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Q08285

- RRP40_YEAST

UniProt

Q08285 - RRP40_YEAST

Protein

Exosome complex component RRP40

Gene

RRP40

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 (21 Sep 2011)
      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. RRP40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.3 Publications

    GO - Molecular functioni

    1. manganese ion binding Source: SGD
    2. protein binding Source: IntAct
    3. RNA binding Source: SGD

    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-33533-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exosome complex component RRP40
    Alternative name(s):
    Ribosomal RNA-processing protein 40
    Gene namesi
    Name:RRP40
    Ordered Locus Names:YOL142W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XV

    Organism-specific databases

    CYGDiYOL142w.
    SGDiS000005502. RRP40.

    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 – 240240Exosome complex component RRP40PRO_0000097453Add
    BLAST

    Proteomic databases

    MaxQBiQ08285.
    PaxDbiQ08285.
    PeptideAtlasiQ08285.

    Expressioni

    Gene expression databases

    GenevestigatoriQ08285.

    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.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CSL4P538595EBI-1831,EBI-1731
    DIS3Q081624EBI-1831,EBI-1740
    SKI6P469484EBI-1831,EBI-1788

    Protein-protein interaction databases

    BioGridi34275. 18 interactions.
    DIPiDIP-5330N.
    IntActiQ08285. 17 interactions.
    MINTiMINT-530842.
    STRINGi4932.YOL142W.

    Structurei

    Secondary structure

    1
    240
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi19 – 213
    Beta strandi25 – 273
    Turni29 – 313
    Beta strandi34 – 363
    Beta strandi40 – 445
    Beta strandi53 – 597
    Beta strandi71 – 799
    Beta strandi81 – 899
    Beta strandi95 – 984
    Beta strandi118 – 1258
    Beta strandi133 – 1375
    Turni139 – 1413
    Beta strandi154 – 1574
    Helixi160 – 1689
    Helixi174 – 1796
    Beta strandi185 – 1895
    Turni190 – 1923
    Beta strandi193 – 1975
    Helixi201 – 21717
    Helixi223 – 23513

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2JA9X-ray2.20A62-236[»]
    4IFDX-ray2.80G1-240[»]
    ProteinModelPortaliQ08285.
    SMRiQ08285. Positions 1-236.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ08285.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini67 – 13771S1 motifAdd
    BLAST

    Sequence similaritiesi

    Belongs to the RRP40 family.Curated
    Contains 1 S1 motif domain.Curated

    Phylogenomic databases

    eggNOGiCOG1097.
    GeneTreeiENSGT00390000012042.
    HOGENOMiHOG000184644.
    KOiK03681.
    OMAiHMDAELE.
    OrthoDBiEOG7FJHC7.

    Family and domain databases

    InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    IPR022967. RNA-binding_domain_S1.
    [Graphical view]
    PANTHERiPTHR21321. PTHR21321. 1 hit.
    SMARTiSM00316. S1. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 1 hit.
    SSF54791. SSF54791. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q08285-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTFIFPGDS FPVDPTTPVK LGPGIYCDPN TQEIRPVNTG VLHVSAKGKS    50
    GVQTAYIDYS SKRYIPSVND FVIGVIIGTF SDSYKVSLQN FSSSVSLSYM 100
    AFPNASKKNR PTLQVGDLVY ARVCTAEKEL EAEIECFDST TGRDAGFGIL 150
    EDGMIIDVNL NFARQLLFNN DFPLLKVLAA HTKFEVAIGL NGKIWVKCEE 200
    LSNTLACYRT IMECCQKNDT AAFKDIAKRQ FKEILTVKEE 240
    Length:240
    Mass (Da):26,556
    Last modified:September 21, 2011 - v2
    Checksum:i62B3A30348BBAA7C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti160 – 1601L → F in CAA99163. (PubMed:9169874)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z74884 Genomic DNA. Translation: CAA99163.1.
    AY692926 Genomic DNA. Translation: AAT92945.1.
    BK006948 Genomic DNA. Translation: DAA10643.2.
    PIRiS61872.
    RefSeqiNP_014499.2. NM_001183396.2.

    Genome annotation databases

    EnsemblFungiiYOL142W; YOL142W; YOL142W.
    GeneIDi854023.
    KEGGisce:YOL142W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z74884 Genomic DNA. Translation: CAA99163.1 .
    AY692926 Genomic DNA. Translation: AAT92945.1 .
    BK006948 Genomic DNA. Translation: DAA10643.2 .
    PIRi S61872.
    RefSeqi NP_014499.2. NM_001183396.2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2JA9 X-ray 2.20 A 62-236 [» ]
    4IFD X-ray 2.80 G 1-240 [» ]
    ProteinModelPortali Q08285.
    SMRi Q08285. Positions 1-236.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34275. 18 interactions.
    DIPi DIP-5330N.
    IntActi Q08285. 17 interactions.
    MINTi MINT-530842.
    STRINGi 4932.YOL142W.

    Proteomic databases

    MaxQBi Q08285.
    PaxDbi Q08285.
    PeptideAtlasi Q08285.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YOL142W ; YOL142W ; YOL142W .
    GeneIDi 854023.
    KEGGi sce:YOL142W.

    Organism-specific databases

    CYGDi YOL142w.
    SGDi S000005502. RRP40.

    Phylogenomic databases

    eggNOGi COG1097.
    GeneTreei ENSGT00390000012042.
    HOGENOMi HOG000184644.
    KOi K03681.
    OMAi HMDAELE.
    OrthoDBi EOG7FJHC7.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33533-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q08285.
    NextBioi 975559.
    PROi Q08285.

    Gene expression databases

    Genevestigatori Q08285.

    Family and domain databases

    InterProi IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    IPR022967. RNA-binding_domain_S1.
    [Graphical view ]
    PANTHERi PTHR21321. PTHR21321. 1 hit.
    SMARTi SM00316. S1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50249. SSF50249. 1 hit.
    SSF54791. SSF54791. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
      Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
      , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
      Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 160.
      Strain: ATCC 204508 / S288c.
    3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    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: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    7. "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.
    8. Erratum
      Liu Q., Greimann J.C., Lima C.D.
      Cell 131:188-189(2007)
    9. "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, INTERACTION OF THE EXOSOME WITH RRP6 AND SKI7, SUBUNIT.
    10. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities."
      Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G., Sanchez-Rotunno M., Arraiano C.M., van Hoof A.
      Nat. Struct. Mol. Biol. 16:56-62(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN RNA EXOSOME COMPLEX STABILITY.

    Entry informationi

    Entry nameiRRP40_YEAST
    AccessioniPrimary (citable) accession number: Q08285
    Secondary accession number(s): D6W1S7, E9P8Z4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 2001
    Last sequence update: September 21, 2011
    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 6050 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 XV
      Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

    External Data

    Dasty 3