6a5n - Revision history

OCA at 09:18, 22 November 2023

2023-11-22T09:18:54Z

←Older revision		Revision as of 09:18, 22 November 2023
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	==Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA==		==Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA==
-	<StructureSection load='6a5n' size='340' side='right' caption='[[6a5n]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='6a5n' size='340' side='right'caption='[[6a5n]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a5n]] is a 3 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=6A5N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6A5N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a5n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A5N FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ZN:ZINC+ION'>ZN</scene~~></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]] 2.4Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUVH6~~, ~~SDG23, SET23, At2g22740, T9I22.18 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])~~<~~/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=6a5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a5n OCA], [https://pdbe.org/6a5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a5n RCSB], [https://www.ebi.ac.uk/pdbsum/6a5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a5n ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43]~~ </~~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=6a5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a5n OCA], [~~http~~://pdbe.org/6a5n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6a5n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6a5n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6a5n ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SUVH6_ARATH SUVH6_ARATH]] Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Seems to act preferentially on dsMRNA.<ref>PMID:15014946</ref> <ref>PMID:16287862</ref>	+	[https://www.uniprot.org/uniprot/SUVH6_ARATH SUVH6_ARATH] Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Seems to act preferentially on dsMRNA.<ref>PMID:15014946</ref> <ref>PMID:16287862</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6a5n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6a5n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone methyltransferase 3D structures\|Histone methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
-	[[Category: ~~Histone-lysine N-methyltransferase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Du, J~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Li, X~~]]	+	[[Category: Du J]]
-	[[Category: ~~Dna methylation]]~~	+	[[Category: Li X]]
-	~~[[Category: Gene regulation]]~~	+
-	~~[[Category: Gene regulation-dna complex]]~~	+
-	~~[[Category: Histone methyltransferase]]~~	+
-	~~[[Category: Set]]~~	+
-	~~[[Category: Sra~~]]	+

OCA at 20:15, 19 September 2018

2018-09-19T20:15:10Z

←Older revision		Revision as of 20:15, 19 September 2018
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	<StructureSection load='6a5n' size='340' side='right' caption='[[6a5n]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6a5n' size='340' side='right' caption='[[6a5n]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a5n]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A5N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a5n]] is a 3 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=6A5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A5N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUVH6, SDG23, SET23, At2g22740, T9I22.18 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </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=6a5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a5n OCA], [http://pdbe.org/6a5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a5n RCSB], [http://www.ebi.ac.uk/pdbsum/6a5n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a5n ProSAT]</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=6a5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a5n OCA], [http://pdbe.org/6a5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a5n RCSB], [http://www.ebi.ac.uk/pdbsum/6a5n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a5n ProSAT]</span></td></tr>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SUVH6_ARATH SUVH6_ARATH]] Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Seems to act preferentially on dsMRNA.<ref>PMID:15014946</ref> <ref>PMID:16287862</ref>		[[http://www.uniprot.org/uniprot/SUVH6_ARATH SUVH6_ARATH]] Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Seems to act preferentially on dsMRNA.<ref>PMID:15014946</ref> <ref>PMID:16287862</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA methylation functions in gene silencing and the maintenance of genome integrity. In plants, non-CG DNA methylation is linked through a self-reinforcing loop with histone 3 lysine 9 dimethylation (H3K9me2). The plant-specific SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG (SUVH) family H3K9 methyltransferases (MTases) bind to DNA methylation marks and catalyze H3K9 methylation. Here, we analyzed the structure and function of Arabidopsis thaliana SUVH6 to understand how this class of enzyme maintains methylation patterns in the genome. We reveal that SUVH6 has a distinct 5-methyl-dC (5mC) base-flipping mechanism involving a thumb loop element. Autoinhibition of H3 substrate entry is regulated by a SET domain loop, and a conformational transition in the post-SET domain upon cofactor binding may control catalysis. In vitro DNA binding and in vivo ChIP-seq data reveal that the different SUVH family H3K9 MTases have distinct DNA binding preferences, targeting H3K9 methylation to sites with different methylated DNA sequences, explaining the context biased non-CG DNA methylation in plants.
		+
		+	Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.,Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang Z, Li S, Jacobsen SE, Du J Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8793-E8802. doi:, 10.1073/pnas.1809841115. Epub 2018 Aug 27. PMID:30150382<ref>PMID:30150382</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6a5n" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Histone-lysine N-methyltransferase]]		[[Category: Histone-lysine N-methyltransferase]]
	[[Category: Du, J]]		[[Category: Du, J]]

OCA at 07:23, 29 August 2018

2018-08-29T07:23:17Z

←Older revision		Revision as of 07:23, 29 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6a5n is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA==
-		+	<StructureSection load='6a5n' size='340' side='right' caption='[[6a5n]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~: Li, X., Du, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6a5n]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A5N FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~Arabidopsis thaliana SUVH6 in complex with methylated DNA~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </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=6a5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a5n OCA], [http://pdbe.org/6a5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a5n RCSB], [http://www.ebi.ac.uk/pdbsum/6a5n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a5n ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SUVH6_ARATH SUVH6_ARATH]] Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Seems to act preferentially on dsMRNA.<ref>PMID:15014946</ref> <ref>PMID:16287862</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Histone-lysine N-methyltransferase]]
	[[Category: Du, J]]		[[Category: Du, J]]
	[[Category: Li, X]]		[[Category: Li, X]]
		+	[[Category: Dna methylation]]
		+	[[Category: Gene regulation]]
		+	[[Category: Gene regulation-dna complex]]
		+	[[Category: Histone methyltransferase]]
		+	[[Category: Set]]
		+	[[Category: Sra]]

OCA at 03:55, 11 July 2018

2018-07-11T03:55:40Z

←Older revision		Revision as of 03:55, 11 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6a5n is ON HOLD	+	The entry 6a5n is ON HOLD until Paper Publication

	Authors: Li, X., Du, J.		Authors: Li, X., Du, J.

-	Description: ~~crystal~~ structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA	+	Description: Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Du, J]]		[[Category: Du, J]]
	[[Category: Li, X]]		[[Category: Li, X]]

OCA: Protected "6a5n" [edit=sysop:move=sysop]

2018-07-04T05:32:37Z

Protected "6a5n" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:32, 4 July 2018

OCA: New page: '''Unreleased structure''' The entry 6a5n is ON HOLD Authors: Li, X., Du, J. Description: crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA [[Category: Unr...

2018-07-04T05:32:36Z

New page: '''Unreleased structure''' The entry 6a5n is ON HOLD Authors: Li, X., Du, J. Description: crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA [[Category: Unr...

New page

'''Unreleased structure'''

The entry 6a5n is ON HOLD

Authors: Li, X., Du, J.

Description: crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA
[[Category: Unreleased Structures]]
[[Category: Du, J]]
[[Category: Li, X]]