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P46948

- RRP41_YEAST

UniProt

P46948 - RRP41_YEAST

Protein

Exosome complex component SKI6

Gene

SKI6

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 134 (01 Oct 2014)
      Sequence version 1 (01 Nov 1995)
      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. SKI6 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. nonfunctional rRNA decay Source: SGD
    3. nuclear mRNA surveillance Source: SGD
    4. nuclear polyadenylation-dependent CUT catabolic process Source: SGD
    5. nuclear polyadenylation-dependent mRNA 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
    11. rRNA catabolic process Source: SGD
    12. U1 snRNA 3'-end processing Source: SGD
    13. U4 snRNA 3'-end processing Source: SGD
    14. U5 snRNA 3'-end processing Source: SGD

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30881-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exosome complex component SKI6
    Alternative name(s):
    Extracellular mutant protein 20
    Ribosomal RNA-processing protein 41
    Superkiller protein 6
    Gene namesi
    Name:SKI6
    Synonyms:ECM20, RRP41
    Ordered Locus Names:YGR195W
    ORF Names:G7587
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VII

    Organism-specific databases

    CYGDiYGR195w.
    SGDiS000003427. SKI6.

    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

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi62 – 632KS → ED: Impairs RNA-binding (at the proposed ring entry site). 1 Publication
    Mutagenesisi95 – 962RR → EE: Impairs RNA-binding (at the proposed ring exit site). 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 246246Exosome complex component SKI6PRO_0000139962Add
    BLAST

    Proteomic databases

    MaxQBiP46948.
    PaxDbiP46948.

    Expressioni

    Gene expression databases

    GenevestigatoriP46948.

    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.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CSL4P538599EBI-1788,EBI-1731
    DIS3Q0816210EBI-1788,EBI-1740
    MTR3P482404EBI-1788,EBI-1749
    RRP4P387924EBI-1788,EBI-1757
    RRP40Q082854EBI-1788,EBI-1831
    RRP42Q122774EBI-1788,EBI-1765
    RRP43P253594EBI-1788,EBI-1773
    RRP45Q056368EBI-1788,EBI-1810
    RRP46P532565EBI-1788,EBI-1842

    Protein-protein interaction databases

    BioGridi33448. 40 interactions.
    DIPiDIP-2083N.
    IntActiP46948. 22 interactions.
    MINTiMINT-555587.
    STRINGi4932.YGR195W.

    Structurei

    Secondary structure

    1
    246
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi29 – 313
    Turni33 – 353
    Beta strandi37 – 448
    Beta strandi47 – 5711
    Beta strandi67 – 693
    Beta strandi71 – 788
    Beta strandi82 – 854
    Helixi95 – 10814
    Turni109 – 1113
    Helixi114 – 1163
    Beta strandi121 – 13010
    Helixi135 – 14915
    Beta strandi154 – 1563
    Beta strandi158 – 1669
    Beta strandi169 – 1735
    Helixi176 – 1794
    Beta strandi182 – 1909
    Beta strandi193 – 2019
    Helixi207 – 24034

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2WP8X-ray3.00B1-246[»]
    4IFDX-ray2.80B1-246[»]
    ProteinModelPortaliP46948.
    SMRiP46948. Positions 1-242.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP46948.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the RNase PH family.Curated

    Phylogenomic databases

    eggNOGiCOG0689.
    GeneTreeiENSGT00550000074804.
    HOGENOMiHOG000229515.
    KOiK11600.
    OMAiDYVCACT.
    OrthoDBiEOG7Z0K74.

    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.

    P46948-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSRLEIYSPE GLRLDGRRWN ELRRFESSIN THPHAADGSS YMEQGNNKII    50
    TLVKGPKEPR LKSQMDTSKA LLNVSVNITK FSKFERSKSS HKNERRVLEI 100
    QTSLVRMFEK NVMLNIYPRT VIDIEIHVLE QDGGIMGSLI NGITLALIDA 150
    GISMFDYISG ISVGLYDTTP LLDTNSLEEN AMSTVTLGVV GKSEKLSLLL 200
    VEDKIPLDRL ENVLAIGIAG AHRVRDLMDE ELRKHAQKRV SNASAR 246
    Length:246
    Mass (Da):27,561
    Last modified:November 1, 1995 - v1
    Checksum:iC80EFFB528A43044
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X82775 Genomic DNA. Translation: CAA58018.1.
    Z72980 Genomic DNA. Translation: CAA97221.1.
    Z72981 Genomic DNA. Translation: CAA97223.1.
    AY558509 Genomic DNA. Translation: AAS56835.1.
    BK006941 Genomic DNA. Translation: DAA08288.1.
    PIRiS59180.
    RefSeqiNP_011711.3. NM_001181324.3.

    Genome annotation databases

    EnsemblFungiiYGR195W; YGR195W; YGR195W.
    GeneIDi853109.
    KEGGisce:YGR195W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X82775 Genomic DNA. Translation: CAA58018.1 .
    Z72980 Genomic DNA. Translation: CAA97221.1 .
    Z72981 Genomic DNA. Translation: CAA97223.1 .
    AY558509 Genomic DNA. Translation: AAS56835.1 .
    BK006941 Genomic DNA. Translation: DAA08288.1 .
    PIRi S59180.
    RefSeqi NP_011711.3. NM_001181324.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2WP8 X-ray 3.00 B 1-246 [» ]
    4IFD X-ray 2.80 B 1-246 [» ]
    ProteinModelPortali P46948.
    SMRi P46948. Positions 1-242.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33448. 40 interactions.
    DIPi DIP-2083N.
    IntActi P46948. 22 interactions.
    MINTi MINT-555587.
    STRINGi 4932.YGR195W.

    Proteomic databases

    MaxQBi P46948.
    PaxDbi P46948.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YGR195W ; YGR195W ; YGR195W .
    GeneIDi 853109.
    KEGGi sce:YGR195W.

    Organism-specific databases

    CYGDi YGR195w.
    SGDi S000003427. SKI6.

    Phylogenomic databases

    eggNOGi COG0689.
    GeneTreei ENSGT00550000074804.
    HOGENOMi HOG000229515.
    KOi K11600.
    OMAi DYVCACT.
    OrthoDBi EOG7Z0K74.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30881-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P46948.
    NextBioi 973121.
    PROi P46948.

    Gene expression databases

    Genevestigatori P46948.

    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 complete sequence of a 9000 bp fragment of the right arm of Saccharomyces cerevisiae chromosome VII contains four previously unknown open reading frames."
      Guerreiro P., Maia e Silva A., Barreiros T., Arroyo J., Garcia-Gonzalez M., Garcia-Saez M.I., Rodrigues-Pousada C., Nombela C.
      Yeast 11:1087-1091(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. "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.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases."
      Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D.
      Cell 91:457-466(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBUNIT.
    6. "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: IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS SPECTROMETRY.
    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.
    12. "The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation."
      Bonneau F., Basquin J., Ebert J., Lorentzen E., Conti E.
      Cell 139:547-559(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH RRP45 AND DIS3, MUTAGENESIS OF 62-LYS-SER-63 AND 95-ARG-ARG-96.

    Entry informationi

    Entry nameiRRP41_YEAST
    AccessioniPrimary (citable) accession number: P46948
    Secondary accession number(s): D6VUX7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1995
    Last modified: October 1, 2014
    This is version 134 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 5150 molecules/cell in log phase SD medium.1 Publication

    Caution

    Was originally thought to have exonuclease activity but it was later shown (PubMed:17173052 and PubMed:17174896) that only DIS3/RRP44 subunit of the exosome core has this activity.1 Publication

    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