UniProt Accession

 EXOS3_HUMAN; Q9NQT5; A8K0K6; Q5QP85; Q9Y3A8 

Genbank Protein ID

 AF281132; AK289571; AK290864; AL138752; CH471071; BC002437; BC008880; AF151860 

Genbank Nucleotide ID

 AAF82133.1; BAF82260.1; BAF83553.1; CAI13880.1; EAW58264.1; AAH02437.1; AAH08880.1; AAD34097.1 

Protein Name

 Exosome complex component RRP40 

Protein Synonyms/Alias

 Exosome component 3; Ribosomal RNA-processing protein 40; p10 

Gene Name

 EXOSC3 

Gene Synonyms/Alias

 RRP40; CGI-102 

Created Date

 July 27, 2013 

Organism

 Homo sapiens (Human) 

NCBI Taxa ID

 9606 

Lysine Modification

Position	Peptide	Type	References
82	GDRLLVTKCGRLRHK	ubiquitination	[1]
89	KCGRLRHKEPGSGSG	ubiquitination	[1]
107	YWVDSQQKRYVPVKG	ubiquitination	[1, 2]
113	QKRYVPVKGDHVIGI	ubiquitination	[1, 3, 4, 5]
124	VIGIVTAKSGDIFKV	ubiquitination	[1]
151	LSFEGATKRNRPNVQ	ubiquitination	[1, 2, 5, 6, 7]

Reference

 [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] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [3] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [4] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [5] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [6] 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]
 [7] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965] 

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. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5. 

Sequence Annotation

 MOD_RES 2 2 N-acetylalanine.  

Keyword

 3D-structure; Acetylation; Alternative splicing; Complete proteome; Cytoplasm; Direct protein sequencing; Disease mutation; Exosome; Nucleus; Polymorphism; Reference proteome; RNA-binding; rRNA processing. 

Sequence Source

 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 

Protein Length

 275 AA 

Protein Sequence

Gene Ontology

 GO:0000177; C:cytoplasmic exosome (RNase complex); IDA:UniProtKB.
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0000176; C:nuclear exosome (RNase complex); IDA:UniProtKB.
 GO:0005730; C:nucleolus; IDA:UniProtKB.
 GO:0035327; C:transcriptionally active chromatin; IMP:UniProtKB.
 GO:0000175; F:3'-5'-exoribonuclease activity; NAS:UniProtKB.
 GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
 GO:0071034; P:CUT catabolic process; IMP:UniProtKB.
 GO:0045006; P:DNA deamination; IDA:UniProtKB.
 GO:0043928; P:exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay; IMP:UniProtKB.
 GO:0045190; P:isotype switching; ISS:UniProtKB.
 GO:0006364; P:rRNA processing; IDA:UniProtKB. 

Interpro

 IPR026699; Exosome_RNA_bind1/RRP40/RRP4. 

Pfam

  

SMART

  

PROSITE

  

PRINTS