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Exosome complex component RRP46 (Ribosomal RNA-processing protein 46)

 RRP46_YEAST             Reviewed;         223 AA.
P53256; D6VUM7; Q6TQU1;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
31-OCT-2006, sequence version 2.
05-DEC-2018, entry version 152.
RecName: Full=Exosome complex component RRP46;
AltName: Full=Ribosomal RNA-processing protein 46;
Name=RRP46; OrderedLocusNames=YGR095C;
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=9169869;
Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M.,
Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J.,
Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E.,
Clemente M.L., Coblenz A., Coglievina M., Coissac E., Defoor E.,
Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B.,
Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L.,
Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M.,
Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M.,
Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B.,
Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W.,
Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A.,
Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S.,
Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L.,
Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S.,
Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J.,
Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M.,
Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B.,
Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J.,
Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M.,
van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M.,
Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H.,
Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M.,
Zollner A., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
Nature 387:81-84(1997).
[2]
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).
[3]
NUCLEOTIDE SEQUENCE [MRNA] OF 1-67.
STRAIN=ATCC 204511 / S288c / AB972;
Kennedy M.C., Dietrich F.S.;
Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases.
[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]
INTERACTION WITH LRP1.
PubMed=12837249; DOI=10.1016/S0092-8674(03)00466-5;
Peng W.-T., Robinson M.D., Mnaimneh S., Krogan N.J., Cagney G.,
Morris Q.D., Davierwala A.P., Grigull J., Yang X., Zhang W.,
Mitsakakis N., Ryan O.W., Datta N., Jojic V., Pal C., Canadien V.,
Richards D.P., Beattie B., Wu L.F., Altschuler S.J., Roweis S.,
Frey B.J., Emili A., Greenblatt J.F., Hughes T.R.;
"A panoramic view of yeast noncoding RNA processing.";
Cell 113:919-933(2003).
[6]
IDENTIFICATION OF PROBABLE INITIATION SITE.
PubMed=12748633; DOI=10.1038/nature01644;
Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.;
"Sequencing and comparison of yeast species to identify genes and
regulatory elements.";
Nature 423:241-254(2003).
[7]
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).
[8]
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).
[9]
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).
[10]
ERRATUM.
Liu Q., Greimann J.C., Lima C.D.;
Cell 131:188-189(2007).
[11]
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. RRP46 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:10465791, ECO:0000269|PubMed:17173052}.
-!- 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. Interacts with
LRP1. {ECO:0000269|PubMed:10465791, ECO:0000269|PubMed:12837249,
ECO:0000269|PubMed:17173052}.
-!- INTERACTION:
P53859:CSL4; NbExp=16; IntAct=EBI-1842, EBI-1731;
Q08162:DIS3; NbExp=5; IntAct=EBI-1842, EBI-1740;
P46948:SKI6; NbExp=6; IntAct=EBI-1842, EBI-1788;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
Nucleus, nucleolus {ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 10800 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
-!- CAUTION: According to PubMed:17173052 and PubMed:17174896, only
DIS3/RRP44 subunit of the exosome core has exonuclease activity.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAA97098.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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EMBL; Z72880; CAA97098.1; ALT_INIT; Genomic_DNA.
EMBL; AY389297; AAQ97229.1; -; mRNA.
EMBL; BK006941; DAA08188.1; -; Genomic_DNA.
PIR; S64390; S64390.
RefSeq; NP_011609.2; NM_001181224.1.
PDB; 4IFD; X-ray; 2.80 A; D=1-223.
PDB; 4OO1; X-ray; 3.30 A; D=1-223.
PDB; 5C0W; X-ray; 4.60 A; D=1-223.
PDB; 5C0X; X-ray; 3.81 A; D=1-223.
PDB; 5G06; EM; 4.20 A; D=1-223.
PDB; 5JEA; X-ray; 2.65 A; D=1-223.
PDB; 5K36; X-ray; 3.10 A; D=1-223.
PDB; 5OKZ; X-ray; 3.20 A; D/N/X/h=1-223.
PDB; 5VZJ; X-ray; 3.30 A; D=1-223.
PDB; 6FSZ; EM; 4.60 A; DD=1-223.
PDBsum; 4IFD; -.
PDBsum; 4OO1; -.
PDBsum; 5C0W; -.
PDBsum; 5C0X; -.
PDBsum; 5G06; -.
PDBsum; 5JEA; -.
PDBsum; 5K36; -.
PDBsum; 5OKZ; -.
PDBsum; 5VZJ; -.
PDBsum; 6FSZ; -.
ProteinModelPortal; P53256; -.
SMR; P53256; -.
BioGrid; 33338; 34.
ComplexPortal; CPX-599; Nuclear/nucleolar exosome complex, DIS3-RRP6 variant.
ComplexPortal; CPX-603; Cytoplasmic exosome complex, DIS3 variant.
DIP; DIP-6838N; -.
IntAct; P53256; 23.
MINT; P53256; -.
STRING; 4932.YGR095C; -.
iPTMnet; P53256; -.
MaxQB; P53256; -.
PaxDb; P53256; -.
PRIDE; P53256; -.
EnsemblFungi; YGR095C_mRNA; YGR095C_mRNA; YGR095C.
GeneID; 852987; -.
KEGG; sce:YGR095C; -.
SGD; S000003327; RRP46.
GeneTree; ENSGT00940000153348; -.
HOGENOM; HOG000248419; -.
InParanoid; P53256; -.
KO; K12590; -.
OMA; CNYRPKA; -.
OrthoDB; EOG092C4PZH; -.
BioCyc; YEAST:G3O-30805-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.
PRO; PR:P53256; -.
Proteomes; UP000002311; Chromosome VII.
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; IBA:GO_Central.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
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; IMP: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: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:0016075; P:rRNA catabolic process; IBA:GO_Central.
GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
Gene3D; 3.30.230.70; -; 1.
InterPro; IPR001247; ExoRNase_PH_dom1.
InterPro; IPR015847; ExoRNase_PH_dom2.
InterPro; IPR036345; ExoRNase_PH_dom2_sf.
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; 1.
SUPFAM; SSF55666; SSF55666; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Exosome; Nucleus;
Reference proteome; RNA-binding; rRNA processing.
CHAIN 1 223 Exosome complex component RRP46.
/FTId=PRO_0000139978.
STRAND 4 7 {ECO:0000244|PDB:5JEA}.
STRAND 11 21 {ECO:0000244|PDB:5JEA}.
STRAND 24 34 {ECO:0000244|PDB:5JEA}.
TURN 38 40 {ECO:0000244|PDB:5JEA}.
STRAND 43 45 {ECO:0000244|PDB:5JEA}.
STRAND 47 53 {ECO:0000244|PDB:5JEA}.
STRAND 55 57 {ECO:0000244|PDB:5JEA}.
HELIX 61 77 {ECO:0000244|PDB:5JEA}.
HELIX 80 82 {ECO:0000244|PDB:5JEA}.
STRAND 87 96 {ECO:0000244|PDB:5JEA}.
TURN 101 103 {ECO:0000244|PDB:5JEA}.
HELIX 106 123 {ECO:0000244|PDB:5JEA}.
STRAND 127 139 {ECO:0000244|PDB:5JEA}.
TURN 140 142 {ECO:0000244|PDB:5JEA}.
STRAND 145 148 {ECO:0000244|PDB:5JEA}.
HELIX 151 155 {ECO:0000244|PDB:5JEA}.
STRAND 157 168 {ECO:0000244|PDB:5JEA}.
TURN 169 172 {ECO:0000244|PDB:5JEA}.
STRAND 173 186 {ECO:0000244|PDB:5JEA}.
HELIX 188 217 {ECO:0000244|PDB:5JEA}.
HELIX 218 220 {ECO:0000244|PDB:5JEA}.
SEQUENCE 223 AA; 24407 MW; F1307E0EE4FC3133 CRC64;
MSVQAEIGIL DHVDGSSEFV SQDTKVICSV TGPIEPKARQ ELPTQLALEI IVRPAKGVAT
TREKVLEDKL RAVLTPLITR HCYPRQLCQI TCQILESGED EAEFSLRELS CCINAAFLAL
VDAGIALNSM CASIPIAIIK DTSDIIVDPT AEQLKISLSV HTLALEFVNG GKVVKNVLLL
DSNGDFNEDQ LFSLLELGEQ KCQELVTNIR RIIQDNISPR LVV


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