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P38792

- RRP4_YEAST

UniProt

P38792 - RRP4_YEAST

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Protein

Exosome complex component RRP4

Gene

RRP4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.4 Publications

GO - Molecular functioni

  1. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  2. nonfunctional rRNA decay Source: SGD
  3. nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  4. nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
  5. nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  6. nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription Source: SGD
  7. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
  8. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
  9. nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
  10. polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  11. U4 snRNA 3'-end processing Source: SGD
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31119-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP4
Alternative name(s):
Ribosomal RNA-processing protein 4
Gene namesi
Name:RRP4
Ordered Locus Names:YHR069C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VIII

Organism-specific databases

CYGDiYHR069c.
SGDiS000001111. RRP4.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasmic exosome (RNase complex) Source: SGD
  2. nuclear exosome (RNase complex) Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 359358Exosome complex component RRP4PRO_0000097455Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine1 Publication
Modified residuei28 – 281Phosphoserine2 Publications
Modified residuei268 – 2681Phosphoserine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP38792.
PaxDbiP38792.

Expressioni

Gene expression databases

GenevestigatoriP38792.

Interactioni

Subunit structurei

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/RRP47.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CSL4P538597EBI-1757,EBI-1731
DIS3Q081626EBI-1757,EBI-1740
SKI6P469484EBI-1757,EBI-1788

Protein-protein interaction databases

BioGridi36501. 46 interactions.
DIPiDIP-5888N.
IntActiP38792. 21 interactions.
MINTiMINT-649511.
STRINGi4932.YHR069C.

Structurei

Secondary structure

1
359
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 126
Beta strandi60 – 623
Beta strandi67 – 693
Beta strandi73 – 764
Beta strandi79 – 9113
Beta strandi94 – 1018
Beta strandi111 – 12010
Beta strandi123 – 1275
Beta strandi129 – 1324
Beta strandi134 – 1374
Helixi138 – 1403
Helixi146 – 1483
Turni153 – 1575
Helixi159 – 1613
Beta strandi168 – 1769
Beta strandi178 – 1803
Beta strandi182 – 1854
Beta strandi188 – 1936
Beta strandi196 – 2016
Helixi204 – 2063
Beta strandi214 – 2174
Turni218 – 2203
Beta strandi221 – 2255
Beta strandi229 – 2357
Helixi238 – 2425
Helixi276 – 2783
Beta strandi279 – 2813
Helixi291 – 30919
Helixi316 – 32510
Helixi326 – 3283
Beta strandi329 – 3313
Helixi332 – 3365
Helixi338 – 35619

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80H1-359[»]
4OO1X-ray3.30H1-359[»]
ProteinModelPortaliP38792.
SMRiP38792. Positions 2-357.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini107 – 18781S1 motifAdd
BLAST

Sequence similaritiesi

Belongs to the RRP4 family.Curated
Contains 1 S1 motif domain.Curated

Phylogenomic databases

eggNOGiCOG1097.
GeneTreeiENSGT00440000033656.
HOGENOMiHOG000193685.
InParanoidiP38792.
KOiK03679.
OMAiHTHNLPG.
OrthoDBiEOG7712J5.

Family and domain databases

InterProiIPR025721. Exosome_cplx_N_dom.
IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
IPR022967. S1_dom.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF14382. ECR1_N. 1 hit.
[Graphical view]
SMARTiSM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 2 hits.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P38792-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSEVITITKR NGAFQNSSNL SYNNTGISDD ENDEEDIYMH DVNSASKSES
60 70 80 90 100
DSQIVTPGEL VTDDPIWMRG HGTYFLDNMT YSSVAGTVSR VNRLLSVIPL
110 120 130 140 150
KGRYAPETGD HVVGRIAEVG NKRWKVDIGG KQHAVLMLGS VNLPGGILRR
160 170 180 190 200
KSESDELQMR SFLKEGDLLN AEVQSLFQDG SASLHTRSLK YGKLRNGMFC
210 220 230 240 250
QVPSSLIVRA KNHTHNLPGN ITVVLGVNGY IWLRKTSQMD LARDTPSANN
260 270 280 290 300
SSSIKSTGPT GAVSLNPSIT RLEEESSWQI YSDENDPSIS NNIRQAICRY
310 320 330 340 350
ANVIKALAFC EIGITQQRIV SAYEASMVYS NVGELIEKNV MESIGSDILT

AEKMRGNGN
Length:359
Mass (Da):39,427
Last modified:February 1, 1995 - v1
Checksum:i0718A7ABF42E9B9B
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti136 – 1361L → P in RRP4-1; temperature-sensitive(ts) lethal mutation.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00061 Genomic DNA. Translation: AAB68393.1.
BK006934 Genomic DNA. Translation: DAA06762.1.
PIRiS46714.
RefSeqiNP_011936.1. NM_001179199.1.

Genome annotation databases

EnsemblFungiiYHR069C; YHR069C; YHR069C.
GeneIDi856466.
KEGGisce:YHR069C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00061 Genomic DNA. Translation: AAB68393.1 .
BK006934 Genomic DNA. Translation: DAA06762.1 .
PIRi S46714.
RefSeqi NP_011936.1. NM_001179199.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4IFD X-ray 2.80 H 1-359 [» ]
4OO1 X-ray 3.30 H 1-359 [» ]
ProteinModelPortali P38792.
SMRi P38792. Positions 2-357.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 36501. 46 interactions.
DIPi DIP-5888N.
IntActi P38792. 21 interactions.
MINTi MINT-649511.
STRINGi 4932.YHR069C.

Proteomic databases

MaxQBi P38792.
PaxDbi P38792.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YHR069C ; YHR069C ; YHR069C .
GeneIDi 856466.
KEGGi sce:YHR069C.

Organism-specific databases

CYGDi YHR069c.
SGDi S000001111. RRP4.

Phylogenomic databases

eggNOGi COG1097.
GeneTreei ENSGT00440000033656.
HOGENOMi HOG000193685.
InParanoidi P38792.
KOi K03679.
OMAi HTHNLPG.
OrthoDBi EOG7712J5.

Enzyme and pathway databases

BioCyci YEAST:G3O-31119-MONOMER.

Miscellaneous databases

NextBioi 982123.
PROi P38792.

Gene expression databases

Genevestigatori P38792.

Family and domain databases

InterProi IPR025721. Exosome_cplx_N_dom.
IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
IPR022967. S1_dom.
[Graphical view ]
PANTHERi PTHR21321. PTHR21321. 1 hit.
Pfami PF14382. ECR1_N. 1 hit.
[Graphical view ]
SMARTi SM00316. S1. 1 hit.
[Graphical view ]
SUPFAMi SSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 2 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  8. 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. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRRP4_YEAST
AccessioniPrimary (citable) accession number: P38792
Secondary accession number(s): D3DL18
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: October 29, 2014
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 4840 molecules/cell in log phase SD medium.1 Publication

Caution

Was originally (PubMed:9390555 and PubMed:8600032) thought to have exonuclease activity but it was later shown (PubMed:17173052 and PubMed:17174896) that only DIS3/RRP44 subunit of the exosome core has this activity.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome VIII
    Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

External Data

Dasty 3