OCA at 15:37, 18 October 2023

2023-10-18T15:37:44Z

←Older revision		Revision as of 15:37, 18 October 2023
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-	====	+	==Crystal structure of the DRM2-CCT DNA complex==
-	<StructureSection load='7l4m' size='340' side='right'caption='[[7l4m]]' scene=''>	+	<StructureSection load='7l4m' size='340' side='right'caption='[[7l4m]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7l4m]] is a 6 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=7L4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L4M FirstGlance]. <br>
-	</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=7l4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l4m OCA], [https://pdbe.org/7l4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l4m RCSB], [https://www.ebi.ac.uk/pdbsum/7l4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l4m ProSAT]</span></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]] 2.805Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></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=7l4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l4m OCA], [https://pdbe.org/7l4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l4m RCSB], [https://www.ebi.ac.uk/pdbsum/7l4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l4m ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DRM2_ARATH DRM2_ARATH] Involved in de novo DNA methylation. Controls asymmetric and CpNpG methylation. Required for FWA gene silencing but not for the maintenance of SUP gene silencing. Functionally redundant to CMT3 to maintain non-CpG methylation. Involved in RNA-directed DNA methylation (RdDM) (PubMed:12121623, PubMed:12151602, PubMed:14680640). Acts as major DNA methyltransferase in the RdDM pathway, and is essential for RNA-directed de novo DNA methylation of cytosines in all sequence contexts (PubMed:21060858, PubMed:21212233). Associates with long non-coding RNA (lncRNA) produced by RNA polymerase V (Pol V). This association is dependent on AGO4 and IDN2, and results in DNA methylation of RdDM target loci (PubMed:24862207).<ref>PMID:12121623</ref> <ref>PMID:12151602</ref> <ref>PMID:14680640</ref> <ref>PMID:21060858</ref> <ref>PMID:21212233</ref> <ref>PMID:24862207</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA methylation is a major epigenetic mechanism critical for gene expression and genome stability. In plants, domains rearranged methyltransferase 2 (DRM2) preferentially mediates CHH (H = C, T, or A) methylation, a substrate specificity distinct from that of mammalian DNA methyltransferases. However, the underlying mechanism is unknown. Here, we report structure-function characterization of DRM2-mediated methylation. An arginine finger from the catalytic loop intercalates into the nontarget strand of DNA through the minor groove, inducing large DNA deformation that affects the substrate preference of DRM2. The target recognition domain stabilizes the enlarged major groove via shape complementarity rather than base-specific interactions, permitting substrate diversity. The engineered DRM2 C397R mutation introduces base-specific contacts with the +2-flanking guanine, thereby shifting the substrate specificity of DRM2 toward CHG DNA. Together, this study uncovers DNA deformation as a mechanism in regulating the specificity of DRM2 toward diverse CHH substrates and illustrates methylome complexity in plants.
		+
		+	Substrate deformation regulates DRM2-mediated DNA methylation in plants.,Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X, Song J Sci Adv. 2021 Jun 2;7(23):eabd9224. doi: 10.1126/sciadv.abd9224. Print 2021 Jun. PMID:34078593<ref>PMID:34078593</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7l4m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Fang J]]
		+	[[Category: Song J]]

OCA at 10:19, 4 August 2021

2021-08-04T10:19:23Z

←Older revision		Revision as of 10:19, 4 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7l4m ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7l4m' size='340' side='right'caption='[[7l4m]]' scene=''>
-	~~Authors~~: ~~Fang, J~~.~~, Song, J~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of the DRM2~~-~~CCT DNA complex~~	+	</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=7l4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l4m OCA], [https://pdbe.org/7l4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l4m RCSB], [https://www.ebi.ac.uk/pdbsum/7l4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l4m ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Song, J~~]]	+	__TOC__
-	[[Category: ~~Fang, J~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 06:44, 27 January 2021

2021-01-27T06:44:19Z

←Older revision		Revision as of 06:44, 27 January 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7l4m is ON HOLD	+	The entry 7l4m is ON HOLD until Paper Publication

	Authors: Fang, J., Song, J.		Authors: Fang, J., Song, J.

OCA: Protected "7l4m" [edit=sysop:move=sysop]

2020-12-30T05:30:20Z

Protected "7l4m" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:30, 30 December 2020

OCA: New page: '''Unreleased structure''' The entry 7l4m is ON HOLD Authors: Fang, J., Song, J. Description: Crystal structure of the DRM2-CCT DNA complex Category: Unreleased Structures [[Catego...

2020-12-30T05:30:19Z

New page: '''Unreleased structure''' The entry 7l4m is ON HOLD Authors: Fang, J., Song, J. Description: Crystal structure of the DRM2-CCT DNA complex Category: Unreleased Structures [[Catego...

New page

'''Unreleased structure'''

The entry 7l4m is ON HOLD

Authors: Fang, J., Song, J.

Description: Crystal structure of the DRM2-CCT DNA complex
[[Category: Unreleased Structures]]
[[Category: Song, J]]
[[Category: Fang, J]]

7l4m - Revision history

OCA at 15:37, 18 October 2023

OCA at 10:19, 4 August 2021

OCA at 06:44, 27 January 2021

OCA: Protected "7l4m" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7l4m is ON HOLD Authors: Fang, J., Song, J. Description: Crystal structure of the DRM2-CCT DNA complex Category: Unreleased Structures [[Catego...