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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 cannot 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

  • aminoacyl-tRNA hydrolase activity Source: EcoCyc
  • ribosome binding Source: EcoCyc
  • translation release factor activity, codon nonspecific Source: GO_Central

GO - Biological processi

  • 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.

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12354. arfB.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi26 – 27GG → VA: Strong decrease in activity. 1 Publication2
Mutagenesisi27 – 28GQ → AE: Strong decrease in activity. 1 Publication2
Mutagenesisi27G → A: Decrease in activity. 2 Publications1
Mutagenesisi28Q → E: Decrease in activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001668581 – 140Peptidyl-tRNA hydrolase ArfBAdd BLAST140

Proteomic databases

PaxDbiP40711.
PRIDEiP40711.

Interactioni

Subunit structurei

Associated with 70S ribosomes and polysomes.1 Publication

Protein-protein interaction databases

BioGridi4263371. 6 interactors.
IntActiP40711. 8 interactors.
STRINGi511145.b0191.

Structurei

Secondary structure

1140
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 5Combined sources3
Beta strandi14 – 20Combined sources7
Beta strandi27 – 29Combined sources3
Beta strandi36 – 42Combined sources7
Helixi43 – 45Combined sources3
Helixi50 – 57Combined sources8
Turni66 – 68Combined sources3
Beta strandi69 – 74Combined sources6
Beta strandi77 – 82Combined sources6
Helixi83 – 98Combined sources16

3D structure databases

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

eggNOGiENOG4108YZN. Bacteria.
COG1186. LUCA.
HOGENOMiHOG000244440.
InParanoidiP40711.
KOiK15034.
OMAiKAQQHRT.
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.
WP_000635537.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73302; AAC73302; b0191.
BAA77867; BAA77867; BAA77867.
GeneIDi946046.
KEGGiecj:JW0187.
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.
WP_000635537.1. NZ_LN832404.1.

3D structure databases

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

Protein-protein interaction databases

BioGridi4263371. 6 interactors.
IntActiP40711. 8 interactors.
STRINGi511145.b0191.

Proteomic databases

PaxDbiP40711.
PRIDEiP40711.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73302; AAC73302; b0191.
BAA77867; BAA77867; BAA77867.
GeneIDi946046.
KEGGiecj:JW0187.
eco:b0191.
PATRICi32115495. VBIEscCol129921_0199.

Organism-specific databases

EchoBASEiEB2258.
EcoGeneiEG12354. arfB.

Phylogenomic databases

eggNOGiENOG4108YZN. Bacteria.
COG1186. LUCA.
HOGENOMiHOG000244440.
InParanoidiP40711.
KOiK15034.
OMAiKAQQHRT.
PhylomeDBiP40711.

Enzyme and pathway databases

BioCyciEcoCyc:EG12354-MONOMER.
ECOL316407:JW0187-MONOMER.
MetaCyc:EG12354-MONOMER.

Miscellaneous databases

PROiP40711.

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...

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: November 2, 2016
This is version 114 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

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 one 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.