CPLM-012462

Genbank Nucleotide ID

Exosome complex component RRP42

Protein Synonyms/Alias

Exosome component 7; Ribosomal RNA-processing protein 42; p8

Homo sapiens (Human)

Position	Peptide	Type	References
11	VTLSEAEKVYIVHGV	ubiquitination	[1]
52	TSGSARVKLGHTDIL	ubiquitination	[1]
116	LYRIFNNKSSVDLKT	acetylation	[2]
116	LYRIFNNKSSVDLKT	ubiquitination	[1]
122	NKSSVDLKTLCISPR	ubiquitination	[3, 4]
178	LEDEEGSKDIELSDD	ubiquitination	[1]
205	PCIVTLCKIGYRHVV	ubiquitination	[1, 3]
244	TCMRKVGKGSLDPES	ubiquitination	[1]
260	FEMMETGKRVGKVLH	ubiquitination	[1, 5]
264	ETGKRVGKVLHASLQ	ubiquitination	[1]
276	SLQSVVHKEESLGPK	ubiquitination	[4, 6]
283	KEESLGPKRQKVGFL	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] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
[3] 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]
[4] 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]
[5] 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]
[6] 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]

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.

MOD_RES 2 2 N-acetylalanine.
MOD_RES 116 116 N6-acetyllysine.

3D-structure; Acetylation; Complete proteome; Cytoplasm; Direct protein sequencing; Exosome; Nucleus; Polymorphism; 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:0000175; F:3'-5'-exoribonuclease activity; TAS:UniProtKB.
GO:0003723; F:RNA binding; TAS:UniProtKB.
GO:0043928; P:exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay; TAS:Reactome.
GO:0006364; P:rRNA processing; TAS:UniProtKB.

IPR001247; ExoRNase_PH_dom1.
IPR015847; ExoRNase_PH_dom2.
IPR027408; PNPase/RNase_PH_dom.
IPR020568; Ribosomal_S5_D2-typ_fold.

PF01138; RNase_PH
PF03725; RNase_PH_C