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P53859

- CSL4_YEAST

UniProt

P53859 - CSL4_YEAST

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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

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. 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
Complete GO annotation...

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. nucleus Source: SGD
Complete GO annotation...

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. 47 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 – 113Combined sources
Beta strandi16 – 2611Combined sources
Beta strandi29 – 379Combined sources
Beta strandi41 – 488Combined sources
Beta strandi51 – 588Combined sources
Beta strandi60 – 689Combined sources
Beta strandi103 – 1119Combined sources
Beta strandi138 – 1469Combined sources
Beta strandi148 – 15912Combined sources
Beta strandi188 – 1903Combined sources
Turni195 – 1984Combined sources
Beta strandi202 – 2065Combined sources
Helixi207 – 2093Combined sources
Beta strandi212 – 2165Combined sources
Helixi220 – 2223Combined sources
Beta strandi229 – 2368Combined sources
Beta strandi239 – 2468Combined sources
Beta strandi253 – 2586Combined sources
Turni259 – 2635Combined sources
Beta strandi266 – 27611Combined sources
Turni278 – 2803Combined sources
Beta strandi283 – 2853Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80I1-292[»]
4OO1X-ray3.30I1-292[»]
ProteinModelPortaliP53859.
SMRiP53859. Positions 1-291.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the CSL4 family.Curated

Phylogenomic databases

eggNOGiCOG1096.
GeneTreeiENSGT00390000015287.
HOGENOMiHOG000177330.
InParanoidiP53859.
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

        10         20         30         40         50
MACNFQFPEI AYPGKLICPQ YGTENKDGED IIFNYVPGPG TKLIQYEHNG
60 70 80 90 100
RTLEAITATL VGTVRCEEEK KTDQEEEREG TDQSTEEEKS VDASPNDVTR
110 120 130 140 150
RTVKNILVSV LPGTEKGRKT NKYANNDFAN NLPKEGDIVL TRVTRLSLQR
160 170 180 190 200
ANVEILAVED KPSPIDSGIG SNGSGIVAAG GGSGAATFSV SQASSDLGET
210 220 230 240 250
FRGIIRSQDV RSTDRDRVKV IECFKPGDIV RAQVLSLGDG TNYYLTTARN
260 270 280 290
DLGVVFARAA NGAGGLMYAT DWQMMTSPVT GATEKRKCAK PF
Length:292
Mass (Da):31,583
Last modified:October 1, 1996 - v1
Checksum:i52D3416EA183583B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4IFD X-ray 2.80 I 1-292 [» ]
4OO1 X-ray 3.30 I 1-292 [» ]
ProteinModelPortali P53859.
SMRi P53859. Positions 1-291.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 35606. 47 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.
InParanoidi P53859.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 129 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