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Exosome complex component RRP40 (Ribosomal RNA-processing protein 40)

 RRP40_YEAST             Reviewed;         240 AA.
Q08285; D6W1S7; E9P8Z4;
01-JUN-2001, integrated into UniProtKB/Swiss-Prot.
21-SEP-2011, sequence version 2.
22-NOV-2017, entry version 145.
RecName: Full=Exosome complex component RRP40;
AltName: Full=Ribosomal RNA-processing protein 40;
Name=RRP40; OrderedLocusNames=YOL142W;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169874;
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W.,
Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R.,
Boyer J., Camasses A., Casamayor A., Casas C., Cheret G.,
Cziepluch C., Daignan-Fornier B., Dang V.-D., de Haan M., Delius H.,
Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F.,
Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A.,
Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J.,
Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P.,
Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M.,
Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R.,
Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S.,
Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A.,
Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M.,
Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C.,
Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S.,
Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
Nature 387:98-102(1997).
[2]
GENOME REANNOTATION, AND SEQUENCE REVISION TO 160.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[4]
FUNCTION, AND IDENTIFICATION IN THE EXOSOME COMPLEX BY MASS
SPECTROMETRY.
PubMed=10465791; DOI=10.1101/gad.13.16.2148;
Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D.,
Mitchell P.;
"The yeast exosome and human PM-Scl are related complexes of 3'-->5'
exonucleases.";
Genes Dev. 13:2148-2158(1999).
[5]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[6]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[7]
RECONSTITUTION OF THE RNA EXOSOME COMPLEX, AND LACK OF EXONUCLEASE
ACTIVITY.
PubMed=17174896; DOI=10.1016/j.cell.2006.10.037;
Liu Q., Greimann J.C., Lima C.D.;
"Reconstitution, activities, and structure of the eukaryotic RNA
exosome.";
Cell 127:1223-1237(2006).
[8]
ERRATUM.
Liu Q., Greimann J.C., Lima C.D.;
Cell 131:188-189(2007).
[9]
IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, INTERACTION OF THE
EXOSOME WITH RRP6 AND SKI7, AND SUBUNIT.
PubMed=17173052; DOI=10.1038/nsmb1184;
Dziembowski A., Lorentzen E., Conti E., Seraphin B.;
"A single subunit, Dis3, is essentially responsible for yeast exosome
core activity.";
Nat. Struct. Mol. Biol. 14:15-22(2007).
[10]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[11]
FUNCTION IN RNA EXOSOME COMPLEX STABILITY.
PubMed=19060898; DOI=10.1038/nsmb.1528;
Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G.,
Sanchez-Rotunno M., Arraiano C.M., van Hoof A.;
"The exosome contains domains with specific endoribonuclease,
exoribonuclease and cytoplasmic mRNA decay activities.";
Nat. Struct. Mol. Biol. 16:56-62(2009).
-!- FUNCTION: Non-catalytic component of the RNA exosome complex which
has 3'->5' exoribonuclease activity and participates in a
multitude of cellular RNA processing and degradation events. In
the nucleus, the RNA exosome complex is involved in proper
maturation of stable RNA species such as rRNA, snRNA and snoRNA,
in the elimination of RNA processing by-products and non-coding
'pervasive' transcripts, such as antisense RNA species and cryptic
unstable transcripts (CUTs), and of mRNAs with processing defects,
thereby limiting or excluding their export to the cytoplasm. In
the cytoplasm, the RNA exosome complex is involved in general mRNA
turnover and in RNA surveillance pathways, preventing translation
of aberrant mRNAs. The catalytic inactive RNA exosome core complex
of 9 subunits (Exo-9) is proposed to play a pivotal role in the
binding and presentation of RNA for ribonucleolysis, and to serve
as a scaffold for the association with catalytic subunits and
accessory proteins or complexes. RRP40 as peripheral part of the
Exo-9 complex is thought to stabilize the hexameric ring of RNase
PH-domain subunits. {ECO:0000269|PubMed:10465791,
ECO:0000269|PubMed:17173052, ECO:0000269|PubMed:19060898}.
-!- SUBUNIT: Component of the RNA exosome complex. Specifically part
of the catalytically inactive RNA exosome core (Exo-9) complex
which associates with catalytic subunits DIS3 and RRP6 in
cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9
is formed by a hexameric ring of RNase PH domain-containing
subunits and peripheral S1 domain-containing components CSL4, RRP4
and RRP40 located on the top of the ring structure.
{ECO:0000269|PubMed:10465791, ECO:0000269|PubMed:17173052}.
-!- INTERACTION:
P53859:CSL4; NbExp=14; IntAct=EBI-1831, EBI-1731;
Q08162:DIS3; NbExp=3; IntAct=EBI-1831, EBI-1740;
P46948:SKI6; NbExp=4; IntAct=EBI-1831, EBI-1788;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
Nucleus, nucleolus {ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 6050 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the RRP40 family. {ECO:0000305}.
-!- CAUTION: According to PubMed:17173052 and PubMed:17174896, only
DIS3/RRP44 subunit of the exosome core has exonuclease activity.
{ECO:0000305}.
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EMBL; Z74884; CAA99163.1; -; Genomic_DNA.
EMBL; AY692926; AAT92945.1; -; Genomic_DNA.
EMBL; BK006948; DAA10643.2; -; Genomic_DNA.
PIR; S61872; S61872.
RefSeq; NP_014499.2; NM_001183396.2.
PDB; 2JA9; X-ray; 2.20 A; A=62-236.
PDB; 4IFD; X-ray; 2.80 A; G=1-240.
PDB; 4OO1; X-ray; 3.30 A; G=1-240.
PDB; 5C0W; X-ray; 4.60 A; G=1-240.
PDB; 5C0X; X-ray; 3.81 A; G=1-240.
PDB; 5G06; EM; 4.20 A; G=1-240.
PDB; 5JEA; X-ray; 2.65 A; G=1-240.
PDB; 5K36; X-ray; 3.10 A; G=1-240.
PDB; 5OKZ; X-ray; 3.20 A; G/Q/a/k=1-240.
PDB; 5VZJ; X-ray; 3.30 A; G=1-240.
PDBsum; 2JA9; -.
PDBsum; 4IFD; -.
PDBsum; 4OO1; -.
PDBsum; 5C0W; -.
PDBsum; 5C0X; -.
PDBsum; 5G06; -.
PDBsum; 5JEA; -.
PDBsum; 5K36; -.
PDBsum; 5OKZ; -.
PDBsum; 5VZJ; -.
ProteinModelPortal; Q08285; -.
SMR; Q08285; -.
BioGrid; 34275; 17.
DIP; DIP-5330N; -.
IntAct; Q08285; 17.
MINT; MINT-530842; -.
STRING; 4932.YOL142W; -.
MaxQB; Q08285; -.
PRIDE; Q08285; -.
EnsemblFungi; YOL142W; YOL142W; YOL142W.
GeneID; 854023; -.
KEGG; sce:YOL142W; -.
EuPathDB; FungiDB:YOL142W; -.
SGD; S000005502; RRP40.
GeneTree; ENSGT00390000012042; -.
HOGENOM; HOG000184644; -.
InParanoid; Q08285; -.
KO; K03681; -.
OMA; ISYLAFE; -.
OrthoDB; EOG092C4V3H; -.
BioCyc; YEAST:G3O-33533-MONOMER; -.
Reactome; R-SCE-429958; mRNA decay by 3' to 5' exoribonuclease.
Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
EvolutionaryTrace; Q08285; -.
PRO; PR:Q08285; -.
Proteomes; UP000002311; Chromosome XV.
GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IDA:SGD.
GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD.
GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
GO; GO:0030145; F:manganese ion binding; IDA:SGD.
GO; GO:0003723; F:RNA binding; IDA:SGD.
GO; GO:0071034; P:CUT catabolic process; IBA:GO_Central.
GO; GO:0043928; P:exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay; IBA:GO_Central.
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.
GO; GO:0043628; P:ncRNA 3'-end processing; IC:SGD.
GO; GO:0070651; P:nonfunctional rRNA decay; IC:SGD.
GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IC:SGD.
GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
GO; GO:0071049; P:nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription; IBA:GO_Central.
GO; GO:0070478; P:nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay; IC:SGD.
GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IBA:GO_Central.
GO; GO:0070481; P:nuclear-transcribed mRNA catabolic process, non-stop decay; IC:SGD.
GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IBA:GO_Central.
GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
InterPro; IPR026699; Exosome_RNA_bind1/RRP40/RRP4.
InterPro; IPR004088; KH_dom_type_1.
InterPro; IPR036612; KH_dom_type_1_sf.
InterPro; IPR012340; NA-bd_OB-fold.
PANTHER; PTHR21321; PTHR21321; 1.
Pfam; PF15985; KH_6; 1.
SUPFAM; SSF50249; SSF50249; 1.
SUPFAM; SSF54791; SSF54791; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Exosome; Nucleus;
Reference proteome; RNA-binding; rRNA processing.
CHAIN 1 240 Exosome complex component RRP40.
/FTId=PRO_0000097453.
DOMAIN 67 137 S1 motif.
CONFLICT 160 160 L -> F (in Ref. 1; CAA99163).
{ECO:0000305}.
STRAND 3 5 {ECO:0000244|PDB:5JEA}.
STRAND 15 17 {ECO:0000244|PDB:5JEA}.
STRAND 19 21 {ECO:0000244|PDB:5JEA}.
STRAND 25 27 {ECO:0000244|PDB:5JEA}.
TURN 29 31 {ECO:0000244|PDB:5JEA}.
STRAND 34 36 {ECO:0000244|PDB:5JEA}.
STRAND 40 44 {ECO:0000244|PDB:5JEA}.
STRAND 53 58 {ECO:0000244|PDB:5JEA}.
STRAND 71 79 {ECO:0000244|PDB:2JA9}.
STRAND 81 89 {ECO:0000244|PDB:2JA9}.
STRAND 95 98 {ECO:0000244|PDB:2JA9}.
HELIX 99 101 {ECO:0000244|PDB:4OO1}.
STRAND 102 104 {ECO:0000244|PDB:4OO1}.
STRAND 107 109 {ECO:0000244|PDB:2JA9}.
STRAND 118 125 {ECO:0000244|PDB:2JA9}.
STRAND 128 130 {ECO:0000244|PDB:5JEA}.
STRAND 133 137 {ECO:0000244|PDB:2JA9}.
TURN 139 141 {ECO:0000244|PDB:2JA9}.
STRAND 148 150 {ECO:0000244|PDB:2JA9}.
STRAND 154 157 {ECO:0000244|PDB:2JA9}.
HELIX 160 168 {ECO:0000244|PDB:2JA9}.
HELIX 174 179 {ECO:0000244|PDB:2JA9}.
STRAND 185 189 {ECO:0000244|PDB:2JA9}.
TURN 190 192 {ECO:0000244|PDB:2JA9}.
STRAND 193 197 {ECO:0000244|PDB:2JA9}.
HELIX 201 217 {ECO:0000244|PDB:2JA9}.
HELIX 220 222 {ECO:0000244|PDB:2JA9}.
HELIX 223 230 {ECO:0000244|PDB:2JA9}.
TURN 231 233 {ECO:0000244|PDB:2JA9}.
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


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