6u8w - Revision history

OCA at 07:46, 11 October 2023

OCA — Wed, 11 Oct 2023 07:46:34 GMT

←Older revision		Revision as of 07:46, 11 October 2023
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	==Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA==		==Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA==
-	<StructureSection load='6u8w' size='340' side='right'caption='[[6u8w]]' scene=''>	+	<StructureSection load='6u8w' size='340' side='right'caption='[[6u8w]], [[Resolution\|resolution]] 2.95Å' 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=6U8W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6U8W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u8w]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U8W FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6u8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8w OCA], [~~http~~://pdbe.org/6u8w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u8w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u8w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8w 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]] 2.9489155Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYO:1-(BETA-D-RIBOFURANOSYL)-PYRIMIDIN-2-ONE-5-PHOSPHATE'>PYO</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=6u8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8w OCA], [https://pdbe.org/6u8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u8w RCSB], [https://www.ebi.ac.uk/pdbsum/6u8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8w ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN] ICF syndrome. The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:10647011</ref> <ref>PMID:10555141</ref> <ref>PMID:10588719</ref> <ref>PMID:11102980</ref> <ref>PMID:15580563</ref>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN] Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1.<ref>PMID:16357870</ref> <ref>PMID:17303076</ref> <ref>PMID:18413740</ref> <ref>PMID:18567530</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mammalian DNA methylation patterns are established by two de novo DNA methyltransferases, DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.
		+
		+	Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms.,Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S, Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H, Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang GG, Jeltsch A, Song J Nat Commun. 2020 Jul 3;11(1):3355. doi: 10.1038/s41467-020-17109-4. PMID:32620778<ref>PMID:32620778</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6u8w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA methyltransferase 3D structures\|DNA methyltransferase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gao L]]		[[Category: Gao L]]
	[[Category: Song J]]		[[Category: Song J]]
	[[Category: Zhang ZM]]		[[Category: Zhang ZM]]

OCA at 06:27, 10 June 2020

OCA — Wed, 10 Jun 2020 06:27:10 GMT

←Older revision		Revision as of 06:27, 10 June 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6u8w ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA==
-		+	<StructureSection load='6u8w' size='340' side='right'caption='[[6u8w]]' scene=''>
-	~~Authors~~: ~~Gao~~, L., ~~Zhang~~, Z.M., ~~Song~~, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U8W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U8W FirstGlance]. <br>
-	~~Description: Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6u8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8w OCA], [http://pdbe.org/6u8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u8w RCSB], [http://www.ebi.ac.uk/pdbsum/6u8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8w ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Song, J~~]]	+	__TOC__
-	[[Category: ~~Gao, L~~]]	+	</StructureSection>
-	[[Category: Zhang~~, Z.M~~]]	+	[[Category: Large Structures]]
		+	[[Category: Gao L]]
		+	[[Category: Song J]]
		+	[[Category: Zhang ZM]]

OCA at 06:01, 11 March 2020

OCA — Wed, 11 Mar 2020 06:01:50 GMT

←Older revision		Revision as of 06:01, 11 March 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u8w is ON HOLD	+	The entry 6u8w is ON HOLD until Paper Publication

	Authors: Gao, L., Zhang, Z.M., Song, J.		Authors: Gao, L., Zhang, Z.M., Song, J.

OCA at 05:33, 4 March 2020

OCA — Wed, 04 Mar 2020 05:33:27 GMT

←Older revision		Revision as of 05:33, 4 March 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u8w is ON HOLD ~~until Paper Publication~~	+	The entry 6u8w is ON HOLD

	Authors: Gao, L., Zhang, Z.M., Song, J.		Authors: Gao, L., Zhang, Z.M., Song, J.

OCA: Protected "6u8w" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 08:24:36 GMT

Protected "6u8w" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:24, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6u8w is ON HOLD until Paper Publication Authors: Gao, L., Zhang, Z.M., Song, J. Description: Crystal structure of DNMT3B(K777A)-DNMT3L in complex w...

OCA — Wed, 02 Oct 2019 08:24:35 GMT

New page: '''Unreleased structure''' The entry 6u8w is ON HOLD until Paper Publication Authors: Gao, L., Zhang, Z.M., Song, J. Description: Crystal structure of DNMT3B(K777A)-DNMT3L in complex w...

New page

'''Unreleased structure'''

The entry 6u8w is ON HOLD until Paper Publication

Authors: Gao, L., Zhang, Z.M., Song, J.

Description: Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA
[[Category: Unreleased Structures]]
[[Category: Song, J]]
[[Category: Gao, L]]
[[Category: Zhang, Z.M]]