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P25359 (RRP43_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 129. 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 RRP43
Alternative name(s):
Ribosomal RNA-processing protein 43
Gene names
Name:RRP43
Ordered Locus Names:YCR035C
ORF Names:YCR35C, YCR522
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length394 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
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. RRP43 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.8 Ref.9 Ref.14

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 NIP7 and NOP8. Interacts strongly with RRP46. Ref.5 Ref.7 Ref.9 Ref.14

Subcellular location

Cytoplasm. Nucleusnucleolus Ref.10.

Miscellaneous

Present with 3180 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the RNase PH family.

Caution

According to Ref.14 and Ref.12, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.

Ontologies

Keywords
   Biological processrRNA processing
   Cellular componentCytoplasm
Exosome
Nucleus
   LigandRNA-binding
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Direct protein sequencing
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 PubMed 10508172Ref.9Ref.5. Source: SGD

mRNA catabolic process

Inferred from mutant phenotype Ref.9. Source: UniProtKB

ncRNA 3'-end processing

Inferred by curator Ref.7. Source: SGD

nonfunctional rRNA decay

Inferred by curator Ref.7. 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 PubMed 18940861. 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.7. Source: SGD

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

Inferred from mutant phenotype Ref.9. Source: SGD

nuclear-transcribed mRNA catabolic process, non-stop decay

Inferred by curator Ref.7. Source: SGD

polyadenylation-dependent snoRNA 3'-end processing

Inferred by curator Ref.7. Source: SGD

rRNA metabolic process

Inferred from mutant phenotype Ref.9. Source: UniProtKB

   Cellular_componentcytoplasm

Inferred from direct assay PubMed 9891085. Source: SGD

cytoplasmic exosome (RNase complex)

Inferred from direct assay Ref.7PubMed 19046973. Source: SGD

nuclear exosome (RNase complex)

Inferred from direct assay Ref.7PubMed 19046973. Source: SGD

nucleolus

Inferred from direct assay PubMed 9891085. Source: SGD

nucleoplasm

Inferred from direct assay PubMed 9891085. Source: SGD

   Molecular_functionRNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

protein binding

Inferred from physical interaction PubMed 11805826PubMed 15670595PubMed 16429126PubMed 16729021PubMed 16829593PubMed 20528918PubMed 21072061PubMed 9891085. Source: IntAct

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.16
Chain2 – 394393Exosome complex component RRP43
PRO_0000139970

Amino acid modifications

Modified residue21N-acetylalanine Ref.16
Modified residue261Phosphoserine Ref.15

Experimental info

Mutagenesis1621S → F: Interaction with RRP46 abolished; when associated with T-246. Ref.9
Mutagenesis2121V → A: Interaction with RRP46 abolished. Ref.9
Mutagenesis2301C → Y: Interaction with RRP46 abolished; when associated with T-274 and Y-276. Ref.9
Mutagenesis2461A → T: Interaction with RRP46 abolished; when associated with F-162. Ref.9
Mutagenesis2741I → T: Interaction with RRP46 abolished; when associated with Y-230 and Y-276. Ref.9
Mutagenesis2761C → Y: Interaction with RRP46 abolished; when associated with Y-230 and T-274. Ref.9
Sequence conflict1021A → S in CAA40227. Ref.1
Sequence conflict3631V → M in CAA40227. Ref.1

Secondary structure

.......................................................... 394
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P25359 [UniParc].

Last modified June 27, 2003. Version 2.
Checksum: 8801837B8184134D

FASTA39444,011
        10         20         30         40         50         60 
MAESTTLETI EIHPITFPPE VLARISPELS LQRHLSLGIR PCLRKYEEFR DVAIENNTLS 

        70         80         90        100        110        120 
RYADAGNIDT KNNILGSNVL KSGKTIVITS ITGGIIEETS AAIKDLDDFG EEELFEVTKE 

       130        140        150        160        170        180 
EDIIANYASV YPVVEVERGR VGACTDEEMT ISQKLHDSIL HSRILPKKAL KVKAGVRSAN 

       190        200        210        220        230        240 
EDGTFSVLYP DELEDDTLNE TNLKMKRKWS YVLYAKIVVL SRTGPVFDLC WNSLMYALQS 

       250        260        270        280        290        300 
VKLPRAFIDE RASDLRMTIR TRGRSATIRE TYEIICDQTK SVPLMINAKN IAFASNYGIV 

       310        320        330        340        350        360 
ELDPECQLQN SDNSEEEEVD IDMDKLNTVL IADLDTEAEE TSIHSTISIL AAPSGNYKQL 

       370        380        390 
TLVGGGAKIT PEMIKRSLLL SRVRADDLST RFNI 

« Hide

References

« Hide 'large scale' references
[1]"The complete sequence of the 8.2 kb segment left of MAT on chromosome III reveals five ORFs, including a gene for a yeast ribokinase."
Thierry A., Fairhead C., Dujon B.
Yeast 6:521-534(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 96604 / S288c / FY1679.
[2]"The complete DNA sequence of yeast chromosome III."
Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M. expand/collapse author list , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]Valles G., Volckaerts G.
Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases
Cited for: SEQUENCE REVISION TO 102 AND 363.
[4]"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.
[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] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 25-33, FUNCTION, SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY.
[6]"The complete sequence of a 7.5 kb region of chromosome III from Saccharomyces cerevisiae that lies between CRY1 and MAT."
Wicksteed B.L., Roberts A.B., Sagliocco F.A., Brown A.J.P.
Yeast 7:761-772(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 232-394.
[7]"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: IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS SPECTROMETRY.
[8]"The exosome subunit Rrp43p is required for the efficient maturation of 5.8S, 18S and 25S rRNA."
Zanchin N.I., Goldfarb D.S.
Nucleic Acids Res. 27:1283-1288(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[9]"Temperature-sensitive mutants of the exosome subunit Rrp43p show a deficiency in mRNA degradation and no longer interact with the exosome."
Oliveira C.C., Gonzales F.A., Zanchin N.I.
Nucleic Acids Res. 30:4186-4198(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH RRP46, MUTAGENESIS OF SER-162; VAL-212; CYS-230; ALA-246; ILE-274 AND CYS-276.
[10]"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].
[11]"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].
[12]"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.
[13]Erratum
Liu Q., Greimann J.C., Lima C.D.
Cell 131:188-189(2007)
[14]"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.
[15]"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-26, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X56909 Genomic DNA. Translation: CAA40227.1.
X59720 Genomic DNA. Translation: CAC42984.1.
S78624 Genomic DNA. Translation: AAB21261.1.
BK006937 Genomic DNA. Translation: DAA07514.1.
PIRS12917.
RefSeqNP_009964.2. NM_001178749.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80C2-394[»]
ProteinModelPortalP25359.
SMRP25359. Positions 7-394.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31018. 32 interactions.
DIPDIP-5485N.
IntActP25359. 17 interactions.
MINTMINT-564723.
STRING4932.YCR035C.

Proteomic databases

MaxQBP25359.
PaxDbP25359.
PeptideAtlasP25359.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYCR035C; YCR035C; YCR035C.
GeneID850401.
KEGGsce:YCR035C.

Organism-specific databases

CYGDYCR035c.
SGDS000000631. RRP43.

Phylogenomic databases

eggNOGNOG286862.
HOGENOMHOG000057141.
KOK12586.
OMATIYYPDL.
OrthoDBEOG7CCC3J.

Enzyme and pathway databases

BioCycYEAST:G3O-29348-MONOMER.

Gene expression databases

GenevestigatorP25359.

Family and domain databases

InterProIPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamPF01138. RNase_PH. 1 hit.
[Graphical view]
SUPFAMSSF54211. SSF54211. 2 hits.
ProtoNetSearch...

Other

NextBio965938.

Entry information

Entry nameRRP43_YEAST
AccessionPrimary (citable) accession number: P25359
Secondary accession number(s): D6VR45, Q8NKJ5
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: June 27, 2003
Last modified: July 9, 2014
This is version 129 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 III

Yeast (Saccharomyces cerevisiae) chromosome III: 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