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Protein

Exosome complex component RRP42

Gene

RRP42

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. RRP42 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.2 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
  • 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: GO_Central
  • 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 catabolic process Source: SGD
  • 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-29512-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP42
Alternative name(s):
Ribosomal RNA-processing protein 42
Gene namesi
Name:RRP42
Ordered Locus Names:YDL111C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL111C.
SGDiS000002269. RRP42.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic exosome (RNase complex) Source: SGD
  • nuclear exosome (RNase complex) Source: SGD
  • nucleolus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001399661 – 265Exosome complex component RRP42Add BLAST265

Proteomic databases

MaxQBiQ12277.
PRIDEiQ12277.

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.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CSL4P538598EBI-1765,EBI-1731
MTR3P482403EBI-1765,EBI-1749
SKI6P469484EBI-1765,EBI-1788

Protein-protein interaction databases

BioGridi31951. 49 interactors.
DIPiDIP-1463N.
IntActiQ12277. 25 interactors.
MINTiMINT-410864.

Structurei

Secondary structure

1265
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 16Combined sources12
Beta strandi17 – 19Combined sources3
Beta strandi34 – 39Combined sources6
Beta strandi44 – 52Combined sources9
Beta strandi53 – 55Combined sources3
Beta strandi57 – 68Combined sources12
Turni69 – 71Combined sources3
Beta strandi76 – 82Combined sources7
Helixi90 – 102Combined sources13
Turni105 – 108Combined sources4
Helixi111 – 114Combined sources4
Beta strandi117 – 132Combined sources16
Helixi138 – 149Combined sources12
Beta strandi153 – 158Combined sources6
Turni163 – 166Combined sources4
Beta strandi171 – 179Combined sources9
Beta strandi186 – 193Combined sources8
Beta strandi196 – 200Combined sources5
Helixi203 – 208Combined sources6
Beta strandi210 – 218Combined sources9
Beta strandi226 – 228Combined sources3
Beta strandi233 – 235Combined sources3
Helixi241 – 253Combined sources13
Helixi256 – 262Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80E1-265[»]
4OO1X-ray3.30E1-265[»]
5C0WX-ray4.60E1-265[»]
5C0XX-ray3.81E1-265[»]
5G06electron microscopy4.20E1-265[»]
5JEAX-ray2.65E1-265[»]
ProteinModelPortaliQ12277.
SMRiQ12277.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

HOGENOMiHOG000248003.
InParanoidiQ12277.
KOiK12589.
OMAiECIVSVK.
OrthoDBiEOG092C3MSX.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 2 hits.

Sequencei

Sequence statusi: Complete.

Q12277-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLSVAEKSY LYDSLASTPS IRPDGRLPHQ FRPIEIFTDF LPSSNGSSRI
60 70 80 90 100
IASDGSECIV SIKSKVVDHH VENELLQVDV DIAGQRDDAL VVETITSLLN
110 120 130 140 150
KVLKSGSGVD SSKLQLTKKY SFKIFVDVLV ISSHSHPVSL ISFAIYSALN
160 170 180 190 200
STYLPKLISA FDDLEVEELP TFHDYDMVKL DINPPLVFIL AVVGNNMLLD
210 220 230 240 250
PAANESEVAN NGLIISWSNG KITSPIRSVA LNDSNVKSFK PHLLKQGLAM
260
VEKYAPDVVR SLENL
Length:265
Mass (Da):29,055
Last modified:November 1, 1996 - v1
Checksum:i806C60979642C67E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95644 Genomic DNA. Translation: CAA64901.1.
Z74159 Genomic DNA. Translation: CAA98678.1.
BK006938 Genomic DNA. Translation: DAA11749.1.
PIRiS67653.
RefSeqiNP_010172.1. NM_001180170.1.

Genome annotation databases

EnsemblFungiiYDL111C; YDL111C; YDL111C.
GeneIDi851447.
KEGGisce:YDL111C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95644 Genomic DNA. Translation: CAA64901.1.
Z74159 Genomic DNA. Translation: CAA98678.1.
BK006938 Genomic DNA. Translation: DAA11749.1.
PIRiS67653.
RefSeqiNP_010172.1. NM_001180170.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80E1-265[»]
4OO1X-ray3.30E1-265[»]
5C0WX-ray4.60E1-265[»]
5C0XX-ray3.81E1-265[»]
5G06electron microscopy4.20E1-265[»]
5JEAX-ray2.65E1-265[»]
ProteinModelPortaliQ12277.
SMRiQ12277.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31951. 49 interactors.
DIPiDIP-1463N.
IntActiQ12277. 25 interactors.
MINTiMINT-410864.

Proteomic databases

MaxQBiQ12277.
PRIDEiQ12277.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL111C; YDL111C; YDL111C.
GeneIDi851447.
KEGGisce:YDL111C.

Organism-specific databases

EuPathDBiFungiDB:YDL111C.
SGDiS000002269. RRP42.

Phylogenomic databases

HOGENOMiHOG000248003.
InParanoidiQ12277.
KOiK12589.
OMAiECIVSVK.
OrthoDBiEOG092C3MSX.

Enzyme and pathway databases

BioCyciYEAST:G3O-29512-MONOMER.

Miscellaneous databases

PROiQ12277.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 2 hits.
ProtoNetiSearch...

Entry informationi

Entry nameiRRP42_YEAST
AccessioniPrimary (citable) accession number: Q12277
Secondary accession number(s): D6VRN9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 136 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 7110 molecules/cell in log phase SD medium.1 Publication

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 IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: 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.