RRP42_YEAST
ID RRP42_YEAST Reviewed; 265 AA.
AC Q12277; D6VRN9;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 177.
DE RecName: Full=Exosome complex component RRP42;
DE AltName: Full=Ribosomal RNA-processing protein 42;
GN Name=RRP42; OrderedLocusNames=YDL111C;
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 96604 / S288c / FY1679;
RX PubMed=8923743;
RX DOI=10.1002/(sici)1097-0061(199610)12:13%3c1377::aid-yea35%3e3.0.co;2-r;
RA Boskovic J., Soler-Mira A., Garcia-Cantalejo J.M., Ballesta J.P.G.,
RA Jimenez A., Remacha M.A.;
RT "The sequence of a 16,691 bp segment of Saccharomyces cerevisiae chromosome
RT IV identifies the DUN1, PMT1, PMT5, SRP14 and DPR1 genes, and five new open
RT reading frames.";
RL Yeast 12:1377-1384(1996).
RN [2]
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 [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 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 [5]
RP 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 [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).
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. RRP42 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:9390555}.
CC -!- INTERACTION:
CC Q12277; P53859: CSL4; NbExp=16; IntAct=EBI-1765, EBI-1731;
CC Q12277; P48240: MTR3; NbExp=11; IntAct=EBI-1765, EBI-1749;
CC Q12277; P46948: SKI6; NbExp=4; IntAct=EBI-1765, EBI-1788;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 7110 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
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DR EMBL; X95644; CAA64901.1; -; Genomic_DNA.
DR EMBL; Z74159; CAA98678.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11749.1; -; Genomic_DNA.
DR PIR; S67653; S67653.
DR RefSeq; NP_010172.1; NM_001180170.1.
DR PDB; 4IFD; X-ray; 2.80 A; E=1-265.
DR PDB; 4OO1; X-ray; 3.30 A; E=1-265.
DR PDB; 5C0W; X-ray; 4.60 A; E=1-265.
DR PDB; 5C0X; X-ray; 3.81 A; E=1-265.
DR PDB; 5G06; EM; 4.20 A; E=1-265.
DR PDB; 5JEA; X-ray; 2.65 A; E=1-265.
DR PDB; 5K36; X-ray; 3.10 A; E=1-265.
DR PDB; 5OKZ; X-ray; 3.20 A; E/O/Y/i=1-265.
DR PDB; 5VZJ; X-ray; 3.30 A; E=1-265.
DR PDB; 6FSZ; EM; 4.60 A; EE=1-265.
DR PDB; 6LQS; EM; 3.80 A; R2=1-265.
DR PDB; 7AJT; EM; 4.60 A; EF=1-265.
DR PDB; 7AJU; EM; 3.80 A; EF=1-265.
DR PDB; 7D4I; EM; 4.00 A; R2=1-265.
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; Q12277; -.
DR SMR; Q12277; -.
DR BioGRID; 31951; 209.
DR ComplexPortal; CPX-599; Nuclear/nucleolar exosome complex, DIS3-RRP6 variant.
DR ComplexPortal; CPX-603; Cytoplasmic exosome complex, DIS3 variant.
DR DIP; DIP-1463N; -.
DR IntAct; Q12277; 27.
DR MINT; Q12277; -.
DR STRING; 4932.YDL111C; -.
DR MaxQB; Q12277; -.
DR PaxDb; Q12277; -.
DR PRIDE; Q12277; -.
DR EnsemblFungi; YDL111C_mRNA; YDL111C; YDL111C.
DR GeneID; 851447; -.
DR KEGG; sce:YDL111C; -.
DR SGD; S000002269; RRP42.
DR VEuPathDB; FungiDB:YDL111C; -.
DR eggNOG; KOG1612; Eukaryota.
DR GeneTree; ENSGT00950000183130; -.
DR HOGENOM; CLU_046570_1_0_1; -.
DR InParanoid; Q12277; -.
DR OMA; QMSIEIP; -.
DR BioCyc; YEAST:G3O-29512-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:Q12277; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q12277; 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: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; IBA:GO_Central.
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; IMP:SGD.
DR GO; GO:0043628; P:small regulatory ncRNA 3'-end processing; IC:SGD.
DR GO; GO:0034473; P:U1 snRNA 3'-end processing; IBA:GO_Central.
DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
DR GO; GO:0034476; P:U5 snRNA 3'-end processing; IBA:GO_Central.
DR Gene3D; 3.30.230.70; -; 1.
DR InterPro; IPR001247; ExoRNase_PH_dom1.
DR InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR Pfam; PF01138; RNase_PH; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Exosome; Nucleus; Reference proteome; RNA-binding;
KW rRNA processing.
FT CHAIN 1..265
FT /note="Exosome complex component RRP42"
FT /id="PRO_0000139966"
FT HELIX 5..16
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 17..19
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 34..39
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 44..52
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:4OO1"
FT STRAND 57..68
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 69..71
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 76..82
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 90..102
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 105..108
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 111..114
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 117..132
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 138..149
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 153..158
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 163..166
FT /evidence="ECO:0007829|PDB:4IFD"
FT STRAND 171..179
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 186..193
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 196..200
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 203..208
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 210..218
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 226..228
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 233..235
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 241..253
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 256..262
FT /evidence="ECO:0007829|PDB:5JEA"
SQ SEQUENCE 265 AA; 29055 MW; 806C60979642C67E CRC64;
MSLSVAEKSY LYDSLASTPS IRPDGRLPHQ FRPIEIFTDF LPSSNGSSRI IASDGSECIV
SIKSKVVDHH VENELLQVDV DIAGQRDDAL VVETITSLLN KVLKSGSGVD SSKLQLTKKY
SFKIFVDVLV ISSHSHPVSL ISFAIYSALN STYLPKLISA FDDLEVEELP TFHDYDMVKL
DINPPLVFIL AVVGNNMLLD PAANESEVAN NGLIISWSNG KITSPIRSVA LNDSNVKSFK
PHLLKQGLAM VEKYAPDVVR SLENL
