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P53256

- RRP46_YEAST

UniProt

P53256 - RRP46_YEAST

Protein

Exosome complex component RRP46

Gene

RRP46

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 117 (01 Oct 2014)
      Sequence version 2 (31 Oct 2006)
      Previous versions | rss
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    Functioni

    Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. RRP46 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.2 Publications

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. RNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
    2. ncRNA 3'-end processing Source: SGD
    3. nonfunctional rRNA decay Source: SGD
    4. nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
    5. nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
    6. nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
    7. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
    8. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
    9. nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
    10. polyadenylation-dependent snoRNA 3'-end processing Source: SGD

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30805-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exosome complex component RRP46
    Alternative name(s):
    Ribosomal RNA-processing protein 46
    Gene namesi
    Name:RRP46
    Ordered Locus Names:YGR095C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VII

    Organism-specific databases

    CYGDiYGR095c.
    SGDiS000003327. RRP46.

    Subcellular locationi

    Cytoplasm 1 Publication. Nucleusnucleolus 1 Publication

    GO - Cellular componenti

    1. cytoplasmic exosome (RNase complex) Source: SGD
    2. nuclear exosome (RNase complex) Source: SGD
    3. nucleolus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Exosome, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 223223Exosome complex component RRP46PRO_0000139978Add
    BLAST

    Proteomic databases

    MaxQBiP53256.
    PaxDbiP53256.
    PeptideAtlasiP53256.

    Expressioni

    Gene expression databases

    GenevestigatoriP53256.

    Interactioni

    Subunit structurei

    Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which associates with catalytic subunits DIS3 and RRP6 in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits and peripheral S1 domain-containing components CSL4, RRP4 and RRP40 located on the top of the ring structure. Interacts with LRP1.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CSL4P538597EBI-1842,EBI-1731
    DIS3Q081626EBI-1842,EBI-1740
    SKI6P469485EBI-1842,EBI-1788

    Protein-protein interaction databases

    BioGridi33338. 31 interactions.
    DIPiDIP-6838N.
    IntActiP53256. 23 interactions.
    MINTiMINT-2732969.
    STRINGi4932.YGR095C.

    Structurei

    Secondary structure

    1
    223
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 74
    Beta strandi11 – 2111
    Beta strandi24 – 3411
    Turni38 – 403
    Beta strandi43 – 5311
    Beta strandi55 – 573
    Helixi61 – 7717
    Helixi80 – 823
    Beta strandi86 – 9611
    Turni101 – 1033
    Helixi106 – 12318
    Beta strandi127 – 13913
    Turni140 – 1423
    Beta strandi145 – 1484
    Helixi151 – 1555
    Beta strandi157 – 16812
    Turni169 – 1724
    Beta strandi173 – 18614
    Helixi188 – 21730
    Turni218 – 2203

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IFDX-ray2.80D1-223[»]
    ProteinModelPortaliP53256.
    SMRiP53256. Positions 1-223.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the RNase PH family.Curated

    Phylogenomic databases

    eggNOGiCOG0689.
    GeneTreeiENSGT00550000075002.
    HOGENOMiHOG000248419.
    KOiK12590.
    OMAiRRDEHAY.
    OrthoDBiEOG7C8GTX.

    Family and domain databases

    Gene3Di3.30.230.70. 1 hit.
    InterProiIPR001247. ExoRNase_PH_dom1.
    IPR015847. ExoRNase_PH_dom2.
    IPR027408. PNPase/RNase_PH_dom.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    [Graphical view]
    PfamiPF01138. RNase_PH. 1 hit.
    PF03725. RNase_PH_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF54211. SSF54211. 1 hit.
    SSF55666. SSF55666. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P53256-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSVQAEIGIL DHVDGSSEFV SQDTKVICSV TGPIEPKARQ ELPTQLALEI    50
    IVRPAKGVAT TREKVLEDKL RAVLTPLITR HCYPRQLCQI TCQILESGED 100
    EAEFSLRELS CCINAAFLAL VDAGIALNSM CASIPIAIIK DTSDIIVDPT 150
    AEQLKISLSV HTLALEFVNG GKVVKNVLLL DSNGDFNEDQ LFSLLELGEQ 200
    KCQELVTNIR RIIQDNISPR LVV 223
    Length:223
    Mass (Da):24,407
    Last modified:October 31, 2006 - v2
    Checksum:iF1307E0EE4FC3133
    GO

    Sequence cautioni

    The sequence CAA97098.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z72880 Genomic DNA. Translation: CAA97098.1. Different initiation.
    AY389297 mRNA. Translation: AAQ97229.1.
    BK006941 Genomic DNA. Translation: DAA08188.1.
    PIRiS64390.
    RefSeqiNP_011609.2. NM_001181224.1.

    Genome annotation databases

    EnsemblFungiiYGR095C; YGR095C; YGR095C.
    GeneIDi852987.
    KEGGisce:YGR095C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z72880 Genomic DNA. Translation: CAA97098.1 . Different initiation.
    AY389297 mRNA. Translation: AAQ97229.1 .
    BK006941 Genomic DNA. Translation: DAA08188.1 .
    PIRi S64390.
    RefSeqi NP_011609.2. NM_001181224.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4IFD X-ray 2.80 D 1-223 [» ]
    ProteinModelPortali P53256.
    SMRi P53256. Positions 1-223.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33338. 31 interactions.
    DIPi DIP-6838N.
    IntActi P53256. 23 interactions.
    MINTi MINT-2732969.
    STRINGi 4932.YGR095C.

    Proteomic databases

    MaxQBi P53256.
    PaxDbi P53256.
    PeptideAtlasi P53256.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YGR095C ; YGR095C ; YGR095C .
    GeneIDi 852987.
    KEGGi sce:YGR095C.

    Organism-specific databases

    CYGDi YGR095c.
    SGDi S000003327. RRP46.

    Phylogenomic databases

    eggNOGi COG0689.
    GeneTreei ENSGT00550000075002.
    HOGENOMi HOG000248419.
    KOi K12590.
    OMAi RRDEHAY.
    OrthoDBi EOG7C8GTX.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30805-MONOMER.

    Miscellaneous databases

    NextBioi 972806.
    PROi P53256.

    Gene expression databases

    Genevestigatori P53256.

    Family and domain databases

    Gene3Di 3.30.230.70. 1 hit.
    InterProi IPR001247. ExoRNase_PH_dom1.
    IPR015847. ExoRNase_PH_dom2.
    IPR027408. PNPase/RNase_PH_dom.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    [Graphical view ]
    Pfami PF01138. RNase_PH. 1 hit.
    PF03725. RNase_PH_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54211. SSF54211. 1 hit.
    SSF55666. SSF55666. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
      Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
      , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
      Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. Kennedy M.C., Dietrich F.S.
      Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-67.
      Strain: ATCC 204511 / S288c / AB972.
    4. "The yeast exosome and human PM-Scl are related complexes of 3'-->5' exonucleases."
      Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D., Mitchell P.
      Genes Dev. 13:2148-2158(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, IDENTIFICATION IN THE EXOSOME COMPLEX BY MASS SPECTROMETRY.
    5. Cited for: INTERACTION WITH LRP1.
    6. "Sequencing and comparison of yeast species to identify genes and regulatory elements."
      Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.
      Nature 423:241-254(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
    7. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    9. "Reconstitution, activities, and structure of the eukaryotic RNA exosome."
      Liu Q., Greimann J.C., Lima C.D.
      Cell 127:1223-1237(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: RECONSTITUTION OF THE RNA EXOSOME COMPLEX, LACK OF EXONUCLEASE ACTIVITY.
    10. Erratum
      Liu Q., Greimann J.C., Lima C.D.
      Cell 131:188-189(2007)
    11. "A single subunit, Dis3, is essentially responsible for yeast exosome core activity."
      Dziembowski A., Lorentzen E., Conti E., Seraphin B.
      Nat. Struct. Mol. Biol. 14:15-22(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION OF THE RNA EXOSOME COMPLEX, SUBUNIT.

    Entry informationi

    Entry nameiRRP46_YEAST
    AccessioniPrimary (citable) accession number: P53256
    Secondary accession number(s): D6VUM7, Q6TQU1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 31, 2006
    Last modified: October 1, 2014
    This is version 117 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 10800 molecules/cell in log phase SD medium.1 Publication

    Caution

    According to PubMed:17173052 and PubMed:17174896, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.Curated

    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. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

    External Data

    Dasty 3