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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: 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

GO - Biological processi

  • CUT catabolic process Source: GO_Central
  • exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: GO_Central
  • exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • nonfunctional rRNA decay Source: SGD
  • nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  • nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription Source: SGD
  • nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
  • nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
  • polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  • 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.
ReactomeiR-SCE-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

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
Proteomesi
  • UP000002311 Componenti: Chromosome VIII

Organism-specific databases

EuPathDBiFungiDB:YHR069C.
SGDiS000001111. RRP4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic exosome (RNase complex) Source: SGD
  • nuclear exosome (RNase complex) Source: SGD
  • nucleolus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000974552 – 359Exosome complex component RRP4Add BLAST358

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei28PhosphoserineCombined sources1
Modified residuei268PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP38792.
PRIDEiP38792.

PTM databases

iPTMnetiP38792.

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. 45 interactors.
DIPiDIP-5888N.
IntActiP38792. 21 interactors.
MINTiMINT-649511.

Structurei

Secondary structure

1359
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 12Combined sources6
Beta strandi60 – 63Combined sources4
Beta strandi65 – 69Combined sources5
Beta strandi73 – 76Combined sources4
Beta strandi79 – 91Combined sources13
Beta strandi94 – 101Combined sources8
Beta strandi111 – 119Combined sources9
Beta strandi121 – 127Combined sources7
Beta strandi129 – 132Combined sources4
Beta strandi134 – 137Combined sources4
Helixi138 – 140Combined sources3
Helixi146 – 148Combined sources3
Helixi154 – 157Combined sources4
Helixi159 – 162Combined sources4
Beta strandi168 – 176Combined sources9
Beta strandi178 – 180Combined sources3
Beta strandi182 – 185Combined sources4
Beta strandi188 – 193Combined sources6
Beta strandi196 – 201Combined sources6
Helixi204 – 206Combined sources3
Beta strandi213 – 217Combined sources5
Turni218 – 220Combined sources3
Beta strandi221 – 225Combined sources5
Beta strandi229 – 235Combined sources7
Helixi238 – 241Combined sources4
Helixi244 – 248Combined sources5
Helixi270 – 276Combined sources7
Beta strandi279 – 281Combined sources3
Helixi291 – 309Combined sources19
Helixi316 – 326Combined sources11
Beta strandi329 – 331Combined sources3
Helixi332 – 336Combined sources5
Helixi338 – 354Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80H1-359[»]
4OO1X-ray3.30H1-359[»]
5C0WX-ray4.60H1-359[»]
5C0XX-ray3.81H1-359[»]
5G06electron microscopy4.20H1-359[»]
5JEAX-ray2.65H50-359[»]
ProteinModelPortaliP38792.
SMRiP38792.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini107 – 187S1 motifAdd BLAST81

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00440000033656.
HOGENOMiHOG000193685.
InParanoidiP38792.
KOiK03679.
OMAiGINRMEE.
OrthoDBiEOG092C3L9G.

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.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 2 hits.
PfamiPF14382. ECR1_N. 1 hit.
PF15985. KH_6. 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)DescriptionActionsGraphical viewLength
Natural varianti136L → P in RRP4-1; temperature-sensitive(ts) lethal mutation. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
U00061 Genomic DNA. Translation: AAB68393.1.
BK006934 Genomic DNA. Translation: DAA06762.1.
PIRiS46714.
RefSeqiNP_011936.1. NM_001179199.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80H1-359[»]
4OO1X-ray3.30H1-359[»]
5C0WX-ray4.60H1-359[»]
5C0XX-ray3.81H1-359[»]
5G06electron microscopy4.20H1-359[»]
5JEAX-ray2.65H50-359[»]
ProteinModelPortaliP38792.
SMRiP38792.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36501. 45 interactors.
DIPiDIP-5888N.
IntActiP38792. 21 interactors.
MINTiMINT-649511.

PTM databases

iPTMnetiP38792.

Proteomic databases

MaxQBiP38792.
PRIDEiP38792.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YHR069C.
SGDiS000001111. RRP4.

Phylogenomic databases

GeneTreeiENSGT00440000033656.
HOGENOMiHOG000193685.
InParanoidiP38792.
KOiK03679.
OMAiGINRMEE.
OrthoDBiEOG092C3L9G.

Enzyme and pathway databases

BioCyciYEAST:G3O-31119-MONOMER.
ReactomeiR-SCE-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Miscellaneous databases

PROiP38792.

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.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 2 hits.
PfamiPF14382. ECR1_N. 1 hit.
PF15985. KH_6. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 2 hits.
ProtoNetiSearch...

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: November 2, 2016
This is version 142 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.