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Protein

Exosome complex component RRP40

Gene

Exosc3

Organism
Mus musculus (Mouse)
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 promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. 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. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5 (By similarity).By similarity1 Publication

GO - Molecular functioni

  • exonuclease activity Source: UniProtKB-KW
  • RNA binding Source: GO_Central

GO - Biological processi

Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease, RNA-binding
Biological processrRNA processing

Enzyme and pathway databases

ReactomeiR-MMU-429958 mRNA decay by 3' to 5' exoribonuclease
R-MMU-450385 Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-MMU-450604 KSRP (KHSRP) binds and destabilizes mRNA
R-MMU-6791226 Major pathway of rRNA processing in the nucleolus and cytosol

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP40 (EC:3.1.13.-)
Alternative name(s):
Exosome component 3
Ribosomal RNA-processing protein 40
Gene namesi
Name:Exosc3
Synonyms:Rrp40
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 4

Organism-specific databases

MGIiMGI:1913612 Exosc3

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome 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
Initiator methionineiRemovedBy similarity
ChainiPRO_00000871322 – 274Exosome complex component RRP40Add BLAST273

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Cross-linki150Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ7TQK4
MaxQBiQ7TQK4
PaxDbiQ7TQK4
PeptideAtlasiQ7TQK4
PRIDEiQ7TQK4

PTM databases

iPTMnetiQ7TQK4
PhosphoSitePlusiQ7TQK4

Expressioni

Gene expression databases

BgeeiENSMUSG00000028322 Expressed in 212 organ(s), highest expression level in testis
CleanExiMM_EXOSC3
ExpressionAtlasiQ7TQK4 baseline and differential
GenevisibleiQ7TQK4 MM

Interactioni

Subunit structurei

Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which is believed to associate with catalytic subunits EXOSC10, and DIS3 or DIS3L in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits specifically containing the heterodimers EXOSC4-EXOSC9, EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and peripheral S1 domain-containing components EXOSC1, EXOSC2 and EXOSC3 located on the top of the ring structure. Interacts with GTPBP1 (By similarity). Interacts with ZC3HAV1 (By similarity). Interacts with DDX17 only in the presence of ZC3HAV1 in an RNA-independent manner (By similarity). Interacts with DHX36; this interaction occurs in a RNase-insensitive manner (By similarity).By similarity

Protein-protein interaction databases

BioGridi211414, 1 interactor
ComplexPortaliCPX-594 Nuclear exosome complex, Dis3-Exosc10 variant
CPX-595 Nucleolar exosome complex, Exosc10 variant
CPX-596 Cytoplasmic exosome complex, Dis3l variant
CPX-598 Exosome complex, Dis3 variant
CPX-601 Cytoplasmic exosome complex, Dis3l-Exosc10 variant
IntActiQ7TQK4, 2 interactors
MINTiQ7TQK4
STRINGi10090.ENSMUSP00000030003

Structurei

3D structure databases

ProteinModelPortaliQ7TQK4
SMRiQ7TQK4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RRP40 family.Curated

Phylogenomic databases

eggNOGiKOG1004 Eukaryota
COG1097 LUCA
GeneTreeiENSGT00390000012042
HOGENOMiHOG000184644
HOVERGENiHBG051518
InParanoidiQ7TQK4
KOiK03681
OMAiISYLAFE
OrthoDBiEOG091G0Q58
PhylomeDBiQ7TQK4
TreeFamiTF314927

Family and domain databases

CDDicd05790 S1_Rrp40, 1 hit
Gene3Di3.30.1370.10, 1 hit
InterProiView protein in InterPro
IPR026699 Exosome_RNA_bind1/RRP40/RRP4
IPR004088 KH_dom_type_1
IPR036612 KH_dom_type_1_sf
IPR012340 NA-bd_OB-fold
IPR037319 Rrp40_S1
PANTHERiPTHR21321 PTHR21321, 1 hit
PfamiView protein in Pfam
PF15985 KH_6, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
SSF54791 SSF54791, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

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

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q7TQK4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAEVLSAGPE SVAGCRARAV HKVLNQVVLP GEELVLPDHE DVDGLGGAGE
60 70 80 90 100
QPLRLNAGAR PRLRVVCGPG LRRCGDRLLV TKCGRLRHKE PSGGGGGVYW
110 120 130 140 150
VDSQQKRYVP VKGDHVIGIV IAKSGDIFKV DVGGSEPASL SYLAFEGATK
160 170 180 190 200
RNRPNVQVGD LIYGQCVVAN KDMEPEMVCI DSCGRANGMG VIGQDGLLFK
210 220 230 240 250
VTLGLIRKLL APDCEIVQEL GKLYPLEIVF GMNGRIWVKA KTIQQTLILA
260 270
NVLEACEHMT TEQRKQIFAR LAES
Length:274
Mass (Da):29,546
Last modified:January 23, 2007 - v3
Checksum:i0932E5B03DD708D4
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F6TGV1F6TGV1_MOUSE
Exosome complex component RRP40
Exosc3
145Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti32E → P in BAB24501 (PubMed:16141072).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC023669 mRNA Translation: AAH23669.1
BC054085 mRNA Translation: AAH54085.1
AK006281 mRNA Translation: BAB24501.1
AK009165 mRNA Translation: BAB26116.1
CCDSiCCDS18136.1
RefSeqiNP_079789.1, NM_025513.3
UniGeneiMm.275788

Genome annotation databases

EnsembliENSMUST00000030003; ENSMUSP00000030003; ENSMUSG00000028322
GeneIDi66362
KEGGimmu:66362
UCSCiuc008ssk.1 mouse

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC023669 mRNA Translation: AAH23669.1
BC054085 mRNA Translation: AAH54085.1
AK006281 mRNA Translation: BAB24501.1
AK009165 mRNA Translation: BAB26116.1
CCDSiCCDS18136.1
RefSeqiNP_079789.1, NM_025513.3
UniGeneiMm.275788

3D structure databases

ProteinModelPortaliQ7TQK4
SMRiQ7TQK4
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi211414, 1 interactor
ComplexPortaliCPX-594 Nuclear exosome complex, Dis3-Exosc10 variant
CPX-595 Nucleolar exosome complex, Exosc10 variant
CPX-596 Cytoplasmic exosome complex, Dis3l variant
CPX-598 Exosome complex, Dis3 variant
CPX-601 Cytoplasmic exosome complex, Dis3l-Exosc10 variant
IntActiQ7TQK4, 2 interactors
MINTiQ7TQK4
STRINGi10090.ENSMUSP00000030003

PTM databases

iPTMnetiQ7TQK4
PhosphoSitePlusiQ7TQK4

Proteomic databases

EPDiQ7TQK4
MaxQBiQ7TQK4
PaxDbiQ7TQK4
PeptideAtlasiQ7TQK4
PRIDEiQ7TQK4

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000030003; ENSMUSP00000030003; ENSMUSG00000028322
GeneIDi66362
KEGGimmu:66362
UCSCiuc008ssk.1 mouse

Organism-specific databases

CTDi51010
MGIiMGI:1913612 Exosc3

Phylogenomic databases

eggNOGiKOG1004 Eukaryota
COG1097 LUCA
GeneTreeiENSGT00390000012042
HOGENOMiHOG000184644
HOVERGENiHBG051518
InParanoidiQ7TQK4
KOiK03681
OMAiISYLAFE
OrthoDBiEOG091G0Q58
PhylomeDBiQ7TQK4
TreeFamiTF314927

Enzyme and pathway databases

ReactomeiR-MMU-429958 mRNA decay by 3' to 5' exoribonuclease
R-MMU-450385 Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-MMU-450604 KSRP (KHSRP) binds and destabilizes mRNA
R-MMU-6791226 Major pathway of rRNA processing in the nucleolus and cytosol

Miscellaneous databases

ChiTaRSiExosc3 mouse
PROiPR:Q7TQK4
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000028322 Expressed in 212 organ(s), highest expression level in testis
CleanExiMM_EXOSC3
ExpressionAtlasiQ7TQK4 baseline and differential
GenevisibleiQ7TQK4 MM

Family and domain databases

CDDicd05790 S1_Rrp40, 1 hit
Gene3Di3.30.1370.10, 1 hit
InterProiView protein in InterPro
IPR026699 Exosome_RNA_bind1/RRP40/RRP4
IPR004088 KH_dom_type_1
IPR036612 KH_dom_type_1_sf
IPR012340 NA-bd_OB-fold
IPR037319 Rrp40_S1
PANTHERiPTHR21321 PTHR21321, 1 hit
PfamiView protein in Pfam
PF15985 KH_6, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
SSF54791 SSF54791, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiEXOS3_MOUSE
AccessioniPrimary (citable) accession number: Q7TQK4
Secondary accession number(s): Q9CV81, Q9CVW2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: January 23, 2007
Last modified: October 10, 2018
This is version 119 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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