P46948 (RRP41_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex component SKI6

Alternative name(s):
Extracellular mutant protein 20
Ribosomal RNA-processing protein 41
Superkiller protein 6

Gene names

Name:	SKI6
Synonyms:	ECM20, RRP41
Ordered Locus Names:	YGR195W
ORF Names:	G7587

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	246 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 anti-sense 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. Ref.5 Ref.11
Subunit structure	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. Ref.5 Ref.11
Subcellular location	Cytoplasm. Nucleus › nucleolus Ref.7.
Miscellaneous	Present with 5150 molecules/cell in log phase SD medium. Ref.8
Sequence similarities	Belongs to the RNase PH family.
Caution	Was originally (Ref.5) thought to have exonuclease activity but it was later shown (Ref.11 and Ref.9) that only DIS3/RRP44 subunit of the exosome core has this activity.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm Exosome Nucleus
Ligand	RNA-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	U1 snRNA 3'-end processing Inferred from mutant phenotype. Source: SGD U4 snRNA 3'-end processing Inferred from mutant phenotype. Source: SGD U5 snRNA 3'-end processing Inferred from mutant phenotype. Source: SGD exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Inferred from mutant phenotype Ref.5. Source: SGD nonfunctional rRNA decay Inferred by curator Ref.6. Source: SGD nuclear mRNA surveillance Inferred from mutant phenotype. Source: SGD nuclear polyadenylation-dependent CUT catabolic process Inferred from mutant phenotype. Source: SGD nuclear polyadenylation-dependent mRNA catabolic process Inferred by curator Ref.6. Source: SGD nuclear polyadenylation-dependent tRNA catabolic process Inferred from direct assay. Source: SGD nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Inferred from mutant phenotype. Source: SGD nuclear-transcribed mRNA catabolic process, non-stop decay Inferred by curator Ref.6. Source: SGD polyadenylation-dependent snoRNA 3'-end processing Inferred from mutant phenotype. Source: SGD
Cellular component	cytoplasmic exosome (RNase complex) Inferred from direct assay Ref.6. Source: SGD nuclear exosome (RNase complex) Inferred from direct assay Ref.6. Source: SGD nucleolus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
DIS3	Q08162	9	EBI-1788,EBI-1740

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 246

246

Exosome complex component SKI6

PRO_0000139962

Experimental info

Mutagenesis

62 – 63

2

KS → ED: Impairs RNA-binding (at the proposed ring entry site). Ref.12

Mutagenesis

95 – 96

2

RR → EE: Impairs RNA-binding (at the proposed ring exit site). Ref.12

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

246

Helix Strand Turn

Details...

Beta strand

26 – 29

4

Turn

33 – 35

3

Beta strand

40 – 43

4

Beta strand

48 – 54

7

Beta strand

67 – 78

12

Helix

95 – 111

17

Turn

114 – 116

3

Beta strand

119 – 130

12

Helix

144 – 149

6

Beta strand

154 – 156

3

Helix

176 – 181

6

Beta strand

199 – 201

3

Helix

207 – 215

9

Helix

222 – 237

16

Sequences

	Sequence		Length	Mass (Da)
	P46948 [UniParc]. Last modified November 1, 1995. Version 1. Checksum: C80EFFB528A43044	FASTA	246	27,561
	10 20 30 40 50 60 MSRLEIYSPE GLRLDGRRWN ELRRFESSIN THPHAADGSS YMEQGNNKII TLVKGPKEPR 70 80 90 100 110 120 LKSQMDTSKA LLNVSVNITK FSKFERSKSS HKNERRVLEI QTSLVRMFEK NVMLNIYPRT 130 140 150 160 170 180 VIDIEIHVLE QDGGIMGSLI NGITLALIDA GISMFDYISG ISVGLYDTTP LLDTNSLEEN 190 200 210 220 230 240 AMSTVTLGVV GKSEKLSLLL VEDKIPLDRL ENVLAIGIAG AHRVRDLMDE ELRKHAQKRV SNASAR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 7502584] [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: 9169869] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] 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: 9390555] [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: 10465791] [Abstract] Cited for: IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS SPECTROMETRY.
[7]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[8]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] 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: 17174896] [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: 17173052] [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: 19879841] [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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

S59180.

RefSeq

NP_011711.1. NM_001181324.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2WP8	X-ray	3.00	B	1-246	[»]

ProteinModelPortal

P46948.

SMR

P46948. Positions 3-239.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2083N.

IntAct

P46948. 24 interactions.

MINT

MINT-555587.

STRING

P46948.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YGR195W; YGR195W; YGR195W.

GeneID

853109.

KEGG

sce:YGR195W.

NMPDR

fig|4932.3.peg.2838.

Organism-specific databases

CYGD

YGR195w.

SGD

S000003427. SKI6.

Phylogenomic databases

eggNOG

fuNOG04193.

GeneTree

EFGT00050000004219.

HOGENOM

HBG737187.

OMA

HMAPFST.

OrthoDB

EOG45MRFG.

Gene expression databases

ArrayExpress

P46948.

Genevestigator

P46948.

GermOnline

YGR195W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]

KO

K11600.

Pfam

PF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]

SUPFAM

SSF55666. 3_ExoRNase. 1 hit.
SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.

ProtoNet

Search...

Other

NextBio

973121.

Entry information

Entry name

RRP41_YEAST

Accession

Primary (citable) accession number: P46948
Secondary accession number(s): D6VUX7

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	November 1, 1995
Last modified:	December 14, 2011
This is version 110 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program