ID RRP6_YEAST Reviewed; 733 AA.
AC Q12149; D6W267; Q6B280;
DT 01-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 01-MAY-2013, entry version 120.
DE RecName: Full=Exosome complex exonuclease RRP6;
DE EC=3.1.13.-;
DE AltName: Full=Ribosomal RNA-processing protein 6;
GN Name=RRP6; Synonyms=UNC733; OrderedLocusNames=YOR001W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
OC Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8896276;
RX DOI=10.1002/(SICI)1097-0061(199609)12:10B<1091::AID-YEA22>3.3.CO;2-9;
RA Sterky F., Holmberg A., Pettersson B., Uhlen M.;
RT "The sequence of a 30 kb fragment on the left arm of chromosome XV
RT from Saccharomyces cerevisiae reveals 15 open reading frames, five of
RT which correspond to previously identified genes.";
RL Yeast 12:1091-1095(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W.,
RA Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R.,
RA Boyer J., Camasses A., Casamayor A., Casas C., Cheret G.,
RA Cziepluch C., Daignan-Fornier B., Dang V.-D., de Haan M., Delius H.,
RA Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F.,
RA Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A.,
RA Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J.,
RA Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P.,
RA Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M.,
RA Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R.,
RA Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S.,
RA Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A.,
RA Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M.,
RA Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C.,
RA Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S.,
RA Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RG Saccharomyces Genome Database;
RL Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
RA Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
RA Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
RA Kolodner R.D., LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-
RT encoding clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP FUNCTION.
RX PubMed=9582370; DOI=10.1074/jbc.273.21.13255;
RA Briggs M.W., Burkard K.T.D., Butler J.S.;
RT "Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen,
RT is essential for efficient 5.8 S rRNA 3' end formation.";
RL J. Biol. Chem. 273:13255-13263(1998).
RN [6]
RP FUNCTION, IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS
RP SPECTROMETRY, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=10465791;
RA Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D.,
RA Mitchell P.;
RT "The yeast exosome and human PM-Scl are related complexes of 3'-->5'
RT exonucleases.";
RL Genes Dev. 13:2148-2158(1999).
RN [7]
RP CATALYTIC ACTIVITY, FUNCTION, INTERACTION WITH NPL3 AND PAP1,
RP SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=10611239; DOI=10.1128/MCB.20.2.604-616.2000;
RA Burkard K.T.D., Butler J.S.;
RT "A nuclear 3'-5' exonuclease involved in mRNA degradation interacts
RT with Poly(A) polymerase and the hnRNA protein Npl3p.";
RL Mol. Cell. Biol. 20:604-616(2000).
RN [8]
RP INTERACTION WITH LRP1.
RX PubMed=12972615; DOI=10.1128/MCB.23.19.6982-6992.2003;
RA Mitchell P., Petfalski E., Houalla R., Podtelejnikov A., Mann M.,
RA Tollervey D.;
RT "Rrp47p is an exosome-associated protein required for the 3'
RT processing of stable RNAs.";
RL Mol. Cell. Biol. 23:6982-6992(2003).
RN [9]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [10]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
RA Dephoure N., O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [11]
RP FUNCTION, INTERACTION WITH LRP1, AND SUBCELLULAR LOCATION.
RX PubMed=15489286; DOI=10.1101/gad.1241204;
RA Hieronymus H., Yu M.C., Silver P.A.;
RT "Genome-wide mRNA surveillance is coupled to mRNA export.";
RL Genes Dev. 18:2652-2662(2004).
RN [12]
RP RECONSTITUTION OF THE RNA EXOSOME COMPLEX, AND EXONUCLEASE ACTIVITY.
RX PubMed=17174896; DOI=10.1016/j.cell.2006.10.037;
RA Liu Q., Greimann J.C., Lima C.D.;
RT "Reconstitution, activities, and structure of the eukaryotic RNA
RT exosome.";
RL Cell 127:1223-1237(2006).
RN [13]
RP ERRATUM.
RA Liu Q., Greimann J.C., Lima C.D.;
RL Cell 131:188-189(2007).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138 AND SER-645, AND
RP MASS SPECTROMETRY.
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [15]
RP IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH THE RNA EXOSOME,
RP SUBUNIT, AND DISRUPTION PHENOTYPE.
RX PubMed=17173052; DOI=10.1038/nsmb1184;
RA Dziembowski A., Lorentzen E., Conti E., Seraphin B.;
RT "A single subunit, Dis3, is essentially responsible for yeast exosome
RT core activity.";
RL Nat. Struct. Mol. Biol. 14:15-22(2007).
RN [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-110 AND SER-645, AND
RP MASS SPECTROMETRY.
RX PubMed=17563356; DOI=10.1073/pnas.0701622104;
RA Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H.;
RT "Proteome-wide identification of in vivo targets of DNA damage
RT checkpoint kinases.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007).
RN [17]
RP INTERACTION WITH NOP53.
RX PubMed=18631361; DOI=10.1111/j.1742-4658.2008.06565.x;
RA Granato D.C., Machado-Santelli G.M., Oliveira C.C.;
RT "Nop53p interacts with 5.8S rRNA co-transcriptionally, and regulates
RT processing of pre-rRNA by the exosome.";
RL FEBS J. 275:4164-4178(2008).
RN [18]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-110; TYR-406; THR-410;
RP SER-412; THR-520; SER-640 AND SER-645, AND MASS SPECTROMETRY.
RX PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth
RT phosphoproteome analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
CC -!- FUNCTION: Nuclear-specific catalytic component of the RNA exosome
CC complex which has 3'->5' exoribonuclease activity and participates
CC in a multitude of cellular RNA processing and degradation events.
CC In the nucleus, the RNA exosome complex is involved in proper
CC maturation of stable RNA species such as rRNA, snRNA and snoRNA,
CC in the elimination of RNA processing by-products and non-coding
CC 'pervasive' transcripts, such as antisense RNA species and cryptic
CC unstable transcripts (CUTs), and of mRNAs with processing defects,
CC thereby limiting or excluding their export to the cytoplasm. The
CC catalytic inactive RNA exosome core complex of 9 subunits (Exo-9)
CC is proposed to play a pivotal role in the binding and presentation
CC of RNA for ribonucleolysis, and to serve as a scaffold for the
CC association with catalytic subunits and accessory proteins or
CC complexes. RRP6 has 3'-5' exonuclease activity which is not
CC modulated upon association with Exo-9 suggesting that the complex
CC inner RNA-binding path is not used to access its active site.
CC -!- SUBUNIT: Component of the RNA exosome complex. The catalytically
CC inactive RNA exosome core (Exo-9) complex associates with
CC catalytic subunits DIS3 and RRP6 in cytoplasmic- and nuclear-
CC specific RNA exosome complex forms. Exo-9 is formed by a hexameric
CC ring of RNase PH domain-containing subunits and peripheral S1
CC domain-containing components CSL4, RRP4 and RRP40 located on the
CC top of the ring structure. RRP6 specifically is part of the
CC nuclear form of the RNA exosome complex; the association appears
CC to be mediated by Exo-9 and not by DIS3. Interacts with LRP1.
CC Interacts with NPL3, NOP53 and PAP1.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus.
CC -!- DISRUPTION PHENOTYPE: Deletion mutant is impaired in growth at all
CC temperatures and is nonviable at 37 degrees Celsius. It is
CC defective in the 3' processing of the 5.8S rRNA and accumulates a
CC discrete species, 5.8S + 30, that is 3' extended by about 30
CC nucleotides. Deletion also causes an accumulation of 7S RNA and 5'
CC ETS and increases the level of poly(A)+ mRNA.
CC -!- MISCELLANEOUS: Present with 2160 molecules/cell in log phase SD
CC medium.
CC -!- SIMILARITY: Belongs to the exosome component 10/RRP6 family.
CC -!- SIMILARITY: Contains 1 HRDC domain.
CC -----------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution-NoDerivs License
CC -----------------------------------------------------------------------
DR EMBL; Z74909; CAA99189.1; -; Genomic_DNA.
DR EMBL; U43491; AAC49480.1; -; Genomic_DNA.
DR EMBL; AY692850; AAT92869.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10783.1; -; Genomic_DNA.
DR PIR; S61984; S61984.
DR RefSeq; NP_014643.1; NM_001183420.1.
DR PDB; 1M0Y; Model; -; A=207-382.
DR PDB; 2HBJ; X-ray; 2.10 A; A=129-536.
DR PDB; 2HBK; X-ray; 2.25 A; A=129-536.
DR PDB; 2HBL; X-ray; 2.30 A; A=129-536.
DR PDB; 2HBM; X-ray; 2.70 A; A=129-536.
DR PDB; 4IFD; X-ray; 2.80 A; K=518-693.
DR PDBsum; 1M0Y; -.
DR PDBsum; 2HBJ; -.
DR PDBsum; 2HBK; -.
DR PDBsum; 2HBL; -.
DR PDBsum; 2HBM; -.
DR PDBsum; 4IFD; -.
DR ProteinModelPortal; Q12149; -.
DR SMR; Q12149; 129-516.
DR DIP; DIP-4560N; -.
DR IntAct; Q12149; 27.
DR MINT; MINT-534618; -.
DR STRING; 4932.YOR001W; -.
DR PaxDb; Q12149; -.
DR EnsemblFungi; YOR001W; YOR001W; YOR001W.
DR GeneID; 854162; -.
DR KEGG; sce:YOR001W; -.
DR CYGD; YOR001w; -.
DR SGD; S000005527; RRP6.
DR eggNOG; COG0349; -.
DR GeneTree; ENSGT00390000015408; -.
DR HOGENOM; HOG000196525; -.
DR KO; K12591; -.
DR OMA; YGIVCLM; -.
DR OrthoDB; EOG4SJ8P0; -.
DR EvolutionaryTrace; Q12149; -.
DR NextBio; 975938; -.
DR Genevestigator; Q12149; -.
DR GermOnline; YOR001W; Saccharomyces cerevisiae.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IDA:SGD.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; 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.
DR GO; GO:0071044; P:histone mRNA catabolic process; IMP:SGD.
DR GO; GO:0071040; P:nuclear polyadenylation-dependent antisense transcript catabolic process; IMP:SGD.
DR GO; GO:0071039; P:nuclear polyadenylation-dependent CUT catabolic process; IMP:SGD.
DR GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IMP:SGD.
DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
DR GO; GO:0071036; P:nuclear polyadenylation-dependent snoRNA catabolic process; IMP:SGD.
DR GO; GO:0071037; P:nuclear polyadenylation-dependent snRNA catabolic process; IMP:SGD.
DR GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
DR GO; GO:0071049; P:nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription; IGI:SGD.
DR GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IMP:SGD.
DR GO; GO:0000973; P:posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery; IMP:SGD.
DR GO; GO:0034473; P:U1 snRNA 3'-end processing; IMP:SGD.
DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD.
DR GO; GO:0034476; P:U5 snRNA 3'-end processing; IMP:SGD.
DR InterPro; IPR002562; 3'-5'_exonuclease_dom.
DR InterPro; IPR012588; Exosome-assoc_fac_Rrp6_N.
DR InterPro; IPR010997; HRDC-like.
DR InterPro; IPR002121; HRDC_dom.
DR InterPro; IPR012337; RNaseH-like_dom.
DR Pfam; PF01612; DNA_pol_A_exo1; 1.
DR Pfam; PF00570; HRDC; 1.
DR Pfam; PF08066; PMC2NT; 1.
DR SMART; SM00474; 35EXOc; 1.
DR SMART; SM00341; HRDC; 1.
DR SUPFAM; SSF47819; HRDC_like; 1.
DR SUPFAM; SSF53098; RNaseH_fold; 1.
DR PROSITE; PS50967; HRDC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Complete proteome; Exonuclease; Exosome; Hydrolase;
KW Nuclease; Nucleus; Phosphoprotein; Reference proteome; RNA-binding;
KW rRNA processing.
FT CHAIN 1 733 Exosome complex exonuclease RRP6.
FT /FTId=PRO_0000097456.
FT DOMAIN 435 515 HRDC.
FT MOD_RES 110 110 Phosphoserine.
FT MOD_RES 138 138 Phosphoserine.
FT MOD_RES 406 406 Phosphotyrosine.
FT MOD_RES 410 410 Phosphothreonine.
FT MOD_RES 412 412 Phosphoserine.
FT MOD_RES 520 520 Phosphothreonine.
FT MOD_RES 640 640 Phosphoserine.
FT MOD_RES 645 645 Phosphoserine.
FT CONFLICT 402 402 E -> G (in Ref. 4; AAT92869).
FT HELIX 132 135
FT HELIX 162 165
FT STRAND 173 175
FT HELIX 184 189
FT HELIX 194 196
FT HELIX 208 210
FT STRAND 214 216
FT HELIX 219 229
FT STRAND 233 242
FT STRAND 244 248
FT STRAND 250 257
FT STRAND 262 266
FT TURN 267 273
FT HELIX 274 277
FT HELIX 278 281
FT STRAND 286 292
FT HELIX 294 304
FT STRAND 309 313
FT HELIX 314 321
FT HELIX 328 335
FT TURN 343 346
FT HELIX 356 367
FT HELIX 369 382
FT HELIX 386 398
FT HELIX 404 406
FT STRAND 413 416
FT STRAND 421 427
FT HELIX 436 438
FT HELIX 439 456
FT HELIX 460 463
FT HELIX 466 475
FT HELIX 480 484
FT HELIX 492 496
FT HELIX 498 515
FT TURN 534 536
FT HELIX 539 553
FT STRAND 570 572
FT TURN 573 577
FT STRAND 582 585
FT STRAND 591 594
FT HELIX 596 611
FT HELIX 612 614
FT STRAND 617 619
SQ SEQUENCE 733 AA; 84039 MW; B19A0B2ED74C6DA7 CRC64;
MTSENPDVLL SRVINVVRAA SSLASQDVDF YKNLDRGFSK DLKSKADKLA DMANEIILSI
DEHHESFELK EEDISDLWNN FGNIMDNLLE MSDHSLDKLN CAINSKSRGS DLQYLGEFSG
KNFSPTKRVE KPQLKFKSPI DNSESHPFIP LLKEKPNALK PLSESLRLVD DDENNPSHYP
HPYEYEIDHQ EYSPEILQIR EEIPSKSWDD SVPIWVDTST ELESMLEDLK NTKEIAVDLE
HHDYRSYYGI VCLMQISTRE RDYLVDTLKL RENLHILNEV FTNPSIVKVF HGAFMDIIWL
QRDLGLYVVG LFDTYHASKA IGLPRHSLAY LLENFANFKT SKKYQLADWR IRPLSKPMTA
YARADTHFLL NIYDQLRNKL IESNKLAGVL YESRNVAKRR FEYSKYRPLT PSSEVYSPIE
KESPWKILMY QYNIPPEREV LVRELYQWRD LIARRDDESP RFVMPNQLLA ALVAYTPTDV
IGVVSLTNGV TEHVRQNAKL LANLIRDALR NIKNTNEEAT PIPSSETKAD GILLETISVP
QIRDVMERFS VLCNSNISKS RAKPVTNSSI LLGKILPREE HDIAYSKDGL PNKVKTEDIR
IRAQNFKSAL ANLEDIIFEI EKPLVVPVKL EEIKTVDPAS APNHSPEIDN LDDLVVLKKK
NIQKKQPAKE KGVTEKDAVD YSKIPNILSN KPGQNNRQQK KRRFDPSSSD SNGPRAAKKR
RPAAKGKNLS FKR
//
