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Q08285 (RRP40_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 116. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Exosome complex component RRP40
Alternative name(s):
Ribosomal RNA-processing protein 40
Gene names
Name:RRP40
Ordered Locus Names:YOL142W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length240 AA.
Sequence statusComplete.
Protein existenceEvidence 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 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. RRP40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits. Ref.4 Ref.9 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.4 Ref.9

Subcellular location

Cytoplasm. Nucleusnucleolus Ref.5.

Miscellaneous

Present with 6050 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the RRP40 family.

Contains 1 S1 motif domain.

Caution

According to Ref.9 and Ref.7, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.

Ontologies

Keywords
   Biological processrRNA processing
   Cellular componentCytoplasm
Exosome
Nucleus
   LigandRNA-binding
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processexonucleolytic 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.4PubMed 10508172. Source: SGD

ncRNA 3'-end processing

Inferred by curator Ref.4. Source: SGD

nonfunctional rRNA decay

Inferred by curator Ref.4. Source: SGD

nuclear polyadenylation-dependent mRNA catabolic process

Inferred by curator Ref.4. Source: SGD

nuclear polyadenylation-dependent rRNA catabolic process

Inferred from mutant phenotype Ref.4. Source: SGD

nuclear polyadenylation-dependent tRNA catabolic process

Inferred from direct assay PubMed 15828860PubMed 17643380. Source: SGD

nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay

Inferred by curator Ref.4. Source: SGD

nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'

Inferred by curator Ref.4. Source: SGD

nuclear-transcribed mRNA catabolic process, non-stop decay

Inferred by curator Ref.4. Source: SGD

polyadenylation-dependent snoRNA 3'-end processing

Inferred by curator Ref.4. Source: SGD

   Cellular_componentcytoplasmic exosome (RNase complex)

Inferred from direct assay Ref.4PubMed 19046973. Source: SGD

nuclear exosome (RNase complex)

Inferred from direct assay Ref.4PubMed 19046973. Source: SGD

nucleolus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionRNA binding

Inferred from direct assay PubMed 17391830. Source: SGD

manganese ion binding

Inferred from direct assay PubMed 17159918. Source: SGD

protein binding

Inferred from physical interaction PubMed 11805826PubMed 16429126PubMed 16729021PubMed 16829593PubMed 21072061. Source: IntAct

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 240240Exosome complex component RRP40
PRO_0000097453

Regions

Domain67 – 13771S1 motif

Experimental info

Sequence conflict1601L → F in CAA99163. Ref.1

Secondary structure

....................................... 240
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q08285 [UniParc].

Last modified September 21, 2011. Version 2.
Checksum: 62B3A30348BBAA7C

FASTA24026,556
        10         20         30         40         50         60 
MSTFIFPGDS FPVDPTTPVK LGPGIYCDPN TQEIRPVNTG VLHVSAKGKS GVQTAYIDYS 

        70         80         90        100        110        120 
SKRYIPSVND FVIGVIIGTF SDSYKVSLQN FSSSVSLSYM AFPNASKKNR PTLQVGDLVY 

       130        140        150        160        170        180 
ARVCTAEKEL EAEIECFDST TGRDAGFGIL EDGMIIDVNL NFARQLLFNN DFPLLKVLAA 

       190        200        210        220        230        240 
HTKFEVAIGL NGKIWVKCEE LSNTLACYRT IMECCQKNDT AAFKDIAKRQ FKEILTVKEE 

« Hide

References

« Hide 'large scale' references
[1]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. expand/collapse author list , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 160.
Strain: ATCC 204508 / S288c.
[3]"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. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]"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 EXOSOME COMPLEX BY MASS SPECTROMETRY.
[5]"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] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[6]"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] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]"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.
[8]Erratum
Liu Q., Greimann J.C., Lima C.D.
Cell 131:188-189(2007)
[9]"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, INTERACTION OF THE EXOSOME WITH RRP6 AND SKI7, SUBUNIT.
[10]"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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"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 RNA EXOSOME COMPLEX STABILITY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z74884 Genomic DNA. Translation: CAA99163.1.
AY692926 Genomic DNA. Translation: AAT92945.1.
BK006948 Genomic DNA. Translation: DAA10643.2.
PIRS61872.
RefSeqNP_014499.2. NM_001183396.2.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2JA9X-ray2.20A62-236[»]
4IFDX-ray2.80G1-240[»]
ProteinModelPortalQ08285.
SMRQ08285. Positions 1-236.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34275. 18 interactions.
DIPDIP-5330N.
IntActQ08285. 17 interactions.
MINTMINT-530842.
STRING4932.YOL142W.

Proteomic databases

MaxQBQ08285.
PaxDbQ08285.
PeptideAtlasQ08285.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOL142W; YOL142W; YOL142W.
GeneID854023.
KEGGsce:YOL142W.

Organism-specific databases

CYGDYOL142w.
SGDS000005502. RRP40.

Phylogenomic databases

eggNOGCOG1097.
GeneTreeENSGT00390000012042.
HOGENOMHOG000184644.
KOK03681.
OMAHMDAELE.
OrthoDBEOG7FJHC7.

Enzyme and pathway databases

BioCycYEAST:G3O-33533-MONOMER.

Gene expression databases

GenevestigatorQ08285.

Family and domain databases

InterProIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
IPR022967. RNA-binding_domain_S1.
[Graphical view]
PANTHERPTHR21321. PTHR21321. 1 hit.
SMARTSM00316. S1. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ08285.
NextBio975559.
PROQ08285.

Entry information

Entry nameRRP40_YEAST
AccessionPrimary (citable) accession number: Q08285
Secondary accession number(s): D6W1S7, E9P8Z4
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: September 21, 2011
Last modified: July 9, 2014
This is version 116 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XV

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

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references