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Q08285

- RRP40_YEAST

UniProt

Q08285 - RRP40_YEAST

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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: 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

GO - Molecular functioni

  1. manganese ion binding Source: SGD
  2. RNA binding Source: SGD

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. ncRNA 3'-end processing Source: SGD
  3. nonfunctional rRNA decay Source: SGD
  4. nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  5. nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
  6. nuclear polyadenylation-dependent tRNA catabolic process 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
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33533-MONOMER.

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
ProteomesiUP000002311: Chromosome XV

Organism-specific databases

CYGDiYOL142w.
SGDiS000005502. RRP40.

Subcellular locationi

Cytoplasm 1 Publication. Nucleusnucleolus 1 Publication

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
Chaini1 – 240240Exosome complex component RRP40PRO_0000097453Add
BLAST

Proteomic databases

MaxQBiQ08285.
PaxDbiQ08285.
PeptideAtlasiQ08285.

Expressioni

Gene expression databases

GenevestigatoriQ08285.

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

WithEntry#Exp.IntActNotes
CSL4P538595EBI-1831,EBI-1731
DIS3Q081624EBI-1831,EBI-1740
SKI6P469484EBI-1831,EBI-1788

Protein-protein interaction databases

BioGridi34275. 19 interactions.
DIPiDIP-5330N.
IntActiQ08285. 17 interactions.
MINTiMINT-530842.
STRINGi4932.YOL142W.

Structurei

Secondary structure

1
240
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi15 – 173Combined sources
Beta strandi19 – 213Combined sources
Beta strandi25 – 273Combined sources
Turni29 – 313Combined sources
Beta strandi34 – 363Combined sources
Beta strandi40 – 445Combined sources
Beta strandi53 – 597Combined sources
Beta strandi71 – 799Combined sources
Beta strandi81 – 899Combined sources
Beta strandi95 – 984Combined sources
Helixi99 – 1013Combined sources
Beta strandi102 – 1043Combined sources
Beta strandi107 – 1093Combined sources
Beta strandi118 – 1258Combined sources
Beta strandi133 – 1375Combined sources
Turni139 – 1413Combined sources
Beta strandi154 – 1574Combined sources
Helixi160 – 1689Combined sources
Helixi174 – 1796Combined sources
Beta strandi185 – 1895Combined sources
Turni190 – 1923Combined sources
Beta strandi193 – 1975Combined sources
Helixi201 – 21717Combined sources
Helixi220 – 2223Combined sources
Helixi223 – 23513Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JA9X-ray2.20A62-236[»]
4IFDX-ray2.80G1-240[»]
4OO1X-ray3.30G1-240[»]
ProteinModelPortaliQ08285.
SMRiQ08285. Positions 1-236.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08285.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini67 – 13771S1 motifAdd
BLAST

Sequence similaritiesi

Belongs to the RRP40 family.Curated
Contains 1 S1 motif domain.Curated

Phylogenomic databases

eggNOGiCOG1097.
GeneTreeiENSGT00390000012042.
HOGENOMiHOG000184644.
InParanoidiQ08285.
KOiK03681.
OMAiHMDAELE.
OrthoDBiEOG7FJHC7.

Family and domain databases

InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
IPR022967. S1_dom.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
SMARTiSM00316. S1. 1 hit.
[Graphical view]
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti160 – 1601L → F in CAA99163. (PubMed:9169874)Curated

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.

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 .
PIRi S61872.
RefSeqi NP_014499.2. NM_001183396.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2JA9 X-ray 2.20 A 62-236 [» ]
4IFD X-ray 2.80 G 1-240 [» ]
4OO1 X-ray 3.30 G 1-240 [» ]
ProteinModelPortali Q08285.
SMRi Q08285. Positions 1-236.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34275. 19 interactions.
DIPi DIP-5330N.
IntActi Q08285. 17 interactions.
MINTi MINT-530842.
STRINGi 4932.YOL142W.

Proteomic databases

MaxQBi Q08285.
PaxDbi Q08285.
PeptideAtlasi Q08285.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YOL142W ; YOL142W ; YOL142W .
GeneIDi 854023.
KEGGi sce:YOL142W.

Organism-specific databases

CYGDi YOL142w.
SGDi S000005502. RRP40.

Phylogenomic databases

eggNOGi COG1097.
GeneTreei ENSGT00390000012042.
HOGENOMi HOG000184644.
InParanoidi Q08285.
KOi K03681.
OMAi HMDAELE.
OrthoDBi EOG7FJHC7.

Enzyme and pathway databases

BioCyci YEAST:G3O-33533-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q08285.
NextBioi 975559.
PROi Q08285.

Gene expression databases

Genevestigatori Q08285.

Family and domain databases

InterProi 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.
SMARTi SM00316. S1. 1 hit.
[Graphical view ]
SUPFAMi SSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 160.
    Strain: ATCC 204508 / S288c.
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. "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: FUNCTION, IDENTIFICATION IN THE EXOSOME COMPLEX BY MASS SPECTROMETRY.
  5. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. "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.
  8. Erratum
    Liu Q., Greimann J.C., Lima C.D.
    Cell 131:188-189(2007)
  9. "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.
  10. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "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.

Entry informationi

Entry nameiRRP40_YEAST
AccessioniPrimary (citable) accession number: Q08285
Secondary accession number(s): D6W1S7, E9P8Z4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: September 21, 2011
Last modified: November 26, 2014
This is version 119 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

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

External Data

Dasty 3