Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Exosome complex component RRP40

Gene

RRP40

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. RRP40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.3 Publications

Miscellaneous

Present with 6050 molecules/cell in log phase SD medium.1 Publication

Caution

According to PubMed:17173052 and PubMed:17174896, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.Curated

GO - Molecular functioni

  • manganese ion binding Source: SGD
  • RNA binding Source: SGD

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processrRNA processing

Enzyme and pathway databases

BioCyciYEAST:G3O-33533-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 RRP40
Alternative name(s):
Ribosomal RNA-processing protein 40
Gene namesi
Name:RRP40
Ordered Locus Names:YOL142W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

SGDiS000005502 RRP40

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
ChainiPRO_00000974531 – 240Exosome complex component RRP40Add BLAST240

Proteomic databases

MaxQBiQ08285
PaxDbiQ08285
PRIDEiQ08285

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.2 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi34275, 18 interactors
ComplexPortaliCPX-599 Nuclear/nucleolar exosome complex, DIS3-RRP6 variant
CPX-603 Cytoplasmic exosome complex, DIS3 variant
DIPiDIP-5330N
IntActiQ08285, 17 interactors
MINTiQ08285
STRINGi4932.YOL142W

Structurei

Secondary structure

1240
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ08285
SMRiQ08285
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08285

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini67 – 137S1 motifAdd BLAST71

Sequence similaritiesi

Belongs to the RRP40 family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000012042
HOGENOMiHOG000184644
InParanoidiQ08285
KOiK03681
OMAiISYLAFE
OrthoDBiEOG092C4V3H

Family and domain databases

CDDicd05790 S1_Rrp40, 1 hit
Gene3Di3.30.1370.10, 1 hit
InterProiView protein in InterPro
IPR026699 Exosome_RNA_bind1/RRP40/RRP4
IPR004088 KH_dom_type_1
IPR036612 KH_dom_type_1_sf
IPR012340 NA-bd_OB-fold
IPR037319 Rrp40_S1
PANTHERiPTHR21321 PTHR21321, 1 hit
PfamiView protein in Pfam
PF15985 KH_6, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
SSF54791 SSF54791, 1 hit

Sequencei

Sequence statusi: Complete.

Q08285-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSTFIFPGDS FPVDPTTPVK LGPGIYCDPN TQEIRPVNTG VLHVSAKGKS
60 70 80 90 100
GVQTAYIDYS SKRYIPSVND FVIGVIIGTF SDSYKVSLQN FSSSVSLSYM
110 120 130 140 150
AFPNASKKNR PTLQVGDLVY ARVCTAEKEL EAEIECFDST TGRDAGFGIL
160 170 180 190 200
EDGMIIDVNL NFARQLLFNN DFPLLKVLAA HTKFEVAIGL NGKIWVKCEE
210 220 230 240
LSNTLACYRT IMECCQKNDT AAFKDIAKRQ FKEILTVKEE
Length:240
Mass (Da):26,556
Last modified:September 21, 2011 - v2
Checksum:i62B3A30348BBAA7C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti160L → F in CAA99163 (PubMed:9169874).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74884 Genomic DNA Translation: CAA99163.1
AY692926 Genomic DNA Translation: AAT92945.1
BK006948 Genomic DNA Translation: DAA10643.2
PIRiS61872
RefSeqiNP_014499.2, NM_001183396.2

Genome annotation databases

EnsemblFungiiYOL142W; YOL142W; YOL142W
GeneIDi854023
KEGGisce:YOL142W

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74884 Genomic DNA Translation: CAA99163.1
AY692926 Genomic DNA Translation: AAT92945.1
BK006948 Genomic DNA Translation: DAA10643.2
PIRiS61872
RefSeqiNP_014499.2, NM_001183396.2

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JA9X-ray2.20A62-236[»]
4IFDX-ray2.80G1-240[»]
4OO1X-ray3.30G1-240[»]
5C0WX-ray4.60G1-240[»]
5C0XX-ray3.81G1-240[»]
5G06electron microscopy4.20G1-240[»]
5JEAX-ray2.65G1-240[»]
5K36X-ray3.10G1-240[»]
5OKZX-ray3.20G/Q/a/k1-240[»]
5VZJX-ray3.30G1-240[»]
6FSZelectron microscopy4.60GG1-240[»]
ProteinModelPortaliQ08285
SMRiQ08285
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34275, 18 interactors
ComplexPortaliCPX-599 Nuclear/nucleolar exosome complex, DIS3-RRP6 variant
CPX-603 Cytoplasmic exosome complex, DIS3 variant
DIPiDIP-5330N
IntActiQ08285, 17 interactors
MINTiQ08285
STRINGi4932.YOL142W

Proteomic databases

MaxQBiQ08285
PaxDbiQ08285
PRIDEiQ08285

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOL142W; YOL142W; YOL142W
GeneIDi854023
KEGGisce:YOL142W

Organism-specific databases

SGDiS000005502 RRP40

Phylogenomic databases

GeneTreeiENSGT00390000012042
HOGENOMiHOG000184644
InParanoidiQ08285
KOiK03681
OMAiISYLAFE
OrthoDBiEOG092C4V3H

Enzyme and pathway databases

BioCyciYEAST:G3O-33533-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

EvolutionaryTraceiQ08285
PROiPR:Q08285

Family and domain databases

CDDicd05790 S1_Rrp40, 1 hit
Gene3Di3.30.1370.10, 1 hit
InterProiView protein in InterPro
IPR026699 Exosome_RNA_bind1/RRP40/RRP4
IPR004088 KH_dom_type_1
IPR036612 KH_dom_type_1_sf
IPR012340 NA-bd_OB-fold
IPR037319 Rrp40_S1
PANTHERiPTHR21321 PTHR21321, 1 hit
PfamiView protein in Pfam
PF15985 KH_6, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
SSF54791 SSF54791, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRRP40_YEAST
AccessioniPrimary (citable) accession number: Q08285
Secondary accession number(s): D6W1S7, E9P8Z4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: September 21, 2011
Last modified: November 7, 2018
This is version 155 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again