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P40711

- ARFB_ECOLI

UniProt

P40711 - ARFB_ECOLI

Protein

Peptidyl-tRNA hydrolase ArfB

Gene

arfB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
  1. 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

    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

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi26 – 272GG → VA: Strong decrease in activity.
    Mutagenesisi27 – 282GQ → AE: Strong decrease in activity. 2 Publications
    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 – 53
    Beta strandi14 – 207
    Beta strandi27 – 293
    Beta strandi36 – 427
    Helixi43 – 453
    Helixi50 – 578
    Turni66 – 683
    Beta strandi69 – 746
    Beta strandi77 – 826
    Helixi83 – 9816

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2RTXNMR-A1-109[»]
    4DH9X-ray3.20Y1-140[»]
    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.
    KOiK15034.
    OMAiFDINASS.
    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

    MIVISRHVAI PDGELEITAI RAQGAGGQHV NKTSTAIHLR FDIRASSLPE    50
    YYKERLLAAS HHLISSDGVI VIKAQEYRSQ ELNREAALAR LVAMIKELTT 100
    EKKARRPTRP TRASKERRLA SKAQKSSVKA MRGKVRSGRE 140
    Length:140
    Mass (Da):15,623
    Last modified:November 1, 1995 - v2
    Checksum:i8F161ADD8C07EBCB
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi G64743.
    RefSeqi NP_414733.1. NC_000913.3.
    YP_488494.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2RTX NMR - A 1-109 [» ]
    4DH9 X-ray 3.20 Y 1-140 [» ]
    ProteinModelPortali P40711.
    SMRi P40711. Positions 2-133.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P40711. 8 interactions.
    STRINGi 511145.b0191.

    Proteomic databases

    PaxDbi P40711.
    PRIDEi P40711.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73302 ; AAC73302 ; b0191 .
    BAA77867 ; BAA77867 ; BAA77867 .
    GeneIDi 12934377.
    946046.
    KEGGi ecj:Y75_p0188.
    eco:b0191.
    PATRICi 32115495. VBIEscCol129921_0199.

    Organism-specific databases

    EchoBASEi EB2258.
    EcoGenei EG12354. arfB.

    Phylogenomic databases

    eggNOGi COG1186.
    HOGENOMi HOG000244440.
    KOi K15034.
    OMAi FDINASS.
    OrthoDBi EOG628F97.
    PhylomeDBi P40711.

    Enzyme and pathway databases

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

    Miscellaneous databases

    PROi P40711.

    Gene expression databases

    Genevestigatori P40711.

    Family and domain databases

    InterProi IPR000352. Pep_chain_release_fac_I_II.
    [Graphical view ]
    Pfami PF00472. RF-1. 1 hit.
    [Graphical view ]
    PROSITEi PS00745. RF_PROK_I. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 98 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