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| | ==Crystal structure of Arabidopsis thaliana AGO5 MID domain== | | ==Crystal structure of Arabidopsis thaliana AGO5 MID domain== |
| - | <StructureSection load='4g0o' size='340' side='right' caption='[[4g0o]], [[Resolution|resolution]] 2.19Å' scene=''> | + | <StructureSection load='4g0o' size='340' side='right'caption='[[4g0o]], [[Resolution|resolution]] 2.19Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4g0o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G0O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G0O FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4g0o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G0O FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4g0m|4g0m]], [[4g0p|4g0p]], [[4g0q|4g0q]], [[4g0x|4g0x]], [[4g0y|4g0y]], [[4g0z|4g0z]]</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=4g0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g0o OCA], [https://pdbe.org/4g0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g0o RCSB], [https://www.ebi.ac.uk/pdbsum/4g0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g0o ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AGO5, At2g27880, T1E2.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
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| - | <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=4g0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g0o OCA], [http://pdbe.org/4g0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4g0o RCSB], [http://www.ebi.ac.uk/pdbsum/4g0o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4g0o ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/AGO5_ARATH AGO5_ARATH]] Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as a microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Associates with siRNAs of various sizes, from 21-24 nucleotide in length and preferentially recruits small RNAs with a 5' terminal cytosine. Probably involved in antiviral RNA silencing. Associates with siRNAs derived from cucumber mosaic virus (CMV). Targeted by the turnip yellows virus (TuYV) protein P0 (via F-box-like domain) for probable proteasome degradation and thereby inactivating AGO5 function in RNA silencing.<ref>PMID:17869110</ref> <ref>PMID:18342361</ref> <ref>PMID:18344228</ref> | + | [https://www.uniprot.org/uniprot/AGO5_ARATH AGO5_ARATH] Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as a microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Associates with siRNAs of various sizes, from 21-24 nucleotide in length and preferentially recruits small RNAs with a 5' terminal cytosine. Probably involved in antiviral RNA silencing. Associates with siRNAs derived from cucumber mosaic virus (CMV). Targeted by the turnip yellows virus (TuYV) protein P0 (via F-box-like domain) for probable proteasome degradation and thereby inactivating AGO5 function in RNA silencing.<ref>PMID:17869110</ref> <ref>PMID:18342361</ref> <ref>PMID:18344228</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Argonaute|Argonaute]] | + | *[[Argonaute 3D structures|Argonaute 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Frank, F]] | + | [[Category: Large Structures]] |
| - | [[Category: Hauver, J]] | + | [[Category: Frank F]] |
| - | [[Category: Nagar, B]] | + | [[Category: Hauver J]] |
| - | [[Category: Sonenberg, N]] | + | [[Category: Nagar B]] |
| - | [[Category: Gene regulation]]
| + | [[Category: Sonenberg N]] |
| - | [[Category: Mid domain]]
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| - | [[Category: Small rna 5' nucleotide recognition]]
| + | |
| Structural highlights
Function
AGO5_ARATH Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as a microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Associates with siRNAs of various sizes, from 21-24 nucleotide in length and preferentially recruits small RNAs with a 5' terminal cytosine. Probably involved in antiviral RNA silencing. Associates with siRNAs derived from cucumber mosaic virus (CMV). Targeted by the turnip yellows virus (TuYV) protein P0 (via F-box-like domain) for probable proteasome degradation and thereby inactivating AGO5 function in RNA silencing.[1] [2] [3]
Publication Abstract from PubMed
The 5'-nucleotide of small RNAs associates directly with the MID domain of Argonaute (AGO) proteins. In humans, the identity of the 5'-base is sensed by the MID domain nucleotide specificity loop and regulates the integrity of miRNAs. In Arabidopsis thaliana, the 5'-nucleotide also controls sorting of small RNAs into the appropriate member of the AGO family; however, the structural basis for this mechanism is unknown. Here, we present crystal structures of the MID domain from three Arabidopsis AGOs, AtAGO1, AtAGO2 and AtAGO5, and characterize their interactions with nucleoside monophosphates (NMPs). In AtAGOs, the nucleotide specificity loop also senses the identity of the 5'-nucleotide but uses more diverse modes of recognition owing to the greater complexity of small RNAs found in plants. Binding analyses of these interactions reveal a strong correlation between their affinities and evolutionary conservation.
Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs.,Frank F, Hauver J, Sonenberg N, Nagar B EMBO J. 2012 Jul 31. doi: 10.1038/emboj.2012.204. PMID:22850669[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Baumberger N, Tsai CH, Lie M, Havecker E, Baulcombe DC. The Polerovirus silencing suppressor P0 targets ARGONAUTE proteins for degradation. Curr Biol. 2007 Sep 18;17(18):1609-14. PMID:17869110 doi:http://dx.doi.org/10.1016/j.cub.2007.08.039
- ↑ Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell. 2008 Apr 4;133(1):116-27. doi: 10.1016/j.cell.2008.02.034. Epub 2008 Mar, 13. PMID:18342361 doi:http://dx.doi.org/10.1016/j.cell.2008.02.034
- ↑ Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y. The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol. 2008 Apr;49(4):493-500. doi: 10.1093/pcp/pcn043. Epub 2008, Mar 14. PMID:18344228 doi:http://dx.doi.org/10.1093/pcp/pcn043
- ↑ Frank F, Hauver J, Sonenberg N, Nagar B. Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs. EMBO J. 2012 Jul 31. doi: 10.1038/emboj.2012.204. PMID:22850669 doi:10.1038/emboj.2012.204
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