View source for 7yt9


==crystal structure of AGD1-4 of Arabidopsis AGDP3==
<StructureSection load='7yt9' size='340' side='right'caption='[[7yt9]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7yt9]] 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=7YT9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YT9 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</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=7yt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yt9 OCA], [https://pdbe.org/7yt9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yt9 RCSB], [https://www.ebi.ac.uk/pdbsum/7yt9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yt9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/F4IL23_ARATH F4IL23_ARATH] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA methylation, a conserved epigenetic mark, is critical for tuning temporal and spatial gene expression. The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1) initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci. However, how ROS1 is recruited to specific loci is not well understood. Here, we report the discovery of Arabidopsis AGENET Domain Containing Protein 3 (AGDP3) as a cellular factor that is required to prevent gene silencing and DNA hypermethylation. AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette. Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3K9 and unmodified H3K4 are specifically anchored into two different surface pockets. A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity. Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.

The H3K9me2-binding protein AGDP3 limits DNA methylation and transcriptional gene silencing in Arabidopsis.,Zhou X, Wei M, Nie W, Xi Y, Peng L, Zheng Q, Tang K, Satheesh V, Wang Y, Luo J, Du X, Liu R, Yang Z, La H, Zhong Y, Yang Y, Zhu JK, Du J, Lei M J Integr Plant Biol. 2022 Dec;64(12):2385-2395. doi: 10.1111/jipb.13369. Epub , 2022 Oct 21. PMID:36149781<ref>PMID:36149781</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7yt9" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Du J]]
[[Category: Zhou X]]