CPLM-012212

Genbank Nucleotide ID

Exosome complex component RRP4

Protein Synonyms/Alias

Exosome component 2; Ribosomal RNA-processing protein 4

Homo sapiens (Human)

Position	Peptide	Type	References
24	RLGRDTKKHLVVPGD	ubiquitination	[1]
51	GTYMGEEKLIASVAG	ubiquitination	[1]
65	GSVERVNKLICVKAL	ubiquitination	[1]
70	VNKLICVKALKTRYI	ubiquitination	[1]
97	EVQQKRWKVETNSRL	ubiquitination	[1]
165	TRSLKYGKLGQGVLV	ubiquitination	[1, 2]
180	QVSPSLVKRQKTHFH	ubiquitination	[1, 2, 3, 4]
273	HQIKDILKPEIMEEI	ubiquitination	[1]

[1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
[2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
[3] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
[4] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]

Functional Description

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. EXOSC2 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC4 and EXOSC7.

DOMAIN 79 159 S1 motif.
MOD_RES 124 124 Phosphoserine.

3D-structure; Complete proteome; Cytoplasm; Exosome; Nucleus; Phosphoprotein; Reference proteome; RNA-binding; rRNA processing.

UniProt (SWISSPROT/TrEMBL); GenBank; EMBL

GO:0005829; C:cytosol; TAS:Reactome.
GO:0000178; C:exosome (RNase complex); IDA:UniProtKB.
GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
GO:0005634; C:nucleus; IDA:UniProtKB.
GO:0000175; F:3'-5'-exoribonuclease activity; TAS:ProtInc.
GO:0008312; F:7S RNA binding; TAS:ProtInc.
GO:0043928; P:exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay; TAS:Reactome.
GO:0030307; P:positive regulation of cell growth; IMP:UniProtKB.
GO:0006364; P:rRNA processing; TAS:ProtInc.

IPR025721; Exosome_cplx_N_dom.
IPR026699; Exosome_RNA_bind1/RRP40/RRP4.
IPR022967; RNA-binding_domain_S1.