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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: 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

GO - Biological processi

  • 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
  • mRNA catabolic process Source: UniProtKB
  • ncRNA 3'-end processing Source: SGD
  • nonfunctional rRNA decay Source: SGD
  • nuclear mRNA surveillance Source: GO_Central
  • 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-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
  • rRNA metabolic process Source: UniProtKB
  • U1 snRNA 3'-end processing Source: GO_Central
  • U4 snRNA 3'-end processing Source: GO_Central
  • U5 snRNA 3'-end processing Source: GO_Central
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
Proteomesi
  • UP000002311 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:YCR035C.
SGDiS000000631. RRP43.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytoplasmic exosome (RNase complex) Source: SGD
  • nuclear exosome (RNase complex) Source: SGD
  • nucleolus Source: SGD
  • nucleoplasm Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi162S → F: Interaction with RRP46 abolished; when associated with T-246. 1 Publication1
Mutagenesisi212V → A: Interaction with RRP46 abolished. 1 Publication1
Mutagenesisi230C → Y: Interaction with RRP46 abolished; when associated with T-274 and Y-276. 1 Publication1
Mutagenesisi246A → T: Interaction with RRP46 abolished; when associated with F-162. 1 Publication1
Mutagenesisi274I → T: Interaction with RRP46 abolished; when associated with Y-230 and Y-276. 1 Publication1
Mutagenesisi276C → Y: Interaction with RRP46 abolished; when associated with Y-230 and T-274. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001399702 – 394Exosome complex component RRP43Add BLAST393

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei26PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP25359.
PRIDEiP25359.

PTM databases

iPTMnetiP25359.

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
NIP7Q089625EBI-1773,EBI-12067
PIH1P387682EBI-1773,EBI-24499
SKI6P469484EBI-1773,EBI-1788

Protein-protein interaction databases

BioGridi31018. 32 interactors.
DIPiDIP-5485N.
IntActiP25359. 17 interactors.
MINTiMINT-564723.

Structurei

Secondary structure

1394
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 12Combined sources3
Helixi19 – 25Combined sources7
Helixi27 – 35Combined sources9
Turni36 – 38Combined sources3
Beta strandi48 – 50Combined sources3
Beta strandi52 – 60Combined sources9
Helixi61 – 63Combined sources3
Beta strandi65 – 67Combined sources3
Beta strandi75 – 82Combined sources8
Beta strandi85 – 97Combined sources13
Helixi124 – 126Combined sources3
Beta strandi131 – 136Combined sources6
Helixi146 – 161Combined sources16
Helixi167 – 170Combined sources4
Beta strandi175 – 180Combined sources6
Turni181 – 183Combined sources3
Beta strandi184 – 188Combined sources5
Beta strandi209 – 221Combined sources13
Helixi227 – 239Combined sources13
Beta strandi242 – 248Combined sources7
Beta strandi257 – 260Combined sources4
Beta strandi265 – 268Combined sources4
Beta strandi275 – 283Combined sources9
Helixi288 – 290Combined sources3
Beta strandi293 – 302Combined sources10
Helixi304 – 306Combined sources3
Beta strandi327 – 333Combined sources7
Helixi338 – 342Combined sources5
Beta strandi345 – 351Combined sources7
Beta strandi357 – 367Combined sources11
Helixi371 – 390Combined sources20

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80C2-394[»]
4OO1X-ray3.30C1-394[»]
5C0WX-ray4.60C1-394[»]
5C0XX-ray3.81C1-394[»]
5G06electron microscopy4.20C1-394[»]
5JEAX-ray2.65C1-394[»]
ProteinModelPortaliP25359.
SMRiP25359.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

HOGENOMiHOG000057141.
InParanoidiP25359.
KOiK12586.
OMAiYVLYAKI.
OrthoDBiEOG092C5179.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR033196. Rrp43.
[Graphical view]
PANTHERiPTHR11097:SF9. PTHR11097:SF9. 4 hits.
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)DescriptionActionsGraphical viewLength
Sequence conflicti102A → S in CAA40227 (PubMed:1964349).Curated1
Sequence conflicti363V → M in CAA40227 (PubMed:1964349).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

EnsemblFungiiCAC42984; CAC42984; CAC42984.
YCR035C; YCR035C; YCR035C.
GeneIDi850401.
KEGGisce:YCR035C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80C2-394[»]
4OO1X-ray3.30C1-394[»]
5C0WX-ray4.60C1-394[»]
5C0XX-ray3.81C1-394[»]
5G06electron microscopy4.20C1-394[»]
5JEAX-ray2.65C1-394[»]
ProteinModelPortaliP25359.
SMRiP25359.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31018. 32 interactors.
DIPiDIP-5485N.
IntActiP25359. 17 interactors.
MINTiMINT-564723.

PTM databases

iPTMnetiP25359.

Proteomic databases

MaxQBiP25359.
PRIDEiP25359.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAC42984; CAC42984; CAC42984.
YCR035C; YCR035C; YCR035C.
GeneIDi850401.
KEGGisce:YCR035C.

Organism-specific databases

EuPathDBiFungiDB:YCR035C.
SGDiS000000631. RRP43.

Phylogenomic databases

HOGENOMiHOG000057141.
InParanoidiP25359.
KOiK12586.
OMAiYVLYAKI.
OrthoDBiEOG092C5179.

Enzyme and pathway databases

BioCyciYEAST:G3O-29348-MONOMER.

Miscellaneous databases

PROiP25359.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR033196. Rrp43.
[Graphical view]
PANTHERiPTHR11097:SF9. PTHR11097:SF9. 4 hits.
PfamiPF01138. RNase_PH. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 2 hits.
ProtoNetiSearch...

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: November 2, 2016
This is version 151 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.