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P40711 (ARFB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 97. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Peptidyl-tRNA hydrolase ArfB

Short name=PTH
EC=3.1.1.29
Alternative name(s):
Alternative ribosome-rescue factor B
Gene names
Name:arfB
Synonyms:yaeJ
Ordered Locus Names:b0191, JW0187
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length140 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Rescues stalled ribosomes. Can hydrolyze peptidyl-tRNA on ribosomes stalled by both non-stop mRNAs and mRNAs that contain rare codon clusters. May function as a complementary rescue system when the stalled ribosome can not be rescued by the SsrA(tmRNA)-SmpB quality control system or the alternative ribosome-rescue factor A. Ref.8 Ref.9 Ref.10

Catalytic activity

N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA. Ref.8 Ref.9

Subunit structure

Associated with 70S ribosomes and polysomes.

Subcellular location

Cytoplasm Probable.

Domain

The unstructured C-terminal region is required for ribosome binding and peptidyl-tRNA hydrolase activity. The C-terminal tail functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned in the peptidyltransferase center (PTC) to catalyze the hydrolysis of peptidyl-tRNA. The N-terminal domain of ArfB is bound in the A site of the 50S subunit next to the P-site tRNA. Ref.8 Ref.9 Ref.10

Sequence similarities

Belongs to the prokaryotic/mitochondrial release factor family.

Ontologies

Keywords
   Biological processTranslation regulation
   Cellular componentCytoplasm
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processrescue of stalled ribosome

Inferred from direct assay Ref.9Ref.8. Source: EcoCyc

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionaminoacyl-tRNA hydrolase activity

Inferred from direct assay Ref.9Ref.8. Source: EcoCyc

ribosome binding

Inferred from direct assay Ref.8. Source: EcoCyc

translation release factor activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 140140Peptidyl-tRNA hydrolase ArfB
PRO_0000166858

Experimental info

Mutagenesis26 – 272GG → VA: Strong decrease in activity. Ref.8 Ref.9
Mutagenesis27 – 282GQ → AE: Strong decrease in activity. Ref.8 Ref.9
Mutagenesis271G → A: Decrease in activity. Ref.8 Ref.9
Mutagenesis281Q → E: Decrease in activity. Ref.9

Secondary structure

.................. 140
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P40711 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: 8F161ADD8C07EBCB

FASTA14015,623
        10         20         30         40         50         60 
MIVISRHVAI PDGELEITAI RAQGAGGQHV NKTSTAIHLR FDIRASSLPE YYKERLLAAS 

        70         80         90        100        110        120 
HHLISSDGVI VIKAQEYRSQ ELNREAALAR LVAMIKELTT EKKARRPTRP TRASKERRLA 

       130        140 
SKAQKSSVKA MRGKVRSGRE 

« Hide

References

« Hide 'large scale' references
[1]"Identification of cutC and cutF (nlpE) genes involved in copper tolerance in Escherichia coli."
Gupta S.D., Lee B.T.O., Camakaris J., Wu H.C.
J. Bacteriol. 177:4207-4215(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[2]Yamamoto Y.
Submitted (DEC-1995) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region."
Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T., Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S., Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.
Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"Sequence of minutes 4-25 of Escherichia coli."
Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[6]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION TO 36.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]"Overproduction of NlpE, a new outer membrane lipoprotein, suppresses the toxicity of periplasmic LacZ by activation of the Cpx signal transduction pathway."
Snyder W.B., Davis L.J., Danese P.N., Cosma C.L., Silhavy T.J.
J. Bacteriol. 177:4216-4223(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 17-140.
Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[8]"Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways."
Chadani Y., Ono K., Kutsukake K., Abo T.
Mol. Microbiol. 80:772-785(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, GENE NAME, INTERACTION WITH RIBOSOMES, DOMAIN, MUTAGENESIS OF GLY-27.
Strain: K12.
[9]"YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes."
Handa Y., Inaho N., Nameki N.
Nucleic Acids Res. 39:1739-1748(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH RIBOSOMES, DOMAIN, MUTAGENESIS OF 26-GLY-GLY-27; 27-GLY-GLN-28; GLY-27 AND GLN-28.
Strain: K12.
[10]"Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome."
Gagnon M.G., Seetharaman S.V., Bulkley D., Steitz T.A.
Science 335:1370-1372(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) IN COMPLEX WITH THERMUS THERMOPHILUS 70S RIBOSOME, FUNCTION, DOMAIN, REACTION MECHANISM.
Strain: K12.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L38619 Genomic DNA. Translation: AAA82971.1.
D49445 Genomic DNA. Translation: BAA08432.1.
U70214 Genomic DNA. Translation: AAB08619.1.
U00096 Genomic DNA. Translation: AAC73302.1.
AP009048 Genomic DNA. Translation: BAA77867.2.
U18345 Genomic DNA. Translation: AAA86092.1.
PIRG64743.
RefSeqNP_414733.1. NC_000913.3.
YP_488494.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2RTXNMR-A1-109[»]
4DH9X-ray3.20Y1-140[»]
ProteinModelPortalP40711.
SMRP40711. Positions 2-133.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP40711. 8 interactions.
STRING511145.b0191.

Proteomic databases

PaxDbP40711.
PRIDEP40711.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73302; AAC73302; b0191.
BAA77867; BAA77867; BAA77867.
GeneID12934377.
946046.
KEGGecj:Y75_p0188.
eco:b0191.
PATRIC32115495. VBIEscCol129921_0199.

Organism-specific databases

EchoBASEEB2258.
EcoGeneEG12354. arfB.

Phylogenomic databases

eggNOGCOG1186.
HOGENOMHOG000244440.
KOK15034.
OMAFDINASS.
OrthoDBEOG628F97.
PhylomeDBP40711.

Enzyme and pathway databases

BioCycEcoCyc:EG12354-MONOMER.
ECOL316407:JW0187-MONOMER.
MetaCyc:EG12354-MONOMER.
RETL1328306-WGS:GSTH-38-MONOMER.

Gene expression databases

GenevestigatorP40711.

Family and domain databases

InterProIPR000352. Pep_chain_release_fac_I_II.
[Graphical view]
PfamPF00472. RF-1. 1 hit.
[Graphical view]
PROSITEPS00745. RF_PROK_I. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP40711.

Entry information

Entry nameARFB_ECOLI
AccessionPrimary (citable) accession number: P40711
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: November 1, 1995
Last modified: July 9, 2014
This is version 97 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene