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P38792 (RRP4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 121. 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 RRP4
Alternative name(s):
Ribosomal RNA-processing protein 4
Gene names
Name:RRP4
Ordered Locus Names:YHR069C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length359 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. RRP4 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits. Ref.1 Ref.4 Ref.10 Ref.12

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/RRP47. Ref.1 Ref.5 Ref.6 Ref.10

Subcellular location

Cytoplasm. Nucleusnucleolus Ref.5 Ref.7.

Miscellaneous

Present with 4840 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the RRP4 family.

Contains 1 S1 motif domain.

Caution

Was originally (Ref.1 and Ref.4) thought to have exonuclease activity but it was later shown (Ref.10 and Ref.9) that only DIS3/RRP44 subunit of the exosome core has this 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_processU4 snRNA 3'-end processing

Inferred from mutant phenotype PubMed 10611222. 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.5PubMed 10508172Ref.4Ref.1. Source: SGD

nonfunctional rRNA decay

Inferred by curator Ref.5. Source: SGD

nuclear polyadenylation-dependent mRNA catabolic process

Inferred by curator Ref.5. Source: SGD

nuclear polyadenylation-dependent rRNA catabolic process

Inferred from mutant phenotype Ref.5. Source: SGD

nuclear polyadenylation-dependent tRNA catabolic process

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

nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription

Inferred from genetic interaction PubMed 11586364. Source: SGD

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

Inferred by curator Ref.5. Source: SGD

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

Inferred from mutant phenotype PubMed 9482746. Source: SGD

nuclear-transcribed mRNA catabolic process, non-stop decay

Inferred by curator Ref.5. Source: SGD

polyadenylation-dependent snoRNA 3'-end processing

Inferred from mutant phenotype PubMed 10611222. Source: SGD

   Cellular_componentcytoplasmic exosome (RNase complex)

Inferred from direct assay Ref.5PubMed 19046973. Source: SGD

nuclear exosome (RNase complex)

Inferred from direct assay Ref.5PubMed 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 11805826Ref.6PubMed 16429126PubMed 16729021PubMed 16829593PubMed 21072061. Source: IntAct

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.14
Chain2 – 359358Exosome complex component RRP4
PRO_0000097455

Regions

Domain107 – 18781S1 motif

Amino acid modifications

Modified residue21N-acetylserine Ref.14
Modified residue281Phosphoserine Ref.11 Ref.13
Modified residue2681Phosphoserine Ref.11

Natural variations

Natural variant1361L → P in RRP4-1; temperature-sensitive(ts) lethal mutation.

Secondary structure

............................................................ 359
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P38792 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 0718A7ABF42E9B9B

FASTA35939,427
        10         20         30         40         50         60 
MSEVITITKR NGAFQNSSNL SYNNTGISDD ENDEEDIYMH DVNSASKSES DSQIVTPGEL 

        70         80         90        100        110        120 
VTDDPIWMRG HGTYFLDNMT YSSVAGTVSR VNRLLSVIPL KGRYAPETGD HVVGRIAEVG 

       130        140        150        160        170        180 
NKRWKVDIGG KQHAVLMLGS VNLPGGILRR KSESDELQMR SFLKEGDLLN AEVQSLFQDG 

       190        200        210        220        230        240 
SASLHTRSLK YGKLRNGMFC QVPSSLIVRA KNHTHNLPGN ITVVLGVNGY IWLRKTSQMD 

       250        260        270        280        290        300 
LARDTPSANN SSSIKSTGPT GAVSLNPSIT RLEEESSWQI YSDENDPSIS NNIRQAICRY 

       310        320        330        340        350 
ANVIKALAFC EIGITQQRIV SAYEASMVYS NVGELIEKNV MESIGSDILT AEKMRGNGN 

« Hide

References

« Hide 'large scale' references
[1]"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: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 94-101; 256-271 AND 306-318, FUNCTION, SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY.
[2]"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII."
Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. expand/collapse author list , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M.
Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"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.
[4]"The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism."
Mitchell P., Petfalski E., Tollervey D.
Genes Dev. 10:502-513(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, VARIANT RRP4-1.
[5]"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, SUBCELLULAR LOCATION.
[6]"Rrp47p is an exosome-associated protein required for the 3' processing of stable RNAs."
Mitchell P., Petfalski E., Houalla R., Podtelejnikov A., Mann M., Tollervey D.
Mol. Cell. Biol. 23:6982-6992(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LRP1.
[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]"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.
[11]"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-28 AND SER-268, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"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.
[13]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-28, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"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 SER-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
U00061 Genomic DNA. Translation: AAB68393.1.
BK006934 Genomic DNA. Translation: DAA06762.1.
PIRS46714.
RefSeqNP_011936.1. NM_001179199.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80H1-359[»]
ProteinModelPortalP38792.
SMRP38792. Positions 2-357.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid36501. 45 interactions.
DIPDIP-5888N.
IntActP38792. 21 interactions.
MINTMINT-649511.
STRING4932.YHR069C.

Proteomic databases

MaxQBP38792.
PaxDbP38792.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYHR069C; YHR069C; YHR069C.
GeneID856466.
KEGGsce:YHR069C.

Organism-specific databases

CYGDYHR069c.
SGDS000001111. RRP4.

Phylogenomic databases

eggNOGCOG1097.
GeneTreeENSGT00440000033656.
HOGENOMHOG000193685.
KOK03679.
OMAHTHNLPG.
OrthoDBEOG7712J5.

Enzyme and pathway databases

BioCycYEAST:G3O-31119-MONOMER.

Gene expression databases

GenevestigatorP38792.

Family and domain databases

InterProIPR025721. Exosome_cplx_N_dom.
IPR026699. 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.
PfamPF14382. ECR1_N. 1 hit.
[Graphical view]
SMARTSM00316. S1. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 2 hits.
ProtoNetSearch...

Other

NextBio982123.
PROP38792.

Entry information

Entry nameRRP4_YEAST
AccessionPrimary (citable) accession number: P38792
Secondary accession number(s): D3DL18
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: July 9, 2014
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome VIII

Yeast (Saccharomyces cerevisiae) chromosome VIII: 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