CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-011779
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Exosome complex exonuclease RRP6 
Protein Synonyms/Alias
 Ribosomal RNA-processing protein 6 
Gene Name
 RRP6 
Gene Synonyms/Alias
 UNC733; YOR001W 
Created Date
 July 27, 2013 
Organism
 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
NCBI Taxa ID
 559292 
Lysine Modification
Position
Peptide
Type
References
121YLGEFSGKNFSPTKRacetylation[1]
676KEKGVTEKDAVDYSKacetylation[1]
683KDAVDYSKIPNILSNacetylation[1]
Reference
 [1] Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae.
 Henriksen P, Wagner SA, Weinert BT, Sharma S, Bacinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C.
 Mol Cell Proteomics. 2012 Nov;11(11):1510-22. [PMID: 22865919] 
Functional Description
 Nuclear-specific 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. 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. RRP6 has 3'-5' exonuclease activity which is not modulated upon association with Exo-9 suggesting that the complex inner RNA-binding path is not used to access its active site. 
Sequence Annotation
 DOMAIN 435 515 HRDC.
 MOD_RES 138 138 Phosphoserine.
 MOD_RES 520 520 Phosphothreonine.
 MOD_RES 640 640 Phosphoserine.
 MOD_RES 645 645 Phosphoserine.  
Keyword
 3D-structure; Complete proteome; Exonuclease; Exosome; Hydrolase; Nuclease; Nucleus; Phosphoprotein; Reference proteome; RNA-binding; rRNA processing. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 733 AA 
Protein Sequence
MTSENPDVLL SRVINVVRAA SSLASQDVDF YKNLDRGFSK DLKSKADKLA DMANEIILSI 60
DEHHESFELK EEDISDLWNN FGNIMDNLLE MSDHSLDKLN CAINSKSRGS DLQYLGEFSG 120
KNFSPTKRVE KPQLKFKSPI DNSESHPFIP LLKEKPNALK PLSESLRLVD DDENNPSHYP 180
HPYEYEIDHQ EYSPEILQIR EEIPSKSWDD SVPIWVDTST ELESMLEDLK NTKEIAVDLE 240
HHDYRSYYGI VCLMQISTRE RDYLVDTLKL RENLHILNEV FTNPSIVKVF HGAFMDIIWL 300
QRDLGLYVVG LFDTYHASKA IGLPRHSLAY LLENFANFKT SKKYQLADWR IRPLSKPMTA 360
YARADTHFLL NIYDQLRNKL IESNKLAGVL YESRNVAKRR FEYSKYRPLT PSSEVYSPIE 420
KESPWKILMY QYNIPPEREV LVRELYQWRD LIARRDDESP RFVMPNQLLA ALVAYTPTDV 480
IGVVSLTNGV TEHVRQNAKL LANLIRDALR NIKNTNEEAT PIPSSETKAD GILLETISVP 540
QIRDVMERFS VLCNSNISKS RAKPVTNSSI LLGKILPREE HDIAYSKDGL PNKVKTEDIR 600
IRAQNFKSAL ANLEDIIFEI EKPLVVPVKL EEIKTVDPAS APNHSPEIDN LDDLVVLKKK 660
NIQKKQPAKE KGVTEKDAVD YSKIPNILSN KPGQNNRQQK KRRFDPSSSD SNGPRAAKKR 720
RPAAKGKNLS FKR 733 
Gene Ontology
 GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD.
 GO:0005730; C:nucleolus; IDA:SGD.
 GO:0000175; F:3'-5'-exoribonuclease activity; IDA:SGD.
 GO:0000166; F:nucleotide binding; IEA:InterPro.
 GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
 GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
 GO:0071044; P:histone mRNA catabolic process; IMP:SGD.
 GO:0071040; P:nuclear polyadenylation-dependent antisense transcript catabolic process; IMP:SGD.
 GO:0071039; P:nuclear polyadenylation-dependent CUT catabolic process; IMP:SGD.
 GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IMP:SGD.
 GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
 GO:0071036; P:nuclear polyadenylation-dependent snoRNA catabolic process; IMP:SGD.
 GO:0071037; P:nuclear polyadenylation-dependent snRNA catabolic process; IMP:SGD.
 GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
 GO:0071049; P:nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription; IGI:SGD.
 GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IMP:SGD.
 GO:0000973; P:posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery; IMP:SGD.
 GO:0034473; P:U1 snRNA 3'-end processing; IMP:SGD.
 GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD.
 GO:0034476; P:U5 snRNA 3'-end processing; IMP:SGD. 
Interpro
 IPR002562; 3'-5'_exonuclease_dom.
 IPR012588; Exosome-assoc_fac_Rrp6_N.
 IPR010997; HRDC-like.
 IPR002121; HRDC_dom.
 IPR012337; RNaseH-like_dom. 
Pfam
 PF01612; DNA_pol_A_exo1
 PF00570; HRDC
 PF08066; PMC2NT 
SMART
 SM00474; 35EXOc
 SM00341; HRDC 
PROSITE
 PS50967; HRDC 
PRINTS