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P25359

- RRP43_YEAST

UniProt

P25359 - RRP43_YEAST

Protein

Exosome complex component RRP43

Gene

RRP43

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 130 (01 Oct 2014)
      Sequence version 2 (27 Jun 2003)
      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. RRP43 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.4 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. mRNA catabolic process Source: UniProtKB
    3. ncRNA 3'-end processing Source: SGD
    4. nonfunctional rRNA decay Source: SGD
    5. nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
    6. nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
    7. nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
    8. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
    9. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
    10. nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
    11. polyadenylation-dependent snoRNA 3'-end processing Source: SGD
    12. rRNA metabolic process Source: UniProtKB

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29348-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exosome complex component RRP43
    Alternative name(s):
    Ribosomal RNA-processing protein 43
    Gene namesi
    Name:RRP43
    Ordered Locus Names:YCR035C
    ORF Names:YCR35C, YCR522
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome III

    Organism-specific databases

    CYGDiYCR035c.
    SGDiS000000631. RRP43.

    Subcellular locationi

    Cytoplasm 1 Publication. Nucleusnucleolus 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. cytoplasmic exosome (RNase complex) Source: SGD
    3. nuclear exosome (RNase complex) Source: SGD
    4. nucleolus Source: SGD
    5. nucleoplasm Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Exosome, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi162 – 1621S → F: Interaction with RRP46 abolished; when associated with T-246. 1 Publication
    Mutagenesisi212 – 2121V → A: Interaction with RRP46 abolished. 1 Publication
    Mutagenesisi230 – 2301C → Y: Interaction with RRP46 abolished; when associated with T-274 and Y-276. 1 Publication
    Mutagenesisi246 – 2461A → T: Interaction with RRP46 abolished; when associated with F-162. 1 Publication
    Mutagenesisi274 – 2741I → T: Interaction with RRP46 abolished; when associated with Y-230 and Y-276. 1 Publication
    Mutagenesisi276 – 2761C → Y: Interaction with RRP46 abolished; when associated with Y-230 and T-274. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 394393Exosome complex component RRP43PRO_0000139970Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanine1 Publication
    Modified residuei26 – 261Phosphoserine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiP25359.
    PaxDbiP25359.
    PeptideAtlasiP25359.

    Expressioni

    Gene expression databases

    GenevestigatoriP25359.

    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 NIP7 and NOP8. Interacts strongly with RRP46.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CSL4P538597EBI-1773,EBI-1731
    NIP7Q089624EBI-1773,EBI-12067
    PIH1P387682EBI-1773,EBI-24499
    SKI6P469484EBI-1773,EBI-1788

    Protein-protein interaction databases

    BioGridi31018. 32 interactions.
    DIPiDIP-5485N.
    IntActiP25359. 17 interactions.
    MINTiMINT-564723.
    STRINGi4932.YCR035C.

    Structurei

    Secondary structure

    1
    394
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi10 – 123
    Helixi19 – 257
    Helixi27 – 359
    Turni36 – 383
    Beta strandi48 – 503
    Beta strandi53 – 608
    Beta strandi65 – 673
    Beta strandi76 – 827
    Beta strandi85 – 9814
    Helixi124 – 1263
    Beta strandi131 – 1366
    Helixi146 – 16116
    Helixi167 – 1704
    Beta strandi175 – 1806
    Turni181 – 1833
    Beta strandi184 – 1885
    Beta strandi208 – 22114
    Helixi227 – 23812
    Beta strandi242 – 2498
    Beta strandi257 – 2604
    Beta strandi265 – 2684
    Beta strandi275 – 2839
    Turni288 – 2903
    Beta strandi293 – 3019
    Helixi304 – 3063
    Beta strandi328 – 3336
    Helixi336 – 3427
    Beta strandi345 – 3517
    Beta strandi357 – 36711
    Helixi371 – 39121

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IFDX-ray2.80C2-394[»]
    ProteinModelPortaliP25359.
    SMRiP25359. Positions 7-394.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the RNase PH family.Curated

    Phylogenomic databases

    eggNOGiNOG286862.
    HOGENOMiHOG000057141.
    KOiK12586.
    OMAiTIYYPDL.
    OrthoDBiEOG7CCC3J.

    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P25359-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAESTTLETI EIHPITFPPE VLARISPELS LQRHLSLGIR PCLRKYEEFR    50
    DVAIENNTLS RYADAGNIDT KNNILGSNVL KSGKTIVITS ITGGIIEETS 100
    AAIKDLDDFG EEELFEVTKE EDIIANYASV YPVVEVERGR VGACTDEEMT 150
    ISQKLHDSIL HSRILPKKAL KVKAGVRSAN EDGTFSVLYP DELEDDTLNE 200
    TNLKMKRKWS YVLYAKIVVL SRTGPVFDLC WNSLMYALQS VKLPRAFIDE 250
    RASDLRMTIR TRGRSATIRE TYEIICDQTK SVPLMINAKN IAFASNYGIV 300
    ELDPECQLQN SDNSEEEEVD IDMDKLNTVL IADLDTEAEE TSIHSTISIL 350
    AAPSGNYKQL TLVGGGAKIT PEMIKRSLLL SRVRADDLST RFNI 394
    Length:394
    Mass (Da):44,011
    Last modified:June 27, 2003 - v2
    Checksum:i8801837B8184134D
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti102 – 1021A → S in CAA40227. (PubMed:1964349)Curated
    Sequence conflicti363 – 3631V → M in CAA40227. (PubMed:1964349)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X56909 Genomic DNA. Translation: CAA40227.1.
    X59720 Genomic DNA. Translation: CAC42984.1.
    S78624 Genomic DNA. Translation: AAB21261.1.
    BK006937 Genomic DNA. Translation: DAA07514.1.
    PIRiS12917.
    RefSeqiNP_009964.2. NM_001178749.1.

    Genome annotation databases

    EnsemblFungiiYCR035C; YCR035C; YCR035C.
    GeneIDi850401.
    KEGGisce:YCR035C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X56909 Genomic DNA. Translation: CAA40227.1 .
    X59720 Genomic DNA. Translation: CAC42984.1 .
    S78624 Genomic DNA. Translation: AAB21261.1 .
    BK006937 Genomic DNA. Translation: DAA07514.1 .
    PIRi S12917.
    RefSeqi NP_009964.2. NM_001178749.1.

    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 C 2-394 [» ]
    ProteinModelPortali P25359.
    SMRi P25359. Positions 7-394.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31018. 32 interactions.
    DIPi DIP-5485N.
    IntActi P25359. 17 interactions.
    MINTi MINT-564723.
    STRINGi 4932.YCR035C.

    Proteomic databases

    MaxQBi P25359.
    PaxDbi P25359.
    PeptideAtlasi P25359.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YCR035C ; YCR035C ; YCR035C .
    GeneIDi 850401.
    KEGGi sce:YCR035C.

    Organism-specific databases

    CYGDi YCR035c.
    SGDi S000000631. RRP43.

    Phylogenomic databases

    eggNOGi NOG286862.
    HOGENOMi HOG000057141.
    KOi K12586.
    OMAi TIYYPDL.
    OrthoDBi EOG7CCC3J.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29348-MONOMER.

    Miscellaneous databases

    NextBioi 965938.

    Gene expression databases

    Genevestigatori P25359.

    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 complete sequence of the 8.2 kb segment left of MAT on chromosome III reveals five ORFs, including a gene for a yeast ribokinase."
      Thierry A., Fairhead C., Dujon B.
      Yeast 6:521-534(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 96604 / S288c / FY1679.
    2. "The complete DNA sequence of yeast chromosome III."
      Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M.
      , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
      Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Valles G., Volckaerts G.
      Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION TO 102 AND 363.
    4. Cited for: GENOME REANNOTATION.
      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: PROTEIN SEQUENCE OF 25-33, FUNCTION, SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY.
    6. "The complete sequence of a 7.5 kb region of chromosome III from Saccharomyces cerevisiae that lies between CRY1 and MAT."
      Wicksteed B.L., Roberts A.B., Sagliocco F.A., Brown A.J.P.
      Yeast 7:761-772(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 232-394.
    7. "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.
    8. "The exosome subunit Rrp43p is required for the efficient maturation of 5.8S, 18S and 25S rRNA."
      Zanchin N.I., Goldfarb D.S.
      Nucleic Acids Res. 27:1283-1288(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Temperature-sensitive mutants of the exosome subunit Rrp43p show a deficiency in mRNA degradation and no longer interact with the exosome."
      Oliveira C.C., Gonzales F.A., Zanchin N.I.
      Nucleic Acids Res. 30:4186-4198(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH RRP46, MUTAGENESIS OF SER-162; VAL-212; CYS-230; ALA-246; ILE-274 AND CYS-276.
    10. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    12. "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.
    13. Erratum
      Liu Q., Greimann J.C., Lima C.D.
      Cell 131:188-189(2007)
    14. "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.
    15. "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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-26, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiRRP43_YEAST
    AccessioniPrimary (citable) accession number: P25359
    Secondary accession number(s): D6VR45, Q8NKJ5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: June 27, 2003
    Last modified: October 1, 2014
    This is version 130 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 3180 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, Direct protein sequencing, 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 III
      Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

    External Data

    Dasty 3