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| <StructureSection load='2po1' size='340' side='right'caption='[[2po1]], [[Resolution|resolution]] 1.94Å' scene=''> | | <StructureSection load='2po1' size='340' side='right'caption='[[2po1]], [[Resolution|resolution]] 1.94Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[2po1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PO1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PO1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2po1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PO1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PO1 FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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]] 1.94Å</td></tr> |
- | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pnz|2pnz]], [[2po0|2po0]], [[2po2|2po2]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr> |
- | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rrp41 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), Rrp42 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</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=2po1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2po1 OCA], [https://pdbe.org/2po1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2po1 RCSB], [https://www.ebi.ac.uk/pdbsum/2po1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2po1 ProSAT]</span></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=2po1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2po1 OCA], [https://pdbe.org/2po1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2po1 RCSB], [https://www.ebi.ac.uk/pdbsum/2po1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2po1 ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
- | [[https://www.uniprot.org/uniprot/RRP42_PYRAB RRP42_PYRAB]] Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Contributes to the structuring of the Rrp41 active site.[HAMAP-Rule:MF_00622] [[https://www.uniprot.org/uniprot/RRP41_PYRAB RRP41_PYRAB]] Catalytic component of the exosome, which is a complex involved in RNA degradation. Has 3'->5' exoribonuclease activity. Can also synthesize heteropolymeric RNA-tails (Probable).<ref>PMID:18353775</ref>
| + | [https://www.uniprot.org/uniprot/RRP41_PYRAB RRP41_PYRAB] Catalytic component of the exosome, which is a complex involved in RNA degradation. Has 3'->5' exoribonuclease activity. Can also synthesize heteropolymeric RNA-tails (Probable).<ref>PMID:18353775</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: Pyrococcus abyssi erauso et al. 1993]] | |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
- | [[Category: Guimaraes, B G]] | + | [[Category: Pyrococcus abyssi]] |
- | [[Category: Navarro, M V.A S]] | + | [[Category: Guimaraes BG]] |
- | [[Category: Hydrolase-hydrolase-rna complex]] | + | [[Category: Navarro MVAS]] |
- | [[Category: Rnase ph]]
| + | |
| Structural highlights
Function
RRP41_PYRAB Catalytic component of the exosome, which is a complex involved in RNA degradation. Has 3'->5' exoribonuclease activity. Can also synthesize heteropolymeric RNA-tails (Probable).[1]
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
Initially identified in yeast, the exosome has emerged as a central component of the RNA maturation and degradation machinery both in Archaea and eukaryotes. Here we describe a series of high-resolution structures of the RNase PH ring from the Pyrococcus abyssi exosome, one of them containing three 10-mer RNA strands within the exosome catalytic chamber, and report additional nucleotide interactions involving positions N5 and N7. Residues from all three Rrp41-Rrp42 heterodimers interact with a single RNA molecule, providing evidence for the functional relevance of exosome ring-like assembly in RNA processivity. Furthermore, an ADP-bound structure showed a rearrangement of nucleotide interactions at site N1, suggesting a rationale for the elimination of nucleoside diphosphate after catalysis. In combination with RNA degradation assays performed with mutants of key amino acid residues, the structural data presented here provide support for a model of exosome-mediated RNA degradation that integrates the events involving catalytic cleavage, product elimination, and RNA translocation. Finally, comparisons between the archaeal and human exosome structures provide a possible explanation for the eukaryotic exosome inability to catalyze phosphate-dependent RNA degradation.
Insights into the mechanism of progressive RNA degradation by the archaeal exosome.,Navarro MV, Oliveira CC, Zanchin NI, Guimaraes BG J Biol Chem. 2008 May 16;283(20):14120-31. Epub 2008 Mar 19. PMID:18353775[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Navarro MV, Oliveira CC, Zanchin NI, Guimaraes BG. Insights into the mechanism of progressive RNA degradation by the archaeal exosome. J Biol Chem. 2008 May 16;283(20):14120-31. Epub 2008 Mar 19. PMID:18353775 doi:10.1074/jbc.M801005200
- ↑ Navarro MV, Oliveira CC, Zanchin NI, Guimaraes BG. Insights into the mechanism of progressive RNA degradation by the archaeal exosome. J Biol Chem. 2008 May 16;283(20):14120-31. Epub 2008 Mar 19. PMID:18353775 doi:10.1074/jbc.M801005200
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