RRP41_YEAST
ID RRP41_YEAST Reviewed; 246 AA.
AC P46948; D6VUX7;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 189.
DE RecName: Full=Exosome complex component SKI6;
DE AltName: Full=Extracellular mutant protein 20;
DE AltName: Full=Ribosomal RNA-processing protein 41;
DE AltName: Full=Superkiller protein 6;
GN Name=SKI6; Synonyms=ECM20, RRP41; OrderedLocusNames=YGR195W;
GN ORFNames=G7587;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7502584; DOI=10.1002/yea.320111110;
RA Guerreiro P., Maia e Silva A., Barreiros T., Arroyo J., Garcia-Gonzalez M.,
RA Garcia-Saez M.I., Rodrigues-Pousada C., Nombela C.;
RT "The complete sequence of a 9000 bp fragment of the right arm of
RT Saccharomyces cerevisiae chromosome VII contains four previously unknown
RT open reading frames.";
RL Yeast 11:1087-1091(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
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., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, AND SUBUNIT.
RX PubMed=9390555; DOI=10.1016/s0092-8674(00)80432-8;
RA Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D.;
RT "The exosome: a conserved eukaryotic RNA processing complex containing
RT multiple 3'-->5' exoribonucleases.";
RL Cell 91:457-466(1997).
RN [6]
RP IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS SPECTROMETRY.
RX PubMed=10465791; DOI=10.1101/gad.13.16.2148;
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 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 [8]
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., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [9]
RP RECONSTITUTION OF THE RNA EXOSOME COMPLEX, AND LACK OF EXONUCLEASE
RP 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 exosome.";
RL Cell 127:1223-1237(2006).
RN [10]
RP ERRATUM OF PUBMED:17174896.
RA Liu Q., Greimann J.C., Lima C.D.;
RL Cell 131:188-189(2007).
RN [11]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION OF THE RNA EXOSOME COMPLEX,
RP AND SUBUNIT.
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 core
RT activity.";
RL Nat. Struct. Mol. Biol. 14:15-22(2007).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH RRP45 AND DIS3, AND
RP MUTAGENESIS OF 62-LYS-SER-63 AND 95-ARG-ARG-96.
RX PubMed=19879841; DOI=10.1016/j.cell.2009.08.042;
RA Bonneau F., Basquin J., Ebert J., Lorentzen E., Conti E.;
RT "The yeast exosome functions as a macromolecular cage to channel RNA
RT substrates for degradation.";
RL Cell 139:547-559(2009).
CC -!- FUNCTION: Non-catalytic component of the RNA exosome complex which has
CC 3'->5' exoribonuclease activity and participates in a multitude of
CC cellular RNA processing and degradation events. In the nucleus, the RNA
CC exosome complex is involved in proper maturation of stable RNA species
CC such as rRNA, snRNA and snoRNA, in the elimination of RNA processing
CC by-products and non-coding 'pervasive' transcripts, such as antisense
CC RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with
CC processing defects, thereby limiting or excluding their export to the
CC cytoplasm. In the cytoplasm, the RNA exosome complex is involved in
CC general mRNA turnover and in RNA surveillance pathways, preventing
CC translation of aberrant mRNAs. The catalytic inactive RNA exosome core
CC complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the
CC binding and presentation of RNA for ribonucleolysis, and to serve as a
CC scaffold for the association with catalytic subunits and accessory
CC proteins or complexes. SKI6 is part of the hexameric ring of RNase PH
CC domain-containing subunits proposed to form a central channel which
CC threads RNA substrates for degradation. {ECO:0000269|PubMed:17173052,
CC ECO:0000269|PubMed:9390555}.
CC -!- SUBUNIT: Component of the RNA exosome complex. Specifically part of the
CC catalytically inactive RNA exosome core (Exo-9) complex which
CC associates with catalytic subunits DIS3 and RRP6 in cytoplasmic- and
CC nuclear-specific RNA exosome complex forms. Exo-9 is formed by a
CC hexameric ring of RNase PH domain-containing subunits and peripheral S1
CC domain-containing components CSL4, RRP4 and RRP40 located on the top of
CC the ring structure. {ECO:0000269|PubMed:10465791,
CC ECO:0000269|PubMed:17173052, ECO:0000269|PubMed:19879841,
CC ECO:0000269|PubMed:9390555}.
CC -!- INTERACTION:
CC P46948; P53859: CSL4; NbExp=17; IntAct=EBI-1788, EBI-1731;
CC P46948; Q08162: DIS3; NbExp=9; IntAct=EBI-1788, EBI-1740;
CC P46948; P48240: MTR3; NbExp=8; IntAct=EBI-1788, EBI-1749;
CC P46948; P38792: RRP4; NbExp=4; IntAct=EBI-1788, EBI-1757;
CC P46948; Q08285: RRP40; NbExp=4; IntAct=EBI-1788, EBI-1831;
CC P46948; Q12277: RRP42; NbExp=4; IntAct=EBI-1788, EBI-1765;
CC P46948; P25359: RRP43; NbExp=4; IntAct=EBI-1788, EBI-1773;
CC P46948; Q05636: RRP45; NbExp=11; IntAct=EBI-1788, EBI-1810;
CC P46948; P53256: RRP46; NbExp=6; IntAct=EBI-1788, EBI-1842;
CC P46948; Q12149: RRP6; NbExp=3; IntAct=EBI-1788, EBI-1782;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 5150 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to have exonuclease activity but it was
CC later shown (PubMed:17173052 and PubMed:17174896) that only DIS3/RRP44
CC subunit of the exosome core has this activity.
CC {ECO:0000305|PubMed:9390555}.
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DR EMBL; X82775; CAA58018.1; -; Genomic_DNA.
DR EMBL; Z72980; CAA97221.1; -; Genomic_DNA.
DR EMBL; Z72981; CAA97223.1; -; Genomic_DNA.
DR EMBL; AY558509; AAS56835.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08288.1; -; Genomic_DNA.
DR PIR; S59180; S59180.
DR RefSeq; NP_011711.3; NM_001181324.3.
DR PDB; 2WP8; X-ray; 3.00 A; B=1-246.
DR PDB; 4IFD; X-ray; 2.80 A; B=1-246.
DR PDB; 4OO1; X-ray; 3.30 A; B=1-246.
DR PDB; 5C0W; X-ray; 4.60 A; B=1-246.
DR PDB; 5C0X; X-ray; 3.81 A; B=1-246.
DR PDB; 5G06; EM; 4.20 A; B=1-246.
DR PDB; 5JEA; X-ray; 2.65 A; B=1-246.
DR PDB; 5K36; X-ray; 3.10 A; B=1-246.
DR PDB; 5OKZ; X-ray; 3.20 A; B/L/V/f=1-246.
DR PDB; 5VZJ; X-ray; 3.30 A; B=1-246.
DR PDB; 6FSZ; EM; 4.60 A; BB=1-246.
DR PDB; 6LQS; EM; 3.80 A; R1=1-246.
DR PDB; 7AJT; EM; 4.60 A; EC=1-246.
DR PDB; 7AJU; EM; 3.80 A; EC=1-246.
DR PDB; 7D4I; EM; 4.00 A; R1=1-246.
DR PDBsum; 2WP8; -.
DR PDBsum; 4IFD; -.
DR PDBsum; 4OO1; -.
DR PDBsum; 5C0W; -.
DR PDBsum; 5C0X; -.
DR PDBsum; 5G06; -.
DR PDBsum; 5JEA; -.
DR PDBsum; 5K36; -.
DR PDBsum; 5OKZ; -.
DR PDBsum; 5VZJ; -.
DR PDBsum; 6FSZ; -.
DR PDBsum; 6LQS; -.
DR PDBsum; 7AJT; -.
DR PDBsum; 7AJU; -.
DR PDBsum; 7D4I; -.
DR AlphaFoldDB; P46948; -.
DR SMR; P46948; -.
DR BioGRID; 33448; 285.
DR ComplexPortal; CPX-599; Nuclear/nucleolar exosome complex, DIS3-RRP6 variant.
DR ComplexPortal; CPX-603; Cytoplasmic exosome complex, DIS3 variant.
DR DIP; DIP-2083N; -.
DR IntAct; P46948; 24.
DR MINT; P46948; -.
DR STRING; 4932.YGR195W; -.
DR MaxQB; P46948; -.
DR PaxDb; P46948; -.
DR PRIDE; P46948; -.
DR TopDownProteomics; P46948; -.
DR EnsemblFungi; YGR195W_mRNA; YGR195W; YGR195W.
DR GeneID; 853109; -.
DR KEGG; sce:YGR195W; -.
DR SGD; S000003427; SKI6.
DR VEuPathDB; FungiDB:YGR195W; -.
DR eggNOG; KOG1068; Eukaryota.
DR GeneTree; ENSGT00940000153348; -.
DR HOGENOM; CLU_063514_0_1_1; -.
DR InParanoid; P46948; -.
DR OMA; GIAMYDY; -.
DR BioCyc; YEAST:G3O-30881-MON; -.
DR Reactome; R-SCE-429958; mRNA decay by 3' to 5' exoribonuclease.
DR Reactome; R-SCE-450385; Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
DR Reactome; R-SCE-450513; Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR EvolutionaryTrace; P46948; -.
DR PRO; PR:P46948; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P46948; protein.
DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IDA:SGD.
DR GO; GO:0000178; C:exosome (RNase complex); IPI:ComplexPortal.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:ComplexPortal.
DR GO; GO:0005634; C:nucleus; IDA:ComplexPortal.
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:0070651; P:nonfunctional rRNA decay; IC:SGD.
DR GO; GO:0071028; P:nuclear mRNA surveillance; 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; IC:SGD.
DR GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
DR GO; GO:0070478; P:nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay; IMP:SGD.
DR GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IMP:SGD.
DR GO; GO:0070481; P:nuclear-transcribed mRNA catabolic process, non-stop decay; IC:SGD.
DR GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IMP:SGD.
DR GO; GO:0006401; P:RNA catabolic process; IDA:ComplexPortal.
DR GO; GO:0006396; P:RNA processing; IDA:ComplexPortal.
DR GO; GO:0016075; P:rRNA catabolic process; 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 Gene3D; 3.30.230.70; -; 1.
DR InterPro; IPR001247; ExoRNase_PH_dom1.
DR InterPro; IPR015847; ExoRNase_PH_dom2.
DR InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR Pfam; PF01138; RNase_PH; 1.
DR Pfam; PF03725; RNase_PH_C; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55666; SSF55666; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Exosome; Nucleus; Reference proteome; RNA-binding;
KW rRNA processing.
FT CHAIN 1..246
FT /note="Exosome complex component SKI6"
FT /id="PRO_0000139962"
FT MUTAGEN 62..63
FT /note="KS->ED: Impairs RNA-binding (at the proposed ring
FT entry site)."
FT /evidence="ECO:0000269|PubMed:19879841"
FT MUTAGEN 95..96
FT /note="RR->EE: Impairs RNA-binding (at the proposed ring
FT exit site)."
FT /evidence="ECO:0000269|PubMed:19879841"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:4OO1"
FT STRAND 25..31
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 37..44
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 47..57
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 60..64
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 67..69
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 95..108
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 109..111
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 121..130
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 135..149
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 158..166
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 176..179
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 182..190
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 193..201
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 207..209
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 210..241
FT /evidence="ECO:0007829|PDB:5JEA"
SQ SEQUENCE 246 AA; 27561 MW; C80EFFB528A43044 CRC64;
MSRLEIYSPE GLRLDGRRWN ELRRFESSIN THPHAADGSS YMEQGNNKII TLVKGPKEPR
LKSQMDTSKA LLNVSVNITK FSKFERSKSS HKNERRVLEI QTSLVRMFEK NVMLNIYPRT
VIDIEIHVLE QDGGIMGSLI NGITLALIDA GISMFDYISG ISVGLYDTTP LLDTNSLEEN
AMSTVTLGVV GKSEKLSLLL VEDKIPLDRL ENVLAIGIAG AHRVRDLMDE ELRKHAQKRV
SNASAR
