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Exosome complex component RRP42 (Ribosomal RNA-processing protein 42)

 RRP42_YEAST             Reviewed;         265 AA.
Q12277; D6VRN9;
01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
25-APR-2018, entry version 149.
RecName: Full=Exosome complex component RRP42;
AltName: Full=Ribosomal RNA-processing protein 42;
Name=RRP42; OrderedLocusNames=YDL111C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 96604 / S288c / FY1679;
PubMed=8923743;
DOI=10.1002/(SICI)1097-0061(199610)12:13<1377::AID-YEA35>3.0.CO;2-R;
Boskovic J., Soler-Mira A., Garcia-Cantalejo J.M., Ballesta J.P.G.,
Jimenez A., Remacha M.A.;
"The sequence of a 16,691 bp segment of Saccharomyces cerevisiae
chromosome IV identifies the DUN1, PMT1, PMT5, SRP14 and DPR1 genes,
and five new open reading frames.";
Yeast 12:1377-1384(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169867;
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N.,
Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M.,
Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L.,
Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M.,
Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S.,
Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M.,
Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S.,
Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K.,
Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D.,
Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C.,
Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T.,
Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E.,
Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W.,
Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K.,
Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S.,
Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A.,
Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S.,
Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M.,
Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y.,
Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M.,
Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E.,
Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R.,
Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
Mewes H.-W., Zollner A., Zaccaria P.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
Nature 387:75-78(1997).
[3]
GENOME REANNOTATION.
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).
[4]
IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, AND SUBUNIT.
PubMed=9390555; DOI=10.1016/S0092-8674(00)80432-8;
Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D.;
"The exosome: a conserved eukaryotic RNA processing complex containing
multiple 3'-->5' exoribonucleases.";
Cell 91:457-466(1997).
[5]
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).
[6]
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).
[7]
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).
[8]
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).
[9]
ERRATUM.
Liu Q., Greimann J.C., Lima C.D.;
Cell 131:188-189(2007).
[10]
IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION OF THE RNA EXOSOME
COMPLEX, 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).
-!- 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. RRP42 is part of the hexameric
ring of RNase PH domain-containing subunits proposed to form a
central channel which threads RNA substrates for degradation.
{ECO:0000269|PubMed:17173052, ECO:0000269|PubMed:9390555}.
-!- 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,
ECO:0000269|PubMed:9390555}.
-!- INTERACTION:
P53859:CSL4; NbExp=18; IntAct=EBI-1765, EBI-1731;
Q08162:DIS3; NbExp=9; IntAct=EBI-1765, EBI-1740;
P48240:MTR3; NbExp=15; IntAct=EBI-1765, EBI-1749;
P38792:RRP4; NbExp=4; IntAct=EBI-1765, EBI-1757;
P25359:RRP43; NbExp=4; IntAct=EBI-1765, EBI-1773;
Q05636:RRP45; NbExp=6; IntAct=EBI-1765, EBI-1810;
P53256:RRP46; NbExp=10; IntAct=EBI-1765, EBI-1842;
Q12149:RRP6; NbExp=6; IntAct=EBI-1765, EBI-1782;
P46948:SKI6; NbExp=4; IntAct=EBI-1765, EBI-1788;
Q08491:SKI7; NbExp=5; IntAct=EBI-1765, EBI-1389;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
Nucleus, nucleolus {ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 7110 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X95644; CAA64901.1; -; Genomic_DNA.
EMBL; Z74159; CAA98678.1; -; Genomic_DNA.
EMBL; BK006938; DAA11749.1; -; Genomic_DNA.
PIR; S67653; S67653.
RefSeq; NP_010172.1; NM_001180170.1.
PDB; 4IFD; X-ray; 2.80 A; E=1-265.
PDB; 4OO1; X-ray; 3.30 A; E=1-265.
PDB; 5C0W; X-ray; 4.60 A; E=1-265.
PDB; 5C0X; X-ray; 3.81 A; E=1-265.
PDB; 5G06; EM; 4.20 A; E=1-265.
PDB; 5JEA; X-ray; 2.65 A; E=1-265.
PDB; 5K36; X-ray; 3.10 A; E=1-265.
PDB; 5OKZ; X-ray; 3.20 A; E/O/Y/i=1-265.
PDB; 5VZJ; X-ray; 3.30 A; E=1-265.
PDBsum; 4IFD; -.
PDBsum; 4OO1; -.
PDBsum; 5C0W; -.
PDBsum; 5C0X; -.
PDBsum; 5G06; -.
PDBsum; 5JEA; -.
PDBsum; 5K36; -.
PDBsum; 5OKZ; -.
PDBsum; 5VZJ; -.
ProteinModelPortal; Q12277; -.
SMR; Q12277; -.
BioGrid; 31951; 202.
DIP; DIP-1463N; -.
IntAct; Q12277; 31.
MINT; Q12277; -.
STRING; 4932.YDL111C; -.
MaxQB; Q12277; -.
PaxDb; Q12277; -.
PRIDE; Q12277; -.
EnsemblFungi; YDL111C; YDL111C; YDL111C.
GeneID; 851447; -.
KEGG; sce:YDL111C; -.
EuPathDB; FungiDB:YDL111C; -.
SGD; S000002269; RRP42.
HOGENOM; HOG000248003; -.
InParanoid; Q12277; -.
KO; K12589; -.
OMA; ECIVSVK; -.
OrthoDB; EOG092C3MSX; -.
BioCyc; YEAST:G3O-29512-MONOMER; -.
PRO; PR:Q12277; -.
Proteomes; UP000002311; Chromosome IV.
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:0017091; F:AU-rich element binding; 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:0071028; P:nuclear mRNA surveillance; IBA:GO_Central.
GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IBA:GO_Central.
GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IBA:GO_Central.
GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
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; IC:SGD.
GO; GO:0016075; P:rRNA catabolic process; IMP:SGD.
GO; GO:0034473; P:U1 snRNA 3'-end processing; IBA:GO_Central.
GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
GO; GO:0034476; P:U5 snRNA 3'-end processing; IBA:GO_Central.
Gene3D; 3.30.230.70; -; 1.
InterPro; IPR001247; ExoRNase_PH_dom1.
InterPro; IPR015847; ExoRNase_PH_dom2.
InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
Pfam; PF01138; RNase_PH; 1.
Pfam; PF03725; RNase_PH_C; 1.
SUPFAM; SSF54211; SSF54211; 2.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Exosome; Nucleus;
Reference proteome; RNA-binding; rRNA processing.
CHAIN 1 265 Exosome complex component RRP42.
/FTId=PRO_0000139966.
HELIX 5 16 {ECO:0000244|PDB:5JEA}.
STRAND 17 19 {ECO:0000244|PDB:5JEA}.
STRAND 34 39 {ECO:0000244|PDB:5JEA}.
STRAND 44 52 {ECO:0000244|PDB:5JEA}.
STRAND 53 55 {ECO:0000244|PDB:4OO1}.
STRAND 57 68 {ECO:0000244|PDB:5JEA}.
TURN 69 71 {ECO:0000244|PDB:5JEA}.
STRAND 76 82 {ECO:0000244|PDB:5JEA}.
HELIX 90 102 {ECO:0000244|PDB:5JEA}.
TURN 105 108 {ECO:0000244|PDB:5JEA}.
HELIX 111 114 {ECO:0000244|PDB:5JEA}.
STRAND 117 132 {ECO:0000244|PDB:5JEA}.
HELIX 138 149 {ECO:0000244|PDB:5JEA}.
STRAND 153 158 {ECO:0000244|PDB:5JEA}.
TURN 163 166 {ECO:0000244|PDB:4IFD}.
STRAND 171 179 {ECO:0000244|PDB:5JEA}.
STRAND 186 193 {ECO:0000244|PDB:5JEA}.
STRAND 196 200 {ECO:0000244|PDB:5JEA}.
HELIX 203 208 {ECO:0000244|PDB:5JEA}.
STRAND 210 218 {ECO:0000244|PDB:5JEA}.
STRAND 226 228 {ECO:0000244|PDB:5JEA}.
STRAND 233 235 {ECO:0000244|PDB:5JEA}.
HELIX 241 253 {ECO:0000244|PDB:5JEA}.
HELIX 256 262 {ECO:0000244|PDB:5JEA}.
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


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