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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: -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

Miscellaneous

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

GO - Molecular functioni

  • AU-rich element binding Source: GO_Central

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processrRNA processing

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

SGDiS000002269 RRP42

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_00001399661 – 265Exosome complex component RRP42Add BLAST265

Proteomic databases

MaxQBiQ12277
PaxDbiQ12277
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

Protein-protein interaction databases

BioGridi31951, 202 interactors
ComplexPortaliCPX-599 Nuclear/nucleolar exosome complex, DIS3-RRP6 variant
CPX-603 Cytoplasmic exosome complex, DIS3 variant
DIPiDIP-1463N
IntActiQ12277, 26 interactors
MINTiQ12277
STRINGi4932.YDL111C

Structurei

Secondary structure

1265
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ12277
SMRiQ12277
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

HOGENOMiHOG000248003
InParanoidiQ12277
KOiK12589
OMAiDGSECIV
OrthoDBiEOG092C3MSX

Family and domain databases

Gene3Di3.30.230.70, 1 hit
InterProiView protein in InterPro
IPR001247 ExoRNase_PH_dom1
IPR015847 ExoRNase_PH_dom2
IPR027408 PNPase/RNase_PH_dom_sf
IPR020568 Ribosomal_S5_D2-typ_fold
PfamiView protein in Pfam
PF01138 RNase_PH, 1 hit
PF03725 RNase_PH_C, 1 hit
SUPFAMiSSF54211 SSF54211, 1 hit

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

Similar proteinsi

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[»]
5K36X-ray3.10E1-265[»]
5OKZX-ray3.20E/O/Y/i1-265[»]
5VZJX-ray3.30E1-265[»]
6FSZelectron microscopy4.60EE1-265[»]
ProteinModelPortaliQ12277
SMRiQ12277
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31951, 202 interactors
ComplexPortaliCPX-599 Nuclear/nucleolar exosome complex, DIS3-RRP6 variant
CPX-603 Cytoplasmic exosome complex, DIS3 variant
DIPiDIP-1463N
IntActiQ12277, 26 interactors
MINTiQ12277
STRINGi4932.YDL111C

Proteomic databases

MaxQBiQ12277
PaxDbiQ12277
PRIDEiQ12277

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL111C; YDL111C; YDL111C
GeneIDi851447
KEGGisce:YDL111C

Organism-specific databases

SGDiS000002269 RRP42

Phylogenomic databases

HOGENOMiHOG000248003
InParanoidiQ12277
KOiK12589
OMAiDGSECIV
OrthoDBiEOG092C3MSX

Enzyme and pathway databases

BioCyciYEAST:G3O-29512-MONOMER

Miscellaneous databases

PROiPR:Q12277

Family and domain databases

Gene3Di3.30.230.70, 1 hit
InterProiView protein in InterPro
IPR001247 ExoRNase_PH_dom1
IPR015847 ExoRNase_PH_dom2
IPR027408 PNPase/RNase_PH_dom_sf
IPR020568 Ribosomal_S5_D2-typ_fold
PfamiView protein in Pfam
PF01138 RNase_PH, 1 hit
PF03725 RNase_PH_C, 1 hit
SUPFAMiSSF54211 SSF54211, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRRP42_YEAST
AccessioniPrimary (citable) accession number: Q12277
Secondary accession number(s): D6VRN9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 7, 2018
This is version 154 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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
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Main funding by: National Institutes of Health

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