binding in the mRNA entry channel downstream
CC of the A site between the head and shoulder of the 30S subunit. This
CC allows the N-terminal globular domain to sample different
CC conformations, so that its conserved GGQ motif is optimally positioned
CC in the peptidyltransferase center (PTC) to catalyze the hydrolysis of
CC peptidyl-tRNA. The N-terminal domain of ArfB is bound in the A site of
CC the 50S subunit next to the P-site tRNA. {ECO:0000269|PubMed:21051357,
CC ECO:0000269|PubMed:21418110, ECO:0000269|PubMed:22422986}.
CC -!- SIMILARITY: Belongs to the prokaryotic/mitochondrial release factor
CC family. {ECO:0000305}.
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DR EMBL; L38619; AAA82971.1; -; Genomic_DNA.
DR EMBL; D49445; BAA08432.1; -; Genomic_DNA.
DR EMBL; U70214; AAB08619.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73302.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA77867.2; -; Genomic_DNA.
DR EMBL; U18345; AAA86092.1; -; Genomic_DNA.
DR PIR; G64743; G64743.
DR RefSeq; NP_414733.1; NC_000913.3.
DR RefSeq; WP_000635537.1; NZ_SSZK01000004.1.
DR PDB; 2RTX; NMR; -; A=1-109.
DR PDB; 4V95; X-ray; 3.20 A; AY=1-140.
DR PDB; 7JSS; EM; 3.70 A; 8=2-133.
DR PDB; 7JSW; EM; 3.80 A; 8=2-133.
DR PDB; 7JSZ; EM; 3.70 A; 8=2-133.
DR PDB; 7JT1; EM; 3.30 A; 8/9=4-133.
DR PDB; 7JT2; EM; 3.50 A; 8=2-133.
DR PDB; 7JT3; EM; 3.70 A; 8/9=4-133.
DR PDBsum; 2RTX; -.
DR PDBsum; 4V95; -.
DR PDBsum; 7JSS; -.
DR PDBsum; 7JSW; -.
DR PDBsum; 7JSZ; -.
DR PDBsum; 7JT1; -.
DR PDBsum; 7JT2; -.
DR PDBsum; 7JT3; -.
DR AlphaFoldDB; P40711; -.
DR SMR; P40711; -.
DR BioGRID; 4263371; 6.
DR IntAct; P40711; 8.
DR STRING; 511145.b0191; -.
DR PaxDb; P40711; -.
DR PRIDE; P40711; -.
DR EnsemblBacteria; AAC73302; AAC73302; b0191.
DR EnsemblBacteria; BAA77867; BAA77867; BAA77867.
DR GeneID; 946046; -.
DR KEGG; ecj:JW0187; -.
DR KEGG; eco:b0191; -.
DR PATRIC; fig|1411691.4.peg.2087; -.
DR EchoBASE; EB2258; -.
DR eggNOG; COG1186; Bacteria.
DR HOGENOM; CLU_089470_3_0_6; -.
DR InParanoid; P40711; -.
DR OMA; SEHRSQW; -.
DR PhylomeDB; P40711; -.
DR BioCyc; EcoCyc:EG12354-MON; -.
DR BioCyc; MetaCyc:EG12354-MON; -.
DR PRO; PR:P40711; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004045; F:aminoacyl-tRNA hydrolase activity; IDA:EcoCyc.
DR GO; GO:0043022; F:ribosome binding; IDA:EcoCyc.
DR GO; GO:0003747; F:translation release factor activity; IEA:InterPro.
DR GO; GO:0072344; P:rescue of stalled ribosome; IDA:EcoCyc.
DR InterPro; IPR000352; Pep_chain_release_fac_I.
DR InterPro; IPR045853; Pep_chain_release_fac_I_sf.
DR Pfam; PF00472; RF-1; 1.
DR SUPFAM; SSF75620; SSF75620; 1.
DR PROSITE; PS00745; RF_PROK_I; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Hydrolase; Reference proteome;
KW Translation regulation.
FT CHAIN 1..140
FT /note="Peptidyl-tRNA hydrolase ArfB"
FT /id="PRO_0000166858"
FT REGION 100..140
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 100..123
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 26..27
FT /note="GG->VA: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:21051357"
FT MUTAGEN 27..28
FT /note="GQ->AE: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:21051357"
FT MUTAGEN 27
FT /note="G->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:21051357,
FT ECO:0000269|PubMed:21418110"
FT MUTAGEN 28
FT /note="Q->E: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:21051357"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:2RTX"
FT STRAND 14..20
FT /evidence="ECO:0007829|PDB:2RTX"
FT STRAND 27..29
FT /evidence="ECO:0007829|PDB:2RTX"
FT STRAND 36..42
FT /evidence="ECO:0007829|PDB:2RTX"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:2RTX"
FT HELIX 50..57
FT /evidence="ECO:0007829|PDB:2RTX"
FT TURN 66..68
FT /evidence="ECO:0007829|PDB:2RTX"
FT STRAND 69..74
FT /evidence="ECO:0007829|PDB:2RTX"
FT STRAND 77..82
FT /evidence="ECO:0007829|PDB:2RTX"
FT HELIX 83..98
FT /evidence="ECO:0007829|PDB:2RTX"
SQ SEQUENCE 140 AA; 15623 MW; 8F161ADD8C07EBCB CRC64;
MIVISRHVAI PDGELEITAI RAQGAGGQHV NKTSTAIHLR FDIRASSLPE YYKERLLAAS
HHLISSDGVI VIKAQEYRSQ ELNREAALAR LVAMIKELTT EKKARRPTRP TRASKERRLA
SKAQKSSVKA MRGKVRSGRE
