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P46948

- RRP41_YEAST

UniProt

P46948 - RRP41_YEAST

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Protein
Exosome complex component SKI6
Gene
SKI6, ECM20, RRP41, YGR195W, G7587
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. SKI6 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. RNA binding Source: UniProtKB-KW
  2. protein binding Source: IntAct
Complete GO annotation...

GO - Biological processi

  1. U1 snRNA 3'-end processing Source: SGD
  2. U4 snRNA 3'-end processing Source: SGD
  3. U5 snRNA 3'-end processing Source: SGD
  4. exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  5. nonfunctional rRNA decay Source: SGD
  6. nuclear mRNA surveillance Source: SGD
  7. nuclear polyadenylation-dependent CUT catabolic process Source: SGD
  8. nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  9. nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  10. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
  11. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
  12. nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
  13. polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  14. rRNA catabolic process Source: SGD
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30881-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component SKI6
Alternative name(s):
Extracellular mutant protein 20
Ribosomal RNA-processing protein 41
Superkiller protein 6
Gene namesi
Name:SKI6
Synonyms:ECM20, RRP41
Ordered Locus Names:YGR195W
ORF Names:G7587
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VII

Organism-specific databases

CYGDiYGR195w.
SGDiS000003427. SKI6.

Subcellular locationi

Cytoplasm. 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
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi62 – 632KS → ED: Impairs RNA-binding (at the proposed ring entry site). 1 Publication
Mutagenesisi95 – 962RR → EE: Impairs RNA-binding (at the proposed ring exit site). 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 246246Exosome complex component SKI6
PRO_0000139962Add
BLAST

Proteomic databases

MaxQBiP46948.
PaxDbiP46948.

Expressioni

Gene expression databases

GenevestigatoriP46948.

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
CSL4P538599EBI-1788,EBI-1731
DIS3Q0816210EBI-1788,EBI-1740
MTR3P482404EBI-1788,EBI-1749
RRP4P387924EBI-1788,EBI-1757
RRP40Q082854EBI-1788,EBI-1831
RRP42Q122774EBI-1788,EBI-1765
RRP43P253594EBI-1788,EBI-1773
RRP45Q056368EBI-1788,EBI-1810
RRP46P532565EBI-1788,EBI-1842

Protein-protein interaction databases

BioGridi33448. 40 interactions.
DIPiDIP-2083N.
IntActiP46948. 22 interactions.
MINTiMINT-555587.
STRINGi4932.YGR195W.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi29 – 313
Turni33 – 353
Beta strandi37 – 448
Beta strandi47 – 5711
Beta strandi67 – 693
Beta strandi71 – 788
Beta strandi82 – 854
Helixi95 – 10814
Turni109 – 1113
Helixi114 – 1163
Beta strandi121 – 13010
Helixi135 – 14915
Beta strandi154 – 1563
Beta strandi158 – 1669
Beta strandi169 – 1735
Helixi176 – 1794
Beta strandi182 – 1909
Beta strandi193 – 2019
Helixi207 – 24034

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2WP8X-ray3.00B1-246[»]
4IFDX-ray2.80B1-246[»]
ProteinModelPortaliP46948.
SMRiP46948. Positions 1-242.

Miscellaneous databases

EvolutionaryTraceiP46948.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.

Phylogenomic databases

eggNOGiCOG0689.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
KOiK11600.
OMAiDYVCACT.
OrthoDBiEOG7Z0K74.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

P46948-1 [UniParc]FASTAAdd to Basket

« Hide

MSRLEIYSPE GLRLDGRRWN ELRRFESSIN THPHAADGSS YMEQGNNKII    50
TLVKGPKEPR LKSQMDTSKA LLNVSVNITK FSKFERSKSS HKNERRVLEI 100
QTSLVRMFEK NVMLNIYPRT VIDIEIHVLE QDGGIMGSLI NGITLALIDA 150
GISMFDYISG ISVGLYDTTP LLDTNSLEEN AMSTVTLGVV GKSEKLSLLL 200
VEDKIPLDRL ENVLAIGIAG AHRVRDLMDE ELRKHAQKRV SNASAR 246
Length:246
Mass (Da):27,561
Last modified:November 1, 1995 - v1
Checksum:iC80EFFB528A43044
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X82775 Genomic DNA. Translation: CAA58018.1.
Z72980 Genomic DNA. Translation: CAA97221.1.
Z72981 Genomic DNA. Translation: CAA97223.1.
AY558509 Genomic DNA. Translation: AAS56835.1.
BK006941 Genomic DNA. Translation: DAA08288.1.
PIRiS59180.
RefSeqiNP_011711.3. NM_001181324.3.

Genome annotation databases

EnsemblFungiiYGR195W; YGR195W; YGR195W.
GeneIDi853109.
KEGGisce:YGR195W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X82775 Genomic DNA. Translation: CAA58018.1 .
Z72980 Genomic DNA. Translation: CAA97221.1 .
Z72981 Genomic DNA. Translation: CAA97223.1 .
AY558509 Genomic DNA. Translation: AAS56835.1 .
BK006941 Genomic DNA. Translation: DAA08288.1 .
PIRi S59180.
RefSeqi NP_011711.3. NM_001181324.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2WP8 X-ray 3.00 B 1-246 [» ]
4IFD X-ray 2.80 B 1-246 [» ]
ProteinModelPortali P46948.
SMRi P46948. Positions 1-242.
ModBasei Search...

Protein-protein interaction databases

BioGridi 33448. 40 interactions.
DIPi DIP-2083N.
IntActi P46948. 22 interactions.
MINTi MINT-555587.
STRINGi 4932.YGR195W.

Proteomic databases

MaxQBi P46948.
PaxDbi P46948.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YGR195W ; YGR195W ; YGR195W .
GeneIDi 853109.
KEGGi sce:YGR195W.

Organism-specific databases

CYGDi YGR195w.
SGDi S000003427. SKI6.

Phylogenomic databases

eggNOGi COG0689.
GeneTreei ENSGT00550000074804.
HOGENOMi HOG000229515.
KOi K11600.
OMAi DYVCACT.
OrthoDBi EOG7Z0K74.

Enzyme and pathway databases

BioCyci YEAST:G3O-30881-MONOMER.

Miscellaneous databases

EvolutionaryTracei P46948.
NextBioi 973121.
PROi P46948.

Gene expression databases

Genevestigatori P46948.

Family and domain databases

Gene3Di 3.30.230.70. 1 hit.
InterProi IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view ]
Pfami PF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view ]
SUPFAMi SSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The complete sequence of a 9000 bp fragment of the right arm of Saccharomyces cerevisiae chromosome VII contains four previously unknown open reading frames."
    Guerreiro P., Maia e Silva A., Barreiros T., Arroyo J., Garcia-Gonzalez M., Garcia-Saez M.I., Rodrigues-Pousada C., Nombela C.
    Yeast 11:1087-1091(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
    Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
    , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
    Nature 387:81-84(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. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    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: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBUNIT.
  6. "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.
  7. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  9. "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.
  10. Erratum
    Liu Q., Greimann J.C., Lima C.D.
    Cell 131:188-189(2007)
  11. "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.
  12. "The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation."
    Bonneau F., Basquin J., Ebert J., Lorentzen E., Conti E.
    Cell 139:547-559(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH RRP45 AND DIS3, MUTAGENESIS OF 62-LYS-SER-63 AND 95-ARG-ARG-96.

Entry informationi

Entry nameiRRP41_YEAST
AccessioniPrimary (citable) accession number: P46948
Secondary accession number(s): D6VUX7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: July 9, 2014
This is version 133 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 5150 molecules/cell in log phase SD medium.

Caution

Was originally (1 Publication) thought to have exonuclease activity but it was later shown (1 Publication and 1 Publication) that only DIS3/RRP44 subunit of the exosome core has this activity.

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 VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

External Data

Dasty 3

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