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P53859

- CSL4_YEAST

UniProt

P53859 - CSL4_YEAST

Protein

Exosome complex component CSL4

Gene

CSL4

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 127 (01 Oct 2014)
      Sequence version 1 (01 Oct 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.3 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-33232-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exosome complex component CSL4
    Alternative name(s):
    CEP1 synthetic lethal protein 4
    Gene namesi
    Name:CSL4
    Synonyms:SKI4
    Ordered Locus Names:YNL232W
    ORF Names:N1154
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIV

    Organism-specific databases

    CYGDiYNL232w.
    SGDiS000005176. CSL4.

    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: UniProtKB-SubCell
    5. nucleus Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Exosome, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 292292Exosome complex component CSL4PRO_0000079403Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei94 – 941Phosphoserine2 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP53859.
    PaxDbiP53859.
    PeptideAtlasiP53859.
    PRIDEiP53859.

    Expressioni

    Gene expression databases

    GenevestigatoriP53859.

    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
    MTR3P482408EBI-1731,EBI-1749
    RRP4P387927EBI-1731,EBI-1757
    RRP40Q082855EBI-1731,EBI-1831
    RRP42Q122778EBI-1731,EBI-1765
    RRP43P253597EBI-1731,EBI-1773
    RRP45Q056367EBI-1731,EBI-1810
    RRP46P532567EBI-1731,EBI-1842
    SKI6P469489EBI-1731,EBI-1788
    SKI7Q084915EBI-1731,EBI-1389

    Protein-protein interaction databases

    BioGridi35606. 46 interactions.
    DIPiDIP-6785N.
    IntActiP53859. 17 interactions.
    MINTiMINT-614245.
    STRINGi4932.YNL232W.

    Structurei

    Secondary structure

    1
    292
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 113
    Beta strandi16 – 2611
    Beta strandi29 – 379
    Beta strandi41 – 488
    Beta strandi51 – 588
    Beta strandi60 – 689
    Beta strandi103 – 1119
    Beta strandi138 – 1469
    Beta strandi148 – 15912
    Beta strandi188 – 1903
    Turni195 – 1984
    Beta strandi202 – 2065
    Helixi207 – 2093
    Helixi220 – 2223
    Beta strandi229 – 2368
    Beta strandi239 – 2468
    Beta strandi253 – 2586
    Turni259 – 2635
    Beta strandi266 – 27611
    Turni278 – 2803
    Beta strandi283 – 2853

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IFDX-ray2.80I1-292[»]
    ProteinModelPortaliP53859.
    SMRiP53859. Positions 1-291.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the CSL4 family.Curated

    Phylogenomic databases

    eggNOGiCOG1096.
    GeneTreeiENSGT00390000015287.
    HOGENOMiHOG000177330.
    KOiK07573.
    OMAiQRANVEI.
    OrthoDBiEOG74BK39.

    Family and domain databases

    InterProiIPR019495. EXOSC1.
    IPR012340. NA-bd_OB-fold.
    [Graphical view]
    PfamiPF10447. EXOSC1. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 2 hits.

    Sequencei

    Sequence statusi: Complete.

    P53859-1 [UniParc]FASTAAdd to Basket

    « Hide

    MACNFQFPEI AYPGKLICPQ YGTENKDGED IIFNYVPGPG TKLIQYEHNG    50
    RTLEAITATL VGTVRCEEEK KTDQEEEREG TDQSTEEEKS VDASPNDVTR 100
    RTVKNILVSV LPGTEKGRKT NKYANNDFAN NLPKEGDIVL TRVTRLSLQR 150
    ANVEILAVED KPSPIDSGIG SNGSGIVAAG GGSGAATFSV SQASSDLGET 200
    FRGIIRSQDV RSTDRDRVKV IECFKPGDIV RAQVLSLGDG TNYYLTTARN 250
    DLGVVFARAA NGAGGLMYAT DWQMMTSPVT GATEKRKCAK PF 292
    Length:292
    Mass (Da):31,583
    Last modified:October 1, 1996 - v1
    Checksum:i52D3416EA183583B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z69381 Genomic DNA. Translation: CAA93366.1.
    Z71508 Genomic DNA. Translation: CAA96137.1.
    BK006947 Genomic DNA. Translation: DAA10326.1.
    PIRiS63198.
    RefSeqiNP_014167.1. NM_001183070.1.

    Genome annotation databases

    EnsemblFungiiYNL232W; YNL232W; YNL232W.
    GeneIDi855489.
    KEGGisce:YNL232W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z69381 Genomic DNA. Translation: CAA93366.1 .
    Z71508 Genomic DNA. Translation: CAA96137.1 .
    BK006947 Genomic DNA. Translation: DAA10326.1 .
    PIRi S63198.
    RefSeqi NP_014167.1. NM_001183070.1.

    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 I 1-292 [» ]
    ProteinModelPortali P53859.
    SMRi P53859. Positions 1-291.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35606. 46 interactions.
    DIPi DIP-6785N.
    IntActi P53859. 17 interactions.
    MINTi MINT-614245.
    STRINGi 4932.YNL232W.

    Proteomic databases

    MaxQBi P53859.
    PaxDbi P53859.
    PeptideAtlasi P53859.
    PRIDEi P53859.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YNL232W ; YNL232W ; YNL232W .
    GeneIDi 855489.
    KEGGi sce:YNL232W.

    Organism-specific databases

    CYGDi YNL232w.
    SGDi S000005176. CSL4.

    Phylogenomic databases

    eggNOGi COG1096.
    GeneTreei ENSGT00390000015287.
    HOGENOMi HOG000177330.
    KOi K07573.
    OMAi QRANVEI.
    OrthoDBi EOG74BK39.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33232-MONOMER.

    Miscellaneous databases

    NextBioi 979469.
    PROi P53859.

    Gene expression databases

    Genevestigatori P53859.

    Family and domain databases

    InterProi IPR019495. EXOSC1.
    IPR012340. NA-bd_OB-fold.
    [Graphical view ]
    Pfami PF10447. EXOSC1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50249. SSF50249. 2 hits.
    ProtoNeti Search...

    Publicationsi

    1. "The DNA sequence of cosmid 14-5 from chromosome XIV reveals 21 open reading frames including a novel gene encoding a globin-like domain."
      Pandolfo D., de Antoni A., Lanfranchi G., Valle G.
      Yeast 12:1071-1076(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
      Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
      , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
      Nature 387:93-98(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. "Mutations synthetically lethal with cep1 target S. cerevisiae kinetochore components."
      Baker R.E., Harris K., Zhang K.
      Genetics 149:73-85(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE NAME.
    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: FUNCTION, IDENTIFICATION IN THE RNA 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.
    11. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
      Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
      Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-94, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "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-94, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. "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 MRNA DEGRADATION.

    Entry informationi

    Entry nameiCSL4_YEAST
    AccessioniPrimary (citable) accession number: P53859
    Secondary accession number(s): D6W0W0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 127 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 5550 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 XIV
      Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

    External Data

    Dasty 3