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Protein

Exosome complex component RRP40

Gene

RRP40

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. 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

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

EuPathDBiFungiDB:YOL142W.
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.
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

Show more details

Protein-protein interaction databases

BioGridi34275. 17 interactors.
DIPiDIP-5330N.
IntActiQ08285. 17 interactors.
MINTiMINT-530842.
STRINGi4932.YOL142W.

Structurei

Secondary structure

1240
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 5Combined sources3
Beta strandi15 – 17Combined sources3
Beta strandi19 – 21Combined sources3
Beta strandi25 – 27Combined sources3
Turni29 – 31Combined sources3
Beta strandi34 – 36Combined sources3
Beta strandi40 – 44Combined sources5
Beta strandi53 – 58Combined sources6
Beta strandi71 – 79Combined sources9
Beta strandi81 – 89Combined sources9
Beta strandi95 – 102Combined sources8
Beta strandi107 – 109Combined sources3
Beta strandi118 – 125Combined sources8
Beta strandi128 – 130Combined sources3
Beta strandi133 – 137Combined sources5
Turni139 – 141Combined sources3
Beta strandi148 – 150Combined sources3
Beta strandi154 – 157Combined sources4
Helixi160 – 168Combined sources9
Helixi174 – 179Combined sources6
Beta strandi185 – 189Combined sources5
Turni190 – 192Combined sources3
Beta strandi193 – 197Combined sources5
Helixi201 – 216Combined sources16
Helixi220 – 222Combined sources3
Helixi223 – 231Combined sources9

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[»]
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

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.
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

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: October 25, 2017
This is version 144 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Caution

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

Keywords - Technical termi

3D-structure, Complete proteome, 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 XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names