RRP40_YEAST
ID RRP40_YEAST Reviewed; 240 AA.
AC Q08285; D6W1S7; E9P8Z4;
DT 01-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 21-SEP-2011, sequence version 2.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=Exosome complex component RRP40;
DE AltName: Full=Ribosomal RNA-processing protein 40;
GN Name=RRP40; OrderedLocusNames=YOL142W;
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=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [2]
RP GENOME REANNOTATION, AND SEQUENCE REVISION TO 160.
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 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 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 [6]
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 [7]
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 [8]
RP ERRATUM OF PUBMED:17174896.
RA Liu Q., Greimann J.C., Lima C.D.;
RL Cell 131:188-189(2007).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, INTERACTION OF THE EXOSOME
RP WITH RRP6 AND SKI7, 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 [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [11]
RP FUNCTION IN RNA EXOSOME COMPLEX STABILITY.
RX PubMed=19060898; DOI=10.1038/nsmb.1528;
RA Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G.,
RA Sanchez-Rotunno M., Arraiano C.M., van Hoof A.;
RT "The exosome contains domains with specific endoribonuclease,
RT exoribonuclease and cytoplasmic mRNA decay activities.";
RL Nat. Struct. Mol. Biol. 16:56-62(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. RRP40 as peripheral part of the Exo-9 complex is
CC thought to stabilize the hexameric ring of RNase PH-domain subunits.
CC {ECO:0000269|PubMed:10465791, ECO:0000269|PubMed:17173052,
CC ECO:0000269|PubMed:19060898}.
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}.
CC -!- INTERACTION:
CC Q08285; P53859: CSL4; NbExp=14; IntAct=EBI-1831, EBI-1731;
CC Q08285; Q08162: DIS3; NbExp=3; IntAct=EBI-1831, EBI-1740;
CC Q08285; P46948: SKI6; NbExp=4; IntAct=EBI-1831, EBI-1788;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 6050 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RRP40 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; Z74884; CAA99163.1; -; Genomic_DNA.
DR EMBL; AY692926; AAT92945.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10643.2; -; Genomic_DNA.
DR PIR; S61872; S61872.
DR RefSeq; NP_014499.2; NM_001183396.2.
DR PDB; 2JA9; X-ray; 2.20 A; A=62-236.
DR PDB; 4IFD; X-ray; 2.80 A; G=1-240.
DR PDB; 4OO1; X-ray; 3.30 A; G=1-240.
DR PDB; 5C0W; X-ray; 4.60 A; G=1-240.
DR PDB; 5C0X; X-ray; 3.81 A; G=1-240.
DR PDB; 5G06; EM; 4.20 A; G=1-240.
DR PDB; 5JEA; X-ray; 2.65 A; G=1-240.
DR PDB; 5K36; X-ray; 3.10 A; G=1-240.
DR PDB; 5OKZ; X-ray; 3.20 A; G/Q/a/k=1-240.
DR PDB; 5VZJ; X-ray; 3.30 A; G=1-240.
DR PDB; 6FSZ; EM; 4.60 A; GG=1-240.
DR PDB; 6LQS; EM; 3.80 A; R0=1-240.
DR PDB; 7AJT; EM; 4.60 A; EH=1-240.
DR PDB; 7AJU; EM; 3.80 A; EH=1-240.
DR PDB; 7D4I; EM; 4.00 A; R0=1-240.
DR PDBsum; 2JA9; -.
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; Q08285; -.
DR SMR; Q08285; -.
DR BioGRID; 34275; 24.
DR ComplexPortal; CPX-599; Nuclear/nucleolar exosome complex, DIS3-RRP6 variant.
DR ComplexPortal; CPX-603; Cytoplasmic exosome complex, DIS3 variant.
DR DIP; DIP-5330N; -.
DR IntAct; Q08285; 18.
DR MINT; Q08285; -.
DR STRING; 4932.YOL142W; -.
DR iPTMnet; Q08285; -.
DR MaxQB; Q08285; -.
DR PaxDb; Q08285; -.
DR PRIDE; Q08285; -.
DR EnsemblFungi; YOL142W_mRNA; YOL142W; YOL142W.
DR GeneID; 854023; -.
DR KEGG; sce:YOL142W; -.
DR SGD; S000005502; RRP40.
DR VEuPathDB; FungiDB:YOL142W; -.
DR eggNOG; KOG1004; Eukaryota.
DR GeneTree; ENSGT00940000153596; -.
DR HOGENOM; CLU_069847_0_0_1; -.
DR InParanoid; Q08285; -.
DR OMA; SYMAFPN; -.
DR BioCyc; YEAST:G3O-33533-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; Q08285; -.
DR PRO; PR:Q08285; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q08285; 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:0030145; F:manganese ion binding; IDA:SGD.
DR GO; GO:0003723; F:RNA binding; IDA:SGD.
DR GO; GO:0071034; P:CUT catabolic process; IBA:GO_Central.
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:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IC: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:0043628; P:small regulatory ncRNA 3'-end processing; IC:SGD.
DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
DR CDD; cd05790; S1_Rrp40; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.1370.10; -; 1.
DR InterPro; IPR026699; Exosome_RNA_bind1/RRP40/RRP4.
DR InterPro; IPR004088; KH_dom_type_1.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR041054; Rrp40_N.
DR InterPro; IPR037319; Rrp40_S1.
DR PANTHER; PTHR21321; PTHR21321; 1.
DR Pfam; PF15985; KH_6; 1.
DR Pfam; PF18311; Rrp40_N; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF54791; SSF54791; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Exosome; Nucleus; Reference proteome; RNA-binding;
KW rRNA processing.
FT CHAIN 1..240
FT /note="Exosome complex component RRP40"
FT /id="PRO_0000097453"
FT DOMAIN 67..137
FT /note="S1 motif"
FT CONFLICT 160
FT /note="L -> F (in Ref. 1; CAA99163)"
FT /evidence="ECO:0000305"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 29..31
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 40..44
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 53..58
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 71..79
FT /evidence="ECO:0007829|PDB:2JA9"
FT STRAND 81..89
FT /evidence="ECO:0007829|PDB:2JA9"
FT STRAND 95..98
FT /evidence="ECO:0007829|PDB:2JA9"
FT HELIX 99..101
FT /evidence="ECO:0007829|PDB:4OO1"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:4OO1"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:2JA9"
FT STRAND 118..125
FT /evidence="ECO:0007829|PDB:2JA9"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 133..137
FT /evidence="ECO:0007829|PDB:2JA9"
FT TURN 139..141
FT /evidence="ECO:0007829|PDB:2JA9"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:2JA9"
FT STRAND 154..157
FT /evidence="ECO:0007829|PDB:2JA9"
FT HELIX 160..168
FT /evidence="ECO:0007829|PDB:2JA9"
FT HELIX 174..179
FT /evidence="ECO:0007829|PDB:2JA9"
FT STRAND 185..189
FT /evidence="ECO:0007829|PDB:2JA9"
FT TURN 190..192
FT /evidence="ECO:0007829|PDB:2JA9"
FT STRAND 193..197
FT /evidence="ECO:0007829|PDB:2JA9"
FT HELIX 201..217
FT /evidence="ECO:0007829|PDB:2JA9"
FT HELIX 220..222
FT /evidence="ECO:0007829|PDB:2JA9"
FT HELIX 223..230
FT /evidence="ECO:0007829|PDB:2JA9"
FT TURN 231..233
FT /evidence="ECO:0007829|PDB:2JA9"
SQ SEQUENCE 240 AA; 26556 MW; 62B3A30348BBAA7C CRC64;
MSTFIFPGDS FPVDPTTPVK LGPGIYCDPN TQEIRPVNTG VLHVSAKGKS GVQTAYIDYS
SKRYIPSVND FVIGVIIGTF SDSYKVSLQN FSSSVSLSYM AFPNASKKNR PTLQVGDLVY
ARVCTAEKEL EAEIECFDST TGRDAGFGIL EDGMIIDVNL NFARQLLFNN DFPLLKVLAA
HTKFEVAIGL NGKIWVKCEE LSNTLACYRT IMECCQKNDT AAFKDIAKRQ FKEILTVKEE
