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Protein

Exosome complex component SKI6

Gene

SKI6

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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

GO - Biological processi

  • exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • nonfunctional rRNA decay Source: SGD
  • nuclear mRNA surveillance Source: SGD
  • nuclear polyadenylation-dependent CUT catabolic process Source: SGD
  • nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  • nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
  • nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
  • polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  • rRNA catabolic process Source: SGD
  • U1 snRNA 3'-end processing Source: SGD
  • U4 snRNA 3'-end processing Source: SGD
  • U5 snRNA 3'-end processing Source: SGD
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30881-MONOMER.
ReactomeiR-SCE-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

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
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGR195W.
SGDiS000003427. SKI6.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic exosome (RNase complex) Source: SGD
  • nuclear exosome (RNase complex) Source: SGD
  • nucleolus Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi62 – 63KS → ED: Impairs RNA-binding (at the proposed ring entry site). 1 Publication2
Mutagenesisi95 – 96RR → EE: Impairs RNA-binding (at the proposed ring exit site). 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001399621 – 246Exosome complex component SKI6Add BLAST246

Proteomic databases

MaxQBiP46948.
PRIDEiP46948.
TopDownProteomicsiP46948.

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.4 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. 39 interactors.
DIPiDIP-2083N.
IntActiP46948. 22 interactors.
MINTiMINT-555587.

Structurei

Secondary structure

1246
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi14 – 16Combined sources3
Beta strandi25 – 31Combined sources7
Turni33 – 35Combined sources3
Beta strandi37 – 44Combined sources8
Beta strandi47 – 57Combined sources11
Beta strandi60 – 64Combined sources5
Beta strandi67 – 69Combined sources3
Beta strandi71 – 78Combined sources8
Beta strandi82 – 85Combined sources4
Helixi95 – 108Combined sources14
Turni109 – 111Combined sources3
Helixi114 – 116Combined sources3
Beta strandi121 – 130Combined sources10
Helixi135 – 149Combined sources15
Beta strandi154 – 156Combined sources3
Beta strandi158 – 166Combined sources9
Beta strandi169 – 173Combined sources5
Helixi176 – 179Combined sources4
Beta strandi182 – 190Combined sources9
Beta strandi193 – 201Combined sources9
Helixi207 – 209Combined sources3
Helixi210 – 241Combined sources32

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2WP8X-ray3.00B1-246[»]
4IFDX-ray2.80B1-246[»]
4OO1X-ray3.30B1-246[»]
5C0WX-ray4.60B1-246[»]
5C0XX-ray3.81B1-246[»]
5G06electron microscopy4.20B1-246[»]
5JEAX-ray2.65B1-246[»]
ProteinModelPortaliP46948.
SMRiP46948.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP46948.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
InParanoidiP46948.
KOiK11600.
OMAiDITLLQM.
OrthoDBiEOG092C4S0G.

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

        10         20         30         40         50
MSRLEIYSPE GLRLDGRRWN ELRRFESSIN THPHAADGSS YMEQGNNKII
60 70 80 90 100
TLVKGPKEPR LKSQMDTSKA LLNVSVNITK FSKFERSKSS HKNERRVLEI
110 120 130 140 150
QTSLVRMFEK NVMLNIYPRT VIDIEIHVLE QDGGIMGSLI NGITLALIDA
160 170 180 190 200
GISMFDYISG ISVGLYDTTP LLDTNSLEEN AMSTVTLGVV GKSEKLSLLL
210 220 230 240
VEDKIPLDRL ENVLAIGIAG AHRVRDLMDE ELRKHAQKRV SNASAR
Length:246
Mass (Da):27,561
Last modified:November 1, 1995 - v1
Checksum:iC80EFFB528A43044
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2WP8X-ray3.00B1-246[»]
4IFDX-ray2.80B1-246[»]
4OO1X-ray3.30B1-246[»]
5C0WX-ray4.60B1-246[»]
5C0XX-ray3.81B1-246[»]
5G06electron microscopy4.20B1-246[»]
5JEAX-ray2.65B1-246[»]
ProteinModelPortaliP46948.
SMRiP46948.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33448. 39 interactors.
DIPiDIP-2083N.
IntActiP46948. 22 interactors.
MINTiMINT-555587.

Proteomic databases

MaxQBiP46948.
PRIDEiP46948.
TopDownProteomicsiP46948.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YGR195W.
SGDiS000003427. SKI6.

Phylogenomic databases

GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
InParanoidiP46948.
KOiK11600.
OMAiDITLLQM.
OrthoDBiEOG092C4S0G.

Enzyme and pathway databases

BioCyciYEAST:G3O-30881-MONOMER.
ReactomeiR-SCE-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Miscellaneous databases

EvolutionaryTraceiP46948.
PROiP46948.

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.
ProtoNetiSearch...

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: November 2, 2016
This is version 151 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.1 Publication

Caution

Was originally thought to have exonuclease activity but it was later shown (PubMed:17173052 and PubMed:17174896) that only DIS3/RRP44 subunit of the exosome core has this activity.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 VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.