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P53256 (RRP46_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 RRP46
Alternative name(s):
Ribosomal RNA-processing protein 46
Gene names
Name:RRP46
Ordered Locus Names:YGR095C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length223 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. RRP46 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.4 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. Interacts with LRP1. Ref.4 Ref.5 Ref.11

Subcellular location

Cytoplasm. Nucleusnucleolus Ref.7.

Miscellaneous

Present with 10800 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the RNase PH family.

Caution

According to Ref.11 and Ref.9, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.

Sequence caution

The sequence CAA97098.1 differs from that shown. Reason: Erroneous initiation.

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 from mutant phenotype PubMed 19369424. 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 electronic annotation. Source: UniProtKB-KW

protein binding

Inferred from physical interaction PubMed 11805826PubMed 12972615PubMed 16429126PubMed 16729021PubMed 16829593PubMed 21072061. Source: IntAct

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 223223Exosome complex component RRP46
PRO_0000139978

Secondary structure

..................................... 223
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P53256 [UniParc].

Last modified October 31, 2006. Version 2.
Checksum: F1307E0EE4FC3133

FASTA22324,407
        10         20         30         40         50         60 
MSVQAEIGIL DHVDGSSEFV SQDTKVICSV TGPIEPKARQ ELPTQLALEI IVRPAKGVAT 

        70         80         90        100        110        120 
TREKVLEDKL RAVLTPLITR HCYPRQLCQI TCQILESGED EAEFSLRELS CCINAAFLAL 

       130        140        150        160        170        180 
VDAGIALNSM CASIPIAIIK DTSDIIVDPT AEQLKISLSV HTLALEFVNG GKVVKNVLLL 

       190        200        210        220 
DSNGDFNEDQ LFSLLELGEQ KCQELVTNIR RIIQDNISPR LVV 

« Hide

References

« Hide 'large scale' references
[1]"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. expand/collapse author list , 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.
[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.
Strain: ATCC 204508 / S288c.
[3]Kennedy M.C., Dietrich F.S.
Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-67.
Strain: ATCC 204511 / S288c / AB972.
[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]"A panoramic view of yeast noncoding RNA processing."
Peng W.-T., Robinson M.D., Mnaimneh S., Krogan N.J., Cagney G., Morris Q.D., Davierwala A.P., Grigull J., Yang X., Zhang W., Mitsakakis N., Ryan O.W., Datta N., Jojic V., Pal C., Canadien V., Richards D.P., Beattie B. expand/collapse author list , Wu L.F., Altschuler S.J., Roweis S., Frey B.J., Emili A., Greenblatt J.F., Hughes T.R.
Cell 113:919-933(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LRP1.
[6]"Sequencing and comparison of yeast species to identify genes and regulatory elements."
Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.
Nature 423:241-254(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
[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] [Europe PMC] [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] [Europe PMC] [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] [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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z72880 Genomic DNA. Translation: CAA97098.1. Different initiation.
AY389297 mRNA. Translation: AAQ97229.1.
BK006941 Genomic DNA. Translation: DAA08188.1.
PIRS64390.
RefSeqNP_011609.2. NM_001181224.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80D1-223[»]
ProteinModelPortalP53256.
SMRP53256. Positions 1-223.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33338. 31 interactions.
DIPDIP-6838N.
IntActP53256. 23 interactions.
MINTMINT-2732969.
STRING4932.YGR095C.

Proteomic databases

MaxQBP53256.
PaxDbP53256.
PeptideAtlasP53256.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYGR095C; YGR095C; YGR095C.
GeneID852987.
KEGGsce:YGR095C.

Organism-specific databases

CYGDYGR095c.
SGDS000003327. RRP46.

Phylogenomic databases

eggNOGCOG0689.
GeneTreeENSGT00550000075002.
HOGENOMHOG000248419.
KOK12590.
OMARRDEHAY.
OrthoDBEOG7C8GTX.

Enzyme and pathway databases

BioCycYEAST:G3O-30805-MONOMER.

Gene expression databases

GenevestigatorP53256.

Family and domain databases

Gene3D3.30.230.70. 1 hit.
InterProIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNetSearch...

Other

NextBio972806.
PROP53256.

Entry information

Entry nameRRP46_YEAST
AccessionPrimary (citable) accession number: P53256
Secondary accession number(s): D6VUM7, Q6TQU1
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 31, 2006
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 VII

Yeast (Saccharomyces cerevisiae) chromosome VII: 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