RRP46_YEAST
ID RRP46_YEAST Reviewed; 223 AA.
AC P53256; D6VUM7; Q6TQU1;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 31-OCT-2006, sequence version 2.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=Exosome complex component RRP46;
DE AltName: Full=Ribosomal RNA-processing protein 46;
GN Name=RRP46; OrderedLocusNames=YGR095C;
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 [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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-67.
RC STRAIN=ATCC 204511 / S288c / AB972;
RA Kennedy M.C., Dietrich F.S.;
RL Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, AND IDENTIFICATION IN THE 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 [5]
RP INTERACTION WITH LRP1.
RX PubMed=12837249; DOI=10.1016/s0092-8674(03)00466-5;
RA Peng W.-T., Robinson M.D., Mnaimneh S., Krogan N.J., Cagney G.,
RA Morris Q.D., Davierwala A.P., Grigull J., Yang X., Zhang W., Mitsakakis N.,
RA Ryan O.W., Datta N., Jojic V., Pal C., Canadien V., Richards D.P.,
RA Beattie B., Wu L.F., Altschuler S.J., Roweis S., Frey B.J., Emili A.,
RA Greenblatt J.F., Hughes T.R.;
RT "A panoramic view of yeast noncoding RNA processing.";
RL Cell 113:919-933(2003).
RN [6]
RP IDENTIFICATION OF PROBABLE INITIATION SITE.
RX PubMed=12748633; DOI=10.1038/nature01644;
RA Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.;
RT "Sequencing and comparison of yeast species to identify genes and
RT regulatory elements.";
RL Nature 423:241-254(2003).
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).
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. RRP46 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:10465791,
CC ECO:0000269|PubMed:17173052}.
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. Interacts with LRP1. {ECO:0000269|PubMed:10465791,
CC ECO:0000269|PubMed:12837249, ECO:0000269|PubMed:17173052}.
CC -!- INTERACTION:
CC P53256; P53859: CSL4; NbExp=16; IntAct=EBI-1842, EBI-1731;
CC P53256; Q08162: DIS3; NbExp=5; IntAct=EBI-1842, EBI-1740;
CC P53256; P46948: SKI6; NbExp=6; IntAct=EBI-1842, EBI-1788;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 10800 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
CC -!- CAUTION: According to PubMed:17173052 and PubMed:17174896, only
CC DIS3/RRP44 subunit of the exosome core has exonuclease activity.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA97098.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; Z72880; CAA97098.1; ALT_INIT; Genomic_DNA.
DR EMBL; AY389297; AAQ97229.1; -; mRNA.
DR EMBL; BK006941; DAA08188.1; -; Genomic_DNA.
DR PIR; S64390; S64390.
DR RefSeq; NP_011609.2; NM_001181224.1.
DR PDB; 4IFD; X-ray; 2.80 A; D=1-223.
DR PDB; 4OO1; X-ray; 3.30 A; D=1-223.
DR PDB; 5C0W; X-ray; 4.60 A; D=1-223.
DR PDB; 5C0X; X-ray; 3.81 A; D=1-223.
DR PDB; 5G06; EM; 4.20 A; D=1-223.
DR PDB; 5JEA; X-ray; 2.65 A; D=1-223.
DR PDB; 5K36; X-ray; 3.10 A; D=1-223.
DR PDB; 5OKZ; X-ray; 3.20 A; D/N/X/h=1-223.
DR PDB; 5VZJ; X-ray; 3.30 A; D=1-223.
DR PDB; 6FSZ; EM; 4.60 A; DD=1-223.
DR PDB; 6LQS; EM; 3.80 A; R6=1-223.
DR PDB; 7AJT; EM; 4.60 A; EE=1-223.
DR PDB; 7AJU; EM; 3.80 A; EE=1-223.
DR PDB; 7D4I; EM; 4.00 A; R6=1-223.
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; P53256; -.
DR SMR; P53256; -.
DR BioGRID; 33338; 42.
DR ComplexPortal; CPX-599; Nuclear/nucleolar exosome complex, DIS3-RRP6 variant.
DR ComplexPortal; CPX-603; Cytoplasmic exosome complex, DIS3 variant.
DR DIP; DIP-6838N; -.
DR IntAct; P53256; 24.
DR MINT; P53256; -.
DR STRING; 4932.YGR095C; -.
DR iPTMnet; P53256; -.
DR MaxQB; P53256; -.
DR PaxDb; P53256; -.
DR PRIDE; P53256; -.
DR EnsemblFungi; YGR095C_mRNA; YGR095C; YGR095C.
DR GeneID; 852987; -.
DR KEGG; sce:YGR095C; -.
DR SGD; S000003327; RRP46.
DR VEuPathDB; FungiDB:YGR095C; -.
DR eggNOG; KOG1069; Eukaryota.
DR GeneTree; ENSGT00940000153348; -.
DR HOGENOM; CLU_063514_2_1_1; -.
DR InParanoid; P53256; -.
DR OMA; CIINEQG; -.
DR BioCyc; YEAST:G3O-30805-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 PRO; PR:P53256; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P53256; 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; IBA:GO_Central.
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: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; IC:SGD.
DR GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IBA:GO_Central.
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; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0043628; P:small regulatory ncRNA 3'-end processing; IC:SGD.
DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
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..223
FT /note="Exosome complex component RRP46"
FT /id="PRO_0000139978"
FT STRAND 4..7
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 11..21
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 24..34
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 38..40
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 43..45
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 47..53
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 55..57
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 61..77
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 87..96
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 101..103
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 106..123
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 127..139
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 140..142
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 145..148
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 151..155
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 157..168
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 169..172
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 173..186
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 188..217
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:5JEA"
SQ SEQUENCE 223 AA; 24407 MW; F1307E0EE4FC3133 CRC64;
MSVQAEIGIL DHVDGSSEFV SQDTKVICSV TGPIEPKARQ ELPTQLALEI IVRPAKGVAT
TREKVLEDKL RAVLTPLITR HCYPRQLCQI TCQILESGED EAEFSLRELS CCINAAFLAL
VDAGIALNSM CASIPIAIIK DTSDIIVDPT AEQLKISLSV HTLALEFVNG GKVVKNVLLL
DSNGDFNEDQ LFSLLELGEQ KCQELVTNIR RIIQDNISPR LVV
