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| | <StructureSection load='2ja9' size='340' side='right'caption='[[2ja9]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='2ja9' size='340' side='right'caption='[[2ja9]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2ja9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JA9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JA9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2ja9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JA9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JA9 FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ja9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja9 OCA], [https://pdbe.org/2ja9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ja9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ja9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ja9 ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ja9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja9 OCA], [https://pdbe.org/2ja9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ja9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ja9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ja9 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RRP40_YEAST RRP40_YEAST]] 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.<ref>PMID:10465791</ref> <ref>PMID:17173052</ref> <ref>PMID:19060898</ref>
| + | [https://www.uniprot.org/uniprot/RRP40_YEAST RRP40_YEAST] 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.<ref>PMID:10465791</ref> <ref>PMID:17173052</ref> <ref>PMID:19060898</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Basquin, J]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Conti, E]] | + | [[Category: Basquin J]] |
| - | [[Category: Gasch, A]] | + | [[Category: Conti E]] |
| - | [[Category: Lorentzen, E]] | + | [[Category: Gasch A]] |
| - | [[Category: Oddone, A]] | + | [[Category: Lorentzen E]] |
| - | [[Category: Rybin, V]] | + | [[Category: Oddone A]] |
| - | [[Category: Sattler, M]] | + | [[Category: Rybin V]] |
| - | [[Category: Exonuclease]]
| + | [[Category: Sattler M]] |
| - | [[Category: Exosome]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Kh domain]]
| + | |
| - | [[Category: Nuclear protein]]
| + | |
| - | [[Category: Nuclease]]
| + | |
| - | [[Category: Nucleic-acid binding]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Rna binding protein]]
| + | |
| - | [[Category: Rna-binding]]
| + | |
| - | [[Category: Rna-binding protein]]
| + | |
| - | [[Category: Rrna processing]]
| + | |
| - | [[Category: S1 domain]]
| + | |
| Structural highlights
Function
RRP40_YEAST 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.[1] [2] [3]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The exosome is a protein complex that is important in both degradation and 3'-processing of eukaryotic RNAs. We present the crystal structure of the Rrp40 exosome subunit from Saccharomyces cerevisiae at a resolution of 2.2 A. The structure comprises an S1 domain and an unusual KH (K homology) domain. Close packing of the S1 and KH domains is stabilized by a GxNG sequence, which is uniquely conserved in exosome KH domains. Nuclear magnetic resonance data reveal the presence of a manganese-binding site at the interface of the two domains. Isothermal titration calorimetry shows that Rrp40 and archaeal Rrp4 alone have very low intrinsic affinity for RNA. The affinity of an archaeal core exosome for RNA is significantly increased in the presence of the S1-KH subunit Rrp4, indicating that multiple subunits might contribute to cooperative binding of RNA substrates by the exosome.
Structural and biochemical characterization of the yeast exosome component Rrp40.,Oddone A, Lorentzen E, Basquin J, Gasch A, Rybin V, Conti E, Sattler M EMBO Rep. 2007 Jan;8(1):63-9. Epub 2006 Dec 8. PMID:17159918[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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. 1999 Aug 15;13(16):2148-58. PMID:10465791
- ↑ Dziembowski A, Lorentzen E, Conti E, Seraphin B. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat Struct Mol Biol. 2007 Jan;14(1):15-22. Epub 2006 Dec 17. PMID:17173052 doi:http://dx.doi.org/nsmb1184
- ↑ Schaeffer D, Tsanova B, Barbas A, Reis FP, Dastidar EG, Sanchez-Rotunno M, Arraiano CM, van Hoof A. The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nat Struct Mol Biol. 2009 Jan;16(1):56-62. doi: 10.1038/nsmb.1528. Epub 2008 Dec , 7. PMID:19060898 doi:http://dx.doi.org/10.1038/nsmb.1528
- ↑ Oddone A, Lorentzen E, Basquin J, Gasch A, Rybin V, Conti E, Sattler M. Structural and biochemical characterization of the yeast exosome component Rrp40. EMBO Rep. 2007 Jan;8(1):63-9. Epub 2006 Dec 8. PMID:17159918
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