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Protein

Exosome complex component ski6

Gene

ski6

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript 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 (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-SPO-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SPO-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-SPO-6791226. Major pathway of rRNA processing in the nucleolus.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component ski6
Alternative name(s):
Ribosomal RNA-processing protein 41
Gene namesi
Name:ski6
Synonyms:rrp41
ORF Names:SPAC3G9.10c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome I

Organism-specific databases

EuPathDBiFungiDB:SPAC3G9.10c.
PomBaseiSPAC3G9.10c.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic exosome (RNase complex) Source: PomBase
  • cytosol Source: PomBase
  • exosome (RNase complex) Source: PomBase
  • mitotic spindle pole body Source: PomBase
  • nuclear exosome (RNase complex) Source: PomBase
  • nucleolus Source: GO_Central
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 242242Exosome complex component ski6PRO_0000139961Add
BLAST

Proteomic databases

MaxQBiO42872.

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 (By similarity).By similarity

Protein-protein interaction databases

BioGridi279871. 11 interactions.
IntActiO42872. 1 interaction.
MINTiMINT-4673653.

Structurei

3D structure databases

ProteinModelPortaliO42872.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

HOGENOMiHOG000229515.
InParanoidiO42872.
KOiK11600.
OMAiDGCKQIR.
OrthoDBiEOG092C4S0G.
PhylomeDBiO42872.

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.

O42872-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSHFEILSLE GLRNDGRRWD EMRNFQCRIG IEPSENGSAF IELGNTKVLC
60 70 80 90 100
IVDGPSEPVI KSKARADRTF VNVEINIASF STIDVKKRFK SDRRIQLQCL
110 120 130 140 150
ALQNTFEEII QTELYPRSQI SVYLHVLQDD GAVMASCINA TTLALIDAGI
160 170 180 190 200
PVKDFVCCST AGIVESDMLL DLNSLEESAL SWLTVAVLGN IKKVVYMQLE
210 220 230 240
TSMHLDYLES VMNMAIAGSE HIYNTMQSAV RQSAKPALAS LS
Length:242
Mass (Da):26,869
Last modified:June 1, 1998 - v1
Checksum:i0EE46F5F994584A9
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti29 – 291I → F in BAA13803 (PubMed:9501991).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D89141 mRNA. Translation: BAA13803.1.
CU329670 Genomic DNA. Translation: CAA15919.1.
PIRiT11646.
T11740.
RefSeqiNP_594082.1. NM_001019503.2.

Genome annotation databases

EnsemblFungiiSPAC3G9.10c.1; SPAC3G9.10c.1:pep; SPAC3G9.10c.
GeneIDi2543451.
KEGGispo:SPAC3G9.10c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D89141 mRNA. Translation: BAA13803.1.
CU329670 Genomic DNA. Translation: CAA15919.1.
PIRiT11646.
T11740.
RefSeqiNP_594082.1. NM_001019503.2.

3D structure databases

ProteinModelPortaliO42872.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi279871. 11 interactions.
IntActiO42872. 1 interaction.
MINTiMINT-4673653.

Proteomic databases

MaxQBiO42872.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPAC3G9.10c.1; SPAC3G9.10c.1:pep; SPAC3G9.10c.
GeneIDi2543451.
KEGGispo:SPAC3G9.10c.

Organism-specific databases

EuPathDBiFungiDB:SPAC3G9.10c.
PomBaseiSPAC3G9.10c.

Phylogenomic databases

HOGENOMiHOG000229515.
InParanoidiO42872.
KOiK11600.
OMAiDGCKQIR.
OrthoDBiEOG092C4S0G.
PhylomeDBiO42872.

Enzyme and pathway databases

ReactomeiR-SPO-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SPO-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-SPO-6791226. Major pathway of rRNA processing in the nucleolus.

Miscellaneous databases

PROiO42872.

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_SCHPO
AccessioniPrimary (citable) accession number: O42872
Secondary accession number(s): P78792
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2002
Last sequence update: June 1, 1998
Last modified: September 7, 2016
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

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.