4g0o

From Proteopedia

(Difference between revisions)

Revision as of 20:47, 25 December 2014

Crystal structure of Arabidopsis thaliana AGO5 MID domain

Structural highlights

4g0o is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	4g0m, 4g0p, 4g0q, 4g0x, 4g0y, 4g0z
Gene:	AGO5, At2g27880, T1E2.20 (Arabidopsis thaliana)
Resources:	FirstGlance, OCA, RCSB, PDBsum

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.

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4g0o"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4g0o]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G0O FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><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>
-<tr><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='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><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 Arabidopsis thaliana])</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 Arabidopsis thaliana])</td></tr>
-<tr><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://www.rcsb.org/pdb/explore.do?structureId=4g0o RCSB], [http://www.ebi.ac.uk/pdbsum/4g0o PDBsum]</span></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=4g0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g0o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g0o RCSB], [http://www.ebi.ac.uk/pdbsum/4g0o PDBsum]</span></td></tr>
-<table>
+</table>
+== 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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 26: @@
 </StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Frank, F.]]
+[[Category: Frank, F]]
-[[Category: Hauver, J.]]
+[[Category: Hauver, J]]
-[[Category: Nagar, B.]]
+[[Category: Nagar, B]]
-[[Category: Sonenberg, N.]]
+[[Category: Sonenberg, N]]
 [[Category: Gene regulation]]
 [[Category: Mid domain]]
 [[Category: Small rna 5' nucleotide recognition]]

4g0o

From Proteopedia

Revision as of 20:47, 25 December 2014

Crystal structure of Arabidopsis thaliana AGO5 MID domain

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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