RRP45_YEAST
ID RRP45_YEAST Reviewed; 305 AA.
AC Q05636; D6VSR0;
DT 01-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 181.
DE RecName: Full=Exosome complex component RRP45;
DE AltName: Full=Ribosomal RNA-processing protein 45;
GN Name=RRP45; OrderedLocusNames=YDR280W; ORFNames=D9954.1;
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=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(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 [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 [4]
RP FUNCTION, AND SUBUNIT.
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 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 [7]
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 [8]
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 [9]
RP ERRATUM OF PUBMED:17174896.
RA Liu Q., Greimann J.C., Lima C.D.;
RL Cell 131:188-189(2007).
RN [10]
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 [11]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SKI6 AND DIS3.
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. RRP45 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 ECO:0000269|PubMed:19879841}.
CC -!- INTERACTION:
CC Q05636; P53859: CSL4; NbExp=15; IntAct=EBI-1810, EBI-1731;
CC Q05636; P46948: SKI6; NbExp=11; IntAct=EBI-1810, EBI-1788;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 4800 molecules/cell in log phase SD medium.
CC {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}.
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DR EMBL; U51030; AAB64446.1; -; Genomic_DNA.
DR EMBL; AY557748; AAS56074.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12120.1; -; Genomic_DNA.
DR PIR; S70136; S70136.
DR RefSeq; NP_010566.1; NM_001180588.1.
DR PDB; 2WP8; X-ray; 3.00 A; A=1-305.
DR PDB; 4IFD; X-ray; 2.80 A; A=2-305.
DR PDB; 4OO1; X-ray; 3.30 A; A=1-305.
DR PDB; 5C0W; X-ray; 4.60 A; A=1-305.
DR PDB; 5C0X; X-ray; 3.81 A; A=1-305.
DR PDB; 5G06; EM; 4.20 A; A=1-305.
DR PDB; 5JEA; X-ray; 2.65 A; A=1-305.
DR PDB; 5K36; X-ray; 3.10 A; A=1-305.
DR PDB; 5OKZ; X-ray; 3.20 A; A/K/U/e=1-305.
DR PDB; 5VZJ; X-ray; 3.30 A; A=1-305.
DR PDB; 6FSZ; EM; 4.60 A; AA=3-305.
DR PDB; 6LQS; EM; 3.80 A; R5=1-305.
DR PDB; 7AJT; EM; 4.60 A; EB=1-305.
DR PDB; 7AJU; EM; 3.80 A; EB=1-305.
DR PDB; 7D4I; EM; 4.00 A; R5=1-305.
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; Q05636; -.
DR SMR; Q05636; -.
DR BioGRID; 32333; 109.
DR ComplexPortal; CPX-599; Nuclear/nucleolar exosome complex, DIS3-RRP6 variant.
DR ComplexPortal; CPX-603; Cytoplasmic exosome complex, DIS3 variant.
DR DIP; DIP-2084N; -.
DR IntAct; Q05636; 30.
DR MINT; Q05636; -.
DR STRING; 4932.YDR280W; -.
DR MaxQB; Q05636; -.
DR PaxDb; Q05636; -.
DR PRIDE; Q05636; -.
DR EnsemblFungi; YDR280W_mRNA; YDR280W; YDR280W.
DR GeneID; 851874; -.
DR KEGG; sce:YDR280W; -.
DR SGD; S000002688; RRP45.
DR VEuPathDB; FungiDB:YDR280W; -.
DR eggNOG; KOG1614; Eukaryota.
DR GeneTree; ENSGT00950000183130; -.
DR HOGENOM; CLU_038194_0_0_1; -.
DR InParanoid; Q05636; -.
DR OMA; CQIAKYG; -.
DR BioCyc; YEAST:G3O-29845-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; Q05636; -.
DR PRO; PR:Q05636; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q05636; 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:SGD.
DR GO; GO:0005634; C:nucleus; IDA:ComplexPortal.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0043928; P:exonucleolytic catabolism of deadenylated mRNA; IBA:GO_Central.
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; IBA:GO_Central.
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; IC: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; IBA:GO_Central.
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 CDD; cd11368; RNase_PH_RRP45; 1.
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 InterPro; IPR033100; Rrp45.
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..305
FT /note="Exosome complex component RRP45"
FT /id="PRO_0000139974"
FT HELIX 9..20
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 36..40
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 46..51
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 54..65
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 69..71
FT /evidence="ECO:0007829|PDB:5OKZ"
FT STRAND 76..80
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:4IFD"
FT HELIX 99..112
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 113..116
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 123..126
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 127..129
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 130..142
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 147..161
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 167..170
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 173..176
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 179..181
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 194..201
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 206..211
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 218..222
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 225..228
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 232..239
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 243..257
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 258..298
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 299..302
FT /evidence="ECO:0007829|PDB:2WP8"
SQ SEQUENCE 305 AA; 33962 MW; 65C9DB5A63678F2D CRC64;
MAKDIEISAS ESKFILEALR QNYRLDGRSF DQFRDVEITF GKEFGDVSVK MGNTKVHCRI
SCQIAQPYED RPFEGLFVIS TEISPMAGSQ FENGNITGED EVLCSRIIEK SVRRSGALDV
EGLCIVAGSK CWAVRADVHF LDCDGGFIDA SCIAVMAGLM HFKKPDITVH GEQIIVHPVN
EREPVPLGIL HIPICVTFSF FNPQDTEENI KGETNSEISI IDATLKEELL RDGVLTVTLN
KNREVVQVSK AGGLPMDALT LMKCCHEAYS IIEKITDQIL QLLKEDSEKR NKYAAMLTSE
NAREI
