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UniProtKB - P36675 (ARFA_ECOLI)

Entry version 116 (31 Jul 2019)
Sequence version 1 (01 Jun 1994)
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Protein

Alternative ribosome-rescue factor A

Gene

arfA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Rescues ribosomes stalled at the 3' end of non-stop mRNAs (PubMed:21062370, PubMed:21435036). This activity is crucial when the stalled ribosome cannot be rescued by the SsrA(tmRNA)-SmpB quality control system (PubMed:21062370, PubMed:21435036). Binds the 30S subunit, contacting 16S rRNA with the N-terminus near the decoding center and its C-terminus in the mRNA entry channel; contacts change in the presence of release factor 2 (RF2, also named PrfB) (PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Requires RF2/PrfB to hydrolyze stalled peptidyl-tRNA on the ribosome; recruits and probably helps position RF2/PrfB correctly in the ribosomal A site so RF2's GGQ motif can hydrolyze the peptidyl-tRNA bond (PubMed:22857598, PubMed:22922063, PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Does not release ribosomes with a programmed pause caused by regulatory chains such as SecM-mediated pausing (PubMed:22857598). Binds tRNA which may stimulate its ribosome rescue activity (PubMed:22857598).9 Publications

Miscellaneous

Active protein is only produced when SsrA(tmRNA)-SmpB-mediated trans translation is limited. ArfA can be synthesized from truncated mRNA, via ribonuclease 3 and the SsrA tagging system. The arfA mRNA is cleaved by ribonuclease 3 within a hairpin structure, probably immediately after the Gly-55 codon, which produces a truncated non-stop transcript and leads to ribosome arrest. In the presence of SsrA, the stalled ribosome is rescued and the incomplete nascent ArfA is tagged for degradation. In the absence of SsrA, truncated ArfA chains are released from the ribosome and are functional. Truncated ArfA could be more active than full-length protein (PubMed:21435036, PubMed:21952205).2 Publications

Caution

In all 3D-structures with RF2/PrfB and the 70S ribosome this protein is seen to contact 16S rRNA (PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). In most is also seen to contact 23S rRNA (PubMed:27906160, PubMed:27934701, PubMed:28077875). Contact with ribosomal protein S12 is also reported sometimes (PubMed:27906160, PubMed:27906161). These discrepancies may be due to interpretation of results.4 Publications

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionRNA-binding, rRNA-binding, tRNA-binding
Biological processTranslation regulation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:MONOMER0-2687
ECOL316407:JW3253-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Alternative ribosome-rescue factor A1 Publication
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:arfA1 Publication
Synonyms:yhdL
Ordered Locus Names:b4550, JW3253
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

Escherichia coli strain K12 genome database

More...EcoGenei		EG11968 arfA

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Cells lacking this gene are viable, but those lacking both arfA and ssrA are non-viable (PubMed:21062370).1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi1 – 18Missing : 90% decrease in kcat for peptidyl-transferase by RF2. 1 PublicationAdd BLAST18
Mutagenesisi8K → A: 75% decrease in kcat for peptidyl-transferase by RF2. 1 Publication1
Mutagenesisi9G → V: 75% decrease in kcat for peptidyl-transferase by RF2. 1 Publication1
Mutagenesisi11I → N: 90% decrease in kcat for peptidyl-transferase by RF2. 1 Publication1
Mutagenesisi18A → C: No change in ribosome rescue activity. 1 Publication1
Mutagenesisi18A → T: Loss of ribosome rescue activity. Does not affect binding to the ribosome or to tRNA. Still recruits RF2 to the ribosome. 3 Publications1
Mutagenesisi20L → C: About 50% ribosome rescue activity, initial rate. 1 Publication1
Mutagenesisi23P → A: 50% decrease in kcat for peptidyl-transferase by RF2. 1 Publication1
Mutagenesisi28R → A: No change in kcat for peptidyl-transferase by RF2. 1 Publication1
Mutagenesisi28R → C: About 50% ribosome rescue activity, initial rate. 1 Publication1
Mutagenesisi30E → A: No change in kcat for peptidyl-transferase by RF2. 1 Publication1
Mutagenesisi34K → A: No change in kcat for peptidyl-transferase by RF2. 1 Publication1
Mutagenesisi34K → C: About 75% ribosome rescue activity, after 10 minutes. About 50% ribosome rescue activity, initial rate. 2 Publications1
Mutagenesisi35G → C: About 50% ribosome rescue activity, initial rate. 1 Publication1
Mutagenesisi36K → A: No change in kcat for peptidyl-transferase by RF2. 1 Publication1
Mutagenesisi39Y → C: About 25% ribosome rescue activity, initial rate. 1 Publication1
Mutagenesisi41R → A: No change in kcat for peptidyl-transferase by RF2. 1 Publication1
Mutagenesisi41R → C: About 20% ribosome rescue activity, initial rate. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001694941 – 72Alternative ribosome-rescue factor AAdd BLAST72

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P36675

PRoteomics IDEntifications database

More...PRIDEi		P36675

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Interacts with the 50S ribosomal subunit (PubMed:21062370, PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875).

Interacts with RF2/PrfB on the ribosome (PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Contacts ribosomal protein S12 (rpsL) (PubMed:27906160, PubMed:27906161).

6 Publications

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		4259344, 8 interactors

STRING: functional protein association networks

More...STRINGi		511145.b4550

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P36675

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the alternative ribosome-rescue factor A family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105VCN Bacteria
COG3036 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000000578

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P36675

KEGG Orthology (KO)

More...KOi		K09890

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR005589 ArfA

Pfam protein domain database

More...Pfami		View protein in Pfam
PF03889 ArfA, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P36675-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSRYQHTKGQ IKDNAIEALL HDPLFRQRVE KNKKGKGSYM RKGKHGNRGN 
        60         70 
WEASGKKVNH FFTTGLLLSG AC
Length:72
Mass (Da):8,171
Last modified:June 1, 1994 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i2F4025A3650CCA16
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
L29458 Genomic DNA Translation: AAA24772.1
U18997 Genomic DNA No translation available.
U00096 Genomic DNA Translation: ABD18700.1
AP009048 Genomic DNA Translation: BAE78000.1

Protein sequence database of the Protein Information Resource

More...PIRi		I67891

NCBI Reference Sequences

More...RefSeqi		WP_000092696.1, NZ_SSZK01000040.1
YP_588467.1, NC_000913.3

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		ABD18700; ABD18700; b4550
BAE78000; BAE78000; BAE78000

Database of genes from NCBI RefSeq genomes

More...GeneIDi		1450289

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW3253
eco:b4550

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.3440

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L29458 Genomic DNA Translation: AAA24772.1
U18997 Genomic DNA No translation available.
U00096 Genomic DNA Translation: ABD18700.1
AP009048 Genomic DNA Translation: BAE78000.1
PIRiI67891
RefSeqiWP_000092696.1, NZ_SSZK01000040.1
YP_588467.1, NC_000913.3

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5H5Uelectron microscopy3.0031-72[»]
5MDVelectron microscopy2.9761-60[»]
5MDWelectron microscopy3.0661-60[»]
5MDYelectron microscopy3.3561-60[»]
5MGPelectron microscopy3.10w2-46[»]
5U4Ielectron microscopy3.50w1-55[»]
5U4Jelectron microscopy3.70w1-55[»]
5U9Felectron microscopy3.20Y1-72[»]
5U9Gelectron microscopy3.20Y1-72[»]
6C4Ielectron microscopy3.24w1-55[»]
SMRiP36675
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4259344, 8 interactors
STRINGi511145.b4550

Proteomic databases

PaxDbiP36675
PRIDEiP36675

Genome annotation databases

EnsemblBacteriaiABD18700; ABD18700; b4550
BAE78000; BAE78000; BAE78000
GeneIDi1450289
KEGGiecj:JW3253
eco:b4550
PATRICifig|1411691.4.peg.3440

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB1911
EcoGeneiEG11968 arfA

Phylogenomic databases

eggNOGiENOG4105VCN Bacteria
COG3036 LUCA
HOGENOMiHOG000000578
InParanoidiP36675
KOiK09890

Enzyme and pathway databases

BioCyciEcoCyc:MONOMER0-2687
ECOL316407:JW3253-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P36675

Family and domain databases

InterProiView protein in InterPro
IPR005589 ArfA
PfamiView protein in Pfam
PF03889 ArfA, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiARFA_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P36675
Secondary accession number(s): Q2EET4, Q2M6V6
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: July 31, 2019
This is version 116 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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