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P25359

- RRP43_YEAST

UniProt

P25359 - RRP43_YEAST

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Protein

Exosome complex component RRP43

Gene

RRP43

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. RRP43 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.4 Publications

GO - Molecular functioni

  1. RNA binding Source: UniProtKB-KW

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. mRNA catabolic process Source: UniProtKB
  3. ncRNA 3'-end processing Source: SGD
  4. nonfunctional rRNA decay Source: SGD
  5. nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  6. nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
  7. nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  8. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
  9. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
  10. nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
  11. polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  12. rRNA metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29348-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP43
Alternative name(s):
Ribosomal RNA-processing protein 43
Gene namesi
Name:RRP43
Ordered Locus Names:YCR035C
ORF Names:YCR35C, YCR522
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome III

Organism-specific databases

CYGDiYCR035c.
SGDiS000000631. RRP43.

Subcellular locationi

Cytoplasm 1 Publication. Nucleusnucleolus 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. cytoplasmic exosome (RNase complex) Source: SGD
  3. nuclear exosome (RNase complex) Source: SGD
  4. nucleolus Source: SGD
  5. nucleoplasm Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi162 – 1621S → F: Interaction with RRP46 abolished; when associated with T-246. 1 Publication
Mutagenesisi212 – 2121V → A: Interaction with RRP46 abolished. 1 Publication
Mutagenesisi230 – 2301C → Y: Interaction with RRP46 abolished; when associated with T-274 and Y-276. 1 Publication
Mutagenesisi246 – 2461A → T: Interaction with RRP46 abolished; when associated with F-162. 1 Publication
Mutagenesisi274 – 2741I → T: Interaction with RRP46 abolished; when associated with Y-230 and Y-276. 1 Publication
Mutagenesisi276 – 2761C → Y: Interaction with RRP46 abolished; when associated with Y-230 and T-274. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 394393Exosome complex component RRP43PRO_0000139970Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine1 Publication
Modified residuei26 – 261Phosphoserine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP25359.
PaxDbiP25359.
PeptideAtlasiP25359.

Expressioni

Gene expression databases

GenevestigatoriP25359.

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 NIP7 and NOP8. Interacts strongly with RRP46.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CSL4P538597EBI-1773,EBI-1731
NIP7Q089624EBI-1773,EBI-12067
PIH1P387682EBI-1773,EBI-24499
SKI6P469484EBI-1773,EBI-1788

Protein-protein interaction databases

BioGridi31018. 33 interactions.
DIPiDIP-5485N.
IntActiP25359. 17 interactions.
MINTiMINT-564723.
STRINGi4932.YCR035C.

Structurei

Secondary structure

1
394
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 123
Helixi19 – 257
Helixi27 – 359
Turni36 – 383
Beta strandi48 – 503
Beta strandi53 – 608
Beta strandi65 – 673
Beta strandi76 – 827
Beta strandi85 – 9814
Helixi124 – 1263
Beta strandi131 – 1366
Helixi146 – 16116
Helixi167 – 1704
Beta strandi175 – 1806
Turni181 – 1833
Beta strandi184 – 1885
Beta strandi208 – 22114
Helixi227 – 23812
Beta strandi242 – 2498
Beta strandi257 – 2604
Beta strandi265 – 2684
Beta strandi275 – 2839
Turni288 – 2903
Beta strandi293 – 3019
Helixi304 – 3063
Beta strandi328 – 3336
Helixi336 – 3427
Beta strandi345 – 3517
Beta strandi357 – 36711
Helixi371 – 39121

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80C2-394[»]
4OO1X-ray3.30C1-394[»]
ProteinModelPortaliP25359.
SMRiP25359. Positions 7-394.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiNOG286862.
HOGENOMiHOG000057141.
InParanoidiP25359.
KOiK12586.
OMAiTIYYPDL.
OrthoDBiEOG7CCC3J.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 2 hits.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P25359-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAESTTLETI EIHPITFPPE VLARISPELS LQRHLSLGIR PCLRKYEEFR
60 70 80 90 100
DVAIENNTLS RYADAGNIDT KNNILGSNVL KSGKTIVITS ITGGIIEETS
110 120 130 140 150
AAIKDLDDFG EEELFEVTKE EDIIANYASV YPVVEVERGR VGACTDEEMT
160 170 180 190 200
ISQKLHDSIL HSRILPKKAL KVKAGVRSAN EDGTFSVLYP DELEDDTLNE
210 220 230 240 250
TNLKMKRKWS YVLYAKIVVL SRTGPVFDLC WNSLMYALQS VKLPRAFIDE
260 270 280 290 300
RASDLRMTIR TRGRSATIRE TYEIICDQTK SVPLMINAKN IAFASNYGIV
310 320 330 340 350
ELDPECQLQN SDNSEEEEVD IDMDKLNTVL IADLDTEAEE TSIHSTISIL
360 370 380 390
AAPSGNYKQL TLVGGGAKIT PEMIKRSLLL SRVRADDLST RFNI
Length:394
Mass (Da):44,011
Last modified:June 27, 2003 - v2
Checksum:i8801837B8184134D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti102 – 1021A → S in CAA40227. (PubMed:1964349)Curated
Sequence conflicti363 – 3631V → M in CAA40227. (PubMed:1964349)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X56909 Genomic DNA. Translation: CAA40227.1.
X59720 Genomic DNA. Translation: CAC42984.1.
S78624 Genomic DNA. Translation: AAB21261.1.
BK006937 Genomic DNA. Translation: DAA07514.1.
PIRiS12917.
RefSeqiNP_009964.2. NM_001178749.1.

Genome annotation databases

EnsemblFungiiYCR035C; YCR035C; YCR035C.
GeneIDi850401.
KEGGisce:YCR035C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X56909 Genomic DNA. Translation: CAA40227.1 .
X59720 Genomic DNA. Translation: CAC42984.1 .
S78624 Genomic DNA. Translation: AAB21261.1 .
BK006937 Genomic DNA. Translation: DAA07514.1 .
PIRi S12917.
RefSeqi NP_009964.2. NM_001178749.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4IFD X-ray 2.80 C 2-394 [» ]
4OO1 X-ray 3.30 C 1-394 [» ]
ProteinModelPortali P25359.
SMRi P25359. Positions 7-394.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31018. 33 interactions.
DIPi DIP-5485N.
IntActi P25359. 17 interactions.
MINTi MINT-564723.
STRINGi 4932.YCR035C.

Proteomic databases

MaxQBi P25359.
PaxDbi P25359.
PeptideAtlasi P25359.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YCR035C ; YCR035C ; YCR035C .
GeneIDi 850401.
KEGGi sce:YCR035C.

Organism-specific databases

CYGDi YCR035c.
SGDi S000000631. RRP43.

Phylogenomic databases

eggNOGi NOG286862.
HOGENOMi HOG000057141.
InParanoidi P25359.
KOi K12586.
OMAi TIYYPDL.
OrthoDBi EOG7CCC3J.

Enzyme and pathway databases

BioCyci YEAST:G3O-29348-MONOMER.

Miscellaneous databases

NextBioi 965938.

Gene expression databases

Genevestigatori P25359.

Family and domain databases

InterProi IPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view ]
Pfami PF01138. RNase_PH. 1 hit.
[Graphical view ]
SUPFAMi SSF54211. SSF54211. 2 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The complete sequence of the 8.2 kb segment left of MAT on chromosome III reveals five ORFs, including a gene for a yeast ribokinase."
    Thierry A., Fairhead C., Dujon B.
    Yeast 6:521-534(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  2. "The complete DNA sequence of yeast chromosome III."
    Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M.
    , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
    Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Valles G., Volckaerts G.
    Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 102 AND 363.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases."
    Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D.
    Cell 91:457-466(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 25-33, FUNCTION, SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY.
  6. "The complete sequence of a 7.5 kb region of chromosome III from Saccharomyces cerevisiae that lies between CRY1 and MAT."
    Wicksteed B.L., Roberts A.B., Sagliocco F.A., Brown A.J.P.
    Yeast 7:761-772(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 232-394.
  7. "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: IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS SPECTROMETRY.
  8. "The exosome subunit Rrp43p is required for the efficient maturation of 5.8S, 18S and 25S rRNA."
    Zanchin N.I., Goldfarb D.S.
    Nucleic Acids Res. 27:1283-1288(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Temperature-sensitive mutants of the exosome subunit Rrp43p show a deficiency in mRNA degradation and no longer interact with the exosome."
    Oliveira C.C., Gonzales F.A., Zanchin N.I.
    Nucleic Acids Res. 30:4186-4198(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RRP46, MUTAGENESIS OF SER-162; VAL-212; CYS-230; ALA-246; ILE-274 AND CYS-276.
  10. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  12. "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.
  13. Erratum
    Liu Q., Greimann J.C., Lima C.D.
    Cell 131:188-189(2007)
  14. "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 OF THE RNA EXOSOME COMPLEX, SUBUNIT.
  15. "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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-26, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRRP43_YEAST
AccessioniPrimary (citable) accession number: P25359
Secondary accession number(s): D6VR45, Q8NKJ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: June 27, 2003
Last modified: October 29, 2014
This is version 131 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 3180 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, 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 III
    Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

External Data

Dasty 3