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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: -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

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

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

Keywordsi

Molecular functionRNA-binding
Biological processrRNA processing

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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
PaxDbiP38792
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

Show more details

Protein-protein interaction databases

BioGridi36501, 270 interactors
ComplexPortaliCPX-599 Nuclear/nucleolar exosome complex, DIS3-RRP6 variant
CPX-603 Cytoplasmic exosome complex, DIS3 variant
DIPiDIP-5888N
IntActiP38792, 22 interactors
MINTiP38792
STRINGi4932.YHR069C

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
Beta strandi151 – 153Combined 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[»]
5K36X-ray3.10H1-359[»]
5OKZX-ray3.20H/R/b/l50-359[»]
5VZJX-ray3.30H1-359[»]
6FSZelectron microscopy4.60HH1-359[»]
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

Phylogenomic databases

GeneTreeiENSGT00440000033656
HOGENOMiHOG000193685
InParanoidiP38792
KOiK03679
OMAiTDDPVWM
OrthoDBiEOG092C3L9G

Family and domain databases

InterProiView protein in InterPro
IPR025721 Exosome_cplx_N_dom
IPR026699 Exosome_RNA_bind1/RRP40/RRP4
IPR004088 KH_dom_type_1
IPR036612 KH_dom_type_1_sf
IPR012340 NA-bd_OB-fold
PANTHERiPTHR21321 PTHR21321, 1 hit
PfamiView protein in Pfam
PF14382 ECR1_N, 1 hit
PF15985 KH_6, 1 hit
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

Similar proteinsi

Entry informationi

Entry nameiRRP4_YEAST
AccessioniPrimary (citable) accession number: P38792
Secondary accession number(s): D3DL18
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: June 20, 2018
This is version 156 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

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

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