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   27-MAR-2024, entry version 177.
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   EMDB; EMD-0952; -.
DR   EMDB; EMD-11807; -.
DR   EMDB; EMD-11808; -.
DR   EMDB; EMD-30574; -.
DR   EMDB; EMD-4301; -.
DR   SMR; P53256; -.
DR   BioGRID; 33338; 82.
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; 4932-YGR095C; -.
DR   PeptideAtlas; P53256; -.
DR   EnsemblFungi; YGR095C_mRNA; YGR095C; YGR095C.
DR   GeneID; 852987; -.
DR   KEGG; sce:YGR095C; -.
DR   AGR; SGD:S000003327; -.
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   OrthoDB; 2996330at2759; -.
DR   BioCyc; YEAST:G3O-30805-MONOMER; -.
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   BioGRID-ORCS; 852987; 4 hits in 10 CRISPR screens.
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: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:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IBA:GO_Central.
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:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
DR   CDD; cd11372; RNase_PH_RRP46; 1.
DR   Gene3D; 3.30.230.70; GHMP Kinase, N-terminal domain; 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_Su5_D2-typ_SF.
DR   PANTHER; PTHR11953; EXOSOME COMPLEX COMPONENT; 1.
DR   PANTHER; PTHR11953:SF1; EXOSOME COMPLEX COMPONENT RRP46; 1.
DR   Pfam; PF01138; RNase_PH; 1.
DR   Pfam; PF03725; RNase_PH_C; 1.
DR   SUPFAM; SSF55666; Ribonuclease PH domain 2-like; 1.
DR   SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 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
//