7yta

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m (Protected "7yta" [edit=sysop:move=sysop])
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'''Unreleased structure'''
 
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The entry 7yta is ON HOLD until Paper Publication
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==crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide==
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<StructureSection load='7yta' size='340' side='right'caption='[[7yta]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[7yta]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YTA FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7yta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yta OCA], [https://pdbe.org/7yta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yta RCSB], [https://www.ebi.ac.uk/pdbsum/7yta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yta ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/A0A1S4CD95_TOBAC A0A1S4CD95_TOBAC]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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Authors:
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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>
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Description:
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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<div class="pdbe-citations 7yta" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Arabidopsis thaliana]]
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[[Category: Large Structures]]
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[[Category: Nicotiana tabacum]]
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[[Category: Du J]]
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[[Category: Zhou X]]

Revision as of 07:48, 11 January 2023

crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide

PDB ID 7yta

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