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Q12277

- RRP42_YEAST

UniProt

Q12277 - RRP42_YEAST

Protein

Exosome complex component RRP42

Gene

RRP42

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 116 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      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. RRP42 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 tRNA catabolic process Source: SGD
    6. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
    7. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
    8. nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
    9. polyadenylation-dependent snoRNA 3'-end processing Source: SGD
    10. rRNA catabolic process Source: SGD

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29512-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exosome complex component RRP42
    Alternative name(s):
    Ribosomal RNA-processing protein 42
    Gene namesi
    Name:RRP42
    Ordered Locus Names:YDL111C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDL111c.
    SGDiS000002269. RRP42.

    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 – 265265Exosome complex component RRP42PRO_0000139966Add
    BLAST

    Proteomic databases

    MaxQBiQ12277.
    PaxDbiQ12277.

    Expressioni

    Gene expression databases

    GenevestigatoriQ12277.

    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.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CSL4P538598EBI-1765,EBI-1731
    MTR3P482403EBI-1765,EBI-1749
    SKI6P469484EBI-1765,EBI-1788

    Protein-protein interaction databases

    BioGridi31951. 49 interactions.
    DIPiDIP-1463N.
    IntActiQ12277. 25 interactions.
    MINTiMINT-410864.
    STRINGi4932.YDL111C.

    Structurei

    Secondary structure

    1
    265
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 1612
    Beta strandi17 – 193
    Beta strandi34 – 396
    Beta strandi44 – 518
    Beta strandi57 – 6812
    Turni69 – 713
    Beta strandi75 – 828
    Helixi90 – 10213
    Turni105 – 1073
    Helixi111 – 1144
    Beta strandi117 – 13216
    Helixi138 – 14912
    Beta strandi153 – 1575
    Turni163 – 1664
    Beta strandi172 – 1798
    Beta strandi186 – 1938
    Beta strandi196 – 2005
    Helixi203 – 2086
    Beta strandi210 – 2189
    Beta strandi221 – 2288
    Beta strandi233 – 2353
    Helixi241 – 26222

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IFDX-ray2.80E1-265[»]
    ProteinModelPortaliQ12277.
    SMRiQ12277. Positions 1-265.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the RNase PH family.Curated

    Phylogenomic databases

    eggNOGiCOG2123.
    HOGENOMiHOG000248003.
    KOiK12589.
    OMAiECIVSVK.
    OrthoDBiEOG71GB6Q.

    Family and domain databases

    InterProiIPR001247. ExoRNase_PH_dom1.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    [Graphical view]
    PfamiPF01138. RNase_PH. 1 hit.
    [Graphical view]
    SUPFAMiSSF54211. SSF54211. 2 hits.

    Sequencei

    Sequence statusi: Complete.

    Q12277-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSLSVAEKSY LYDSLASTPS IRPDGRLPHQ FRPIEIFTDF LPSSNGSSRI    50
    IASDGSECIV SIKSKVVDHH VENELLQVDV DIAGQRDDAL VVETITSLLN 100
    KVLKSGSGVD SSKLQLTKKY SFKIFVDVLV ISSHSHPVSL ISFAIYSALN 150
    STYLPKLISA FDDLEVEELP TFHDYDMVKL DINPPLVFIL AVVGNNMLLD 200
    PAANESEVAN NGLIISWSNG KITSPIRSVA LNDSNVKSFK PHLLKQGLAM 250
    VEKYAPDVVR SLENL 265
    Length:265
    Mass (Da):29,055
    Last modified:November 1, 1996 - v1
    Checksum:i806C60979642C67E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X95644 Genomic DNA. Translation: CAA64901.1.
    Z74159 Genomic DNA. Translation: CAA98678.1.
    BK006938 Genomic DNA. Translation: DAA11749.1.
    PIRiS67653.
    RefSeqiNP_010172.1. NM_001180170.1.

    Genome annotation databases

    EnsemblFungiiYDL111C; YDL111C; YDL111C.
    GeneIDi851447.
    KEGGisce:YDL111C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X95644 Genomic DNA. Translation: CAA64901.1 .
    Z74159 Genomic DNA. Translation: CAA98678.1 .
    BK006938 Genomic DNA. Translation: DAA11749.1 .
    PIRi S67653.
    RefSeqi NP_010172.1. NM_001180170.1.

    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 E 1-265 [» ]
    ProteinModelPortali Q12277.
    SMRi Q12277. Positions 1-265.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31951. 49 interactions.
    DIPi DIP-1463N.
    IntActi Q12277. 25 interactions.
    MINTi MINT-410864.
    STRINGi 4932.YDL111C.

    Proteomic databases

    MaxQBi Q12277.
    PaxDbi Q12277.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDL111C ; YDL111C ; YDL111C .
    GeneIDi 851447.
    KEGGi sce:YDL111C.

    Organism-specific databases

    CYGDi YDL111c.
    SGDi S000002269. RRP42.

    Phylogenomic databases

    eggNOGi COG2123.
    HOGENOMi HOG000248003.
    KOi K12589.
    OMAi ECIVSVK.
    OrthoDBi EOG71GB6Q.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29512-MONOMER.

    Miscellaneous databases

    NextBioi 968699.

    Gene expression databases

    Genevestigatori Q12277.

    Family and domain databases

    InterProi IPR001247. ExoRNase_PH_dom1.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    [Graphical view ]
    Pfami PF01138. RNase_PH. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54211. SSF54211. 2 hits.
    ProtoNeti Search...

    Publicationsi

    1. "The sequence of a 16,691 bp segment of Saccharomyces cerevisiae chromosome IV identifies the DUN1, PMT1, PMT5, SRP14 and DPR1 genes, and five new open reading frames."
      Boskovic J., Soler-Mira A., Garcia-Cantalejo J.M., Ballesta J.P.G., Jimenez A., Remacha M.A.
      Yeast 12:1377-1384(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 96604 / S288c / FY1679.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(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. "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.
    5. "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 EXOSOME COMPLEX BY MASS SPECTROMETRY.
    6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    8. "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.
    9. Erratum
      Liu Q., Greimann J.C., Lima C.D.
      Cell 131:188-189(2007)
    10. "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 nameiRRP42_YEAST
    AccessioniPrimary (citable) accession number: Q12277
    Secondary accession number(s): D6VRN9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 116 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 7110 molecules/cell in log phase SD medium.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 IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3