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| | ==Crystal Structure of rice(Oryza sativa) Rrp46== | | ==Crystal Structure of rice(Oryza sativa) Rrp46== |
| - | <StructureSection load='3hkm' size='340' side='right' caption='[[3hkm]], [[Resolution|resolution]] 1.98Å' scene=''> | + | <StructureSection load='3hkm' size='340' side='right'caption='[[3hkm]], [[Resolution|resolution]] 1.98Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3hkm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HKM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3hkm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HKM FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">putative exonuclease RRP46 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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]] 1.9845Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hkm OCA], [http://pdbe.org/3hkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hkm RCSB], [http://www.ebi.ac.uk/pdbsum/3hkm PDBsum]</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=3hkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hkm OCA], [https://pdbe.org/3hkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hkm RCSB], [https://www.ebi.ac.uk/pdbsum/3hkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hkm ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/EXOS5_ORYSJ EXOS5_ORYSJ]] Probable component of the exosome 3'->5' exoribonuclease complex, a complex that degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3'-untranslated regions. May form a homodimer separately from exosome complexes and function in DNA cleavage process. Binds double-stranded DNA (dsDNA) and single-stranded RNA (ssRNA), and possesses hydrolytic DNase and phosphorolytic RNase activities in vitro.<ref>PMID:20660080</ref> | + | [https://www.uniprot.org/uniprot/EXOS5_ORYSJ EXOS5_ORYSJ] Probable component of the exosome 3'->5' exoribonuclease complex, a complex that degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3'-untranslated regions. May form a homodimer separately from exosome complexes and function in DNA cleavage process. Binds double-stranded DNA (dsDNA) and single-stranded RNA (ssRNA), and possesses hydrolytic DNase and phosphorolytic RNase activities in vitro.<ref>PMID:20660080</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hk/3hkm_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hk/3hkm_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Japanese rice]] | + | [[Category: Large Structures]] |
| - | [[Category: Doudeva, L G]] | + | [[Category: Oryza sativa Japonica Group]] |
| - | [[Category: Hsiao, Y Y]] | + | [[Category: Doudeva LG]] |
| - | [[Category: Wang, Y T]] | + | [[Category: Hsiao Y-Y]] |
| - | [[Category: Yang, C C]] | + | [[Category: Wang Y-T]] |
| - | [[Category: Yuan, H S]] | + | [[Category: Yang C-C]] |
| - | [[Category: Hydrolase]]
| + | [[Category: Yuan HS]] |
| - | [[Category: Phosphorylase]]
| + | |
| - | [[Category: Rnase ph domain]]
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| Structural highlights
Function
EXOS5_ORYSJ Probable component of the exosome 3'->5' exoribonuclease complex, a complex that degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3'-untranslated regions. May form a homodimer separately from exosome complexes and function in DNA cleavage process. Binds double-stranded DNA (dsDNA) and single-stranded RNA (ssRNA), and possesses hydrolytic DNase and phosphorolytic RNase activities in vitro.[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
Rrp46 was first identified as a protein component of the eukaryotic exosome, a protein complex involved in 3' processing of RNA during RNA turnover and surveillance. The Rrp46 homolog, CRN-5, was subsequently characterized as a cell death-related nuclease, participating in DNA fragmentation during apoptosis in Caenorhabditis elegans. Here we report the crystal structures of CRN-5 and rice Rrp46 (oRrp46) at a resolution of 3.9 A and 2.0 A, respectively. We found that recombinant human Rrp46 (hRrp46), oRrp46, and CRN-5 are homodimers, and that endogenous hRrp46 and oRrp46 also form homodimers in a cellular environment, in addition to their association with a protein complex. Dimeric oRrp46 had both phosphorolytic RNase and hydrolytic DNase activities, whereas hRrp46 and CRN-5 bound to DNA without detectable nuclease activity. Site-directed mutagenesis in oRrp46 abolished either its DNase (E160Q) or RNase (K75E/Q76E) activities, confirming the critical importance of these residues in catalysis or substrate binding. Moreover, CRN-5 directly interacted with the apoptotic nuclease CRN-4 and enhanced the DNase activity of CRN-4, suggesting that CRN-5 cooperates with CRN-4 in apoptotic DNA degradation. Taken together all these results strongly suggest that Rrp46 forms a homodimer separately from exosome complexes and, depending on species, is either a structural or catalytic component of the machinery that cleaves DNA during apoptosis.
Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation.,Yang CC, Wang YT, Hsiao YY, Doudeva LG, Kuo PH, Chow SY, Yuan HS RNA. 2010 Sep;16(9):1748-59. Epub 2010 Jul 21. PMID:20660080[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yang CC, Wang YT, Hsiao YY, Doudeva LG, Kuo PH, Chow SY, Yuan HS. Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation. RNA. 2010 Sep;16(9):1748-59. Epub 2010 Jul 21. PMID:20660080 doi:10.1261/rna.2180810
- ↑ Yang CC, Wang YT, Hsiao YY, Doudeva LG, Kuo PH, Chow SY, Yuan HS. Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation. RNA. 2010 Sep;16(9):1748-59. Epub 2010 Jul 21. PMID:20660080 doi:10.1261/rna.2180810
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