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Protein

Peptidyl-tRNA hydrolase ArfB

Gene

arfB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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.3 Publications

Catalytic activityi

N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA.2 Publications

GO - Molecular functioni

  1. aminoacyl-tRNA hydrolase activity Source: EcoCyc
  2. ribosome binding Source: EcoCyc
  3. translation release factor activity Source: InterPro

GO - Biological processi

  1. rescue of stalled ribosome Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Translation regulation

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Peptidyl-tRNA hydrolase ArfB (EC:3.1.1.29)
Short name:
PTH
Alternative name(s):
Alternative ribosome-rescue factor B
Gene namesi
Name:arfB
Synonyms:yaeJ
Ordered Locus Names:b0191, JW0187
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG12354. arfB.

Subcellular locationi

Cytoplasm Curated

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi26 – 272GG → VA: Strong decrease in activity. 1 Publication
Mutagenesisi27 – 282GQ → AE: Strong decrease in activity. 1 Publication
Mutagenesisi27 – 271G → A: Decrease in activity. 2 Publications
Mutagenesisi28 – 281Q → E: Decrease in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 140140Peptidyl-tRNA hydrolase ArfBPRO_0000166858Add
BLAST

Proteomic databases

PaxDbiP40711.
PRIDEiP40711.

Expressioni

Gene expression databases

GenevestigatoriP40711.

Interactioni

Subunit structurei

Associated with 70S ribosomes and polysomes.1 Publication

Protein-protein interaction databases

IntActiP40711. 8 interactions.
STRINGi511145.b0191.

Structurei

Secondary structure

1
140
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 53Combined sources
Beta strandi14 – 207Combined sources
Beta strandi27 – 293Combined sources
Beta strandi36 – 427Combined sources
Helixi43 – 453Combined sources
Helixi50 – 578Combined sources
Turni66 – 683Combined sources
Beta strandi69 – 746Combined sources
Beta strandi77 – 826Combined sources
Helixi83 – 9816Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2RTXNMR-A1-109[»]
4V95X-ray3.20AY1-140[»]
ProteinModelPortaliP40711.
SMRiP40711. Positions 2-133.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

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.3 Publications

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1186.
HOGENOMiHOG000244440.
InParanoidiP40711.
KOiK15034.
OMAiRITQEGV.
OrthoDBiEOG628F97.
PhylomeDBiP40711.

Family and domain databases

InterProiIPR000352. Pep_chain_release_fac_I_II.
[Graphical view]
PfamiPF00472. RF-1. 1 hit.
[Graphical view]
PROSITEiPS00745. RF_PROK_I. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P40711-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIVISRHVAI PDGELEITAI RAQGAGGQHV NKTSTAIHLR FDIRASSLPE
60 70 80 90 100
YYKERLLAAS HHLISSDGVI VIKAQEYRSQ ELNREAALAR LVAMIKELTT
110 120 130 140
EKKARRPTRP TRASKERRLA SKAQKSSVKA MRGKVRSGRE
Length:140
Mass (Da):15,623
Last modified:November 1, 1995 - v2
Checksum:i8F161ADD8C07EBCB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiG64743.
RefSeqiNP_414733.1. NC_000913.3.
YP_488494.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73302; AAC73302; b0191.
BAA77867; BAA77867; BAA77867.
GeneIDi12934377.
946046.
KEGGiecj:Y75_p0188.
eco:b0191.
PATRICi32115495. VBIEscCol129921_0199.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiG64743.
RefSeqiNP_414733.1. NC_000913.3.
YP_488494.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2RTXNMR-A1-109[»]
4V95X-ray3.20AY1-140[»]
ProteinModelPortaliP40711.
SMRiP40711. Positions 2-133.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP40711. 8 interactions.
STRINGi511145.b0191.

Proteomic databases

PaxDbiP40711.
PRIDEiP40711.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73302; AAC73302; b0191.
BAA77867; BAA77867; BAA77867.
GeneIDi12934377.
946046.
KEGGiecj:Y75_p0188.
eco:b0191.
PATRICi32115495. VBIEscCol129921_0199.

Organism-specific databases

EchoBASEiEB2258.
EcoGeneiEG12354. arfB.

Phylogenomic databases

eggNOGiCOG1186.
HOGENOMiHOG000244440.
InParanoidiP40711.
KOiK15034.
OMAiRITQEGV.
OrthoDBiEOG628F97.
PhylomeDBiP40711.

Enzyme and pathway databases

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

Miscellaneous databases

PROiP40711.

Gene expression databases

GenevestigatoriP40711.

Family and domain databases

InterProiIPR000352. Pep_chain_release_fac_I_II.
[Graphical view]
PfamiPF00472. RF-1. 1 hit.
[Graphical view]
PROSITEiPS00745. RF_PROK_I. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiARFB_ECOLI
AccessioniPrimary (citable) accession number: P40711
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: November 1, 1995
Last modified: March 4, 2015
This is version 103 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.