6w8j - Revision history

OCA at 14:18, 18 October 2023

OCA — Wed, 18 Oct 2023 14:18:46 GMT

←Older revision		Revision as of 14:18, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='6w8j' size='340' side='right'caption='[[6w8j]], [[Resolution\|resolution]] 2.44Å' scene=''>		<StructureSection load='6w8j' size='340' side='right'caption='[[6w8j]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6w8j]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W8J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6W8J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w8j]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=6W8J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W8J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SAH:S~~-~~ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.445Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=PYO:1-(BETA-D-RIBOFURANOSYL)-PYRIMIDIN-2-ONE-5-PHOSPHATE'>PYO</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DNMT3A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~, ~~DNMT3L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~<~~/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=6w8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w8j OCA], [https://pdbe.org/6w8j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w8j RCSB], [https://www.ebi.ac.uk/pdbsum/6w8j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w8j 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/DNA_(cytosine~~-5-)-~~methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37]~~ </~~span~~></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=6w8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w8j OCA], [~~http~~://pdbe.org/6w8j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6w8j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6w8j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6w8j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DNM3A_HUMAN DNM3A_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. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZNF238. Can actively repress transcription through the recruitment of HDAC activity (By similarity).<ref>PMID:16357870</ref> [[http://www.uniprot.org/uniprot/DNM3L_HUMAN DNM3L_HUMAN]] Catalytically inactive regulatory factor of DNA methyltransferases. It is essential for the function of DNMT3A and DNMT3B. Activates DNMT3A and DNMT3B by binding to their catalytic domain. Accelerates the binding of DNA and AdoMet to the methyltransferases and dissociates from the complex after DNA binding to the methyltransferases. Recognizes unmethylated histone H3 lysine 4 (H3K4) and induces de novo DNA methylation by recruitment or activation of DNMT3.<ref>PMID:17687327</ref>	+	[https://www.uniprot.org/uniprot/DNM3A_HUMAN DNM3A_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. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZNF238. Can actively repress transcription through the recruitment of HDAC activity (By similarity).<ref>PMID:16357870</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 6w8j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6w8j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA methyltransferase 3D structures\|DNA methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Anteneh, H~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Song, J~~]]	+	[[Category: Anteneh H]]
-	[[Category: ~~Aml]]~~	+	[[Category: Song J]]
-	~~[[Category: Dna methylation]]~~	+
-	~~[[Category: Epigenetic]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 06:14, 20 May 2020

OCA — Wed, 20 May 2020 06:14:23 GMT

←Older revision		Revision as of 06:14, 20 May 2020
Line 1:		Line 1:

	==Structure of DNMT3A (R882H) in complex with CAG DNA==		==Structure of DNMT3A (R882H) in complex with CAG DNA==
-	<StructureSection load='6w8j' size='340' side='right'caption='[[6w8j]]' scene=''>	+	<StructureSection load='6w8j' size='340' side='right'caption='[[6w8j]], [[Resolution\|resolution]] 2.44Å' 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=6W8J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W8J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w8j]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W8J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W8J 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=6w8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w8j OCA], [http://pdbe.org/6w8j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w8j RCSB], [http://www.ebi.ac.uk/pdbsum/6w8j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w8j ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PYO:1-(BETA-D-RIBOFURANOSYL)-PYRIMIDIN-2-ONE-5-PHOSPHATE'>PYO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DNMT3A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DNMT3L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span></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=6w8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w8j OCA], [http://pdbe.org/6w8j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w8j RCSB], [http://www.ebi.ac.uk/pdbsum/6w8j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w8j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DNM3A_HUMAN DNM3A_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. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZNF238. Can actively repress transcription through the recruitment of HDAC activity (By similarity).<ref>PMID:16357870</ref> [[http://www.uniprot.org/uniprot/DNM3L_HUMAN DNM3L_HUMAN]] Catalytically inactive regulatory factor of DNA methyltransferases. It is essential for the function of DNMT3A and DNMT3B. Activates DNMT3A and DNMT3B by binding to their catalytic domain. Accelerates the binding of DNA and AdoMet to the methyltransferases and dissociates from the complex after DNA binding to the methyltransferases. Recognizes unmethylated histone H3 lysine 4 (H3K4) and induces de novo DNA methylation by recruitment or activation of DNMT3.<ref>PMID:17687327</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA methyltransferase DNMT3A is essential for establishment of mammalian DNA methylation during development. The R882H DNMT3A is a hotspot mutation in acute myeloid leukemia (AML) causing aberrant DNA methylation. However, how this mutation affects the structure and function of DNMT3A remains unclear. Here we report structural characterization of wild-type and R882H-mutated DNMT3A in complex with DNA substrates with different sequence contexts. A loop from the target recognition domain (TRD loop) recognizes the CpG dinucleotides in a +1 flanking site-dependent manner. The R882H mutation reduces the DNA binding at the homodimeric interface, as well as the molecular link between the homodimeric interface and TRD loop, leading to enhanced dynamics of TRD loop. Consistently, in vitro methylation analyses indicate that the R882H mutation compromises the enzymatic activity, CpG specificity and flanking sequence preference of DNMT3A. Together, this study uncovers multiple defects of DNMT3A caused by the R882H mutation in AML.
		+
		+	Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation.,Anteneh H, Fang J, Song J Nat Commun. 2020 May 8;11(1):2294. doi: 10.1038/s41467-020-16213-9. PMID:32385248<ref>PMID:32385248</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6w8j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Anteneh H]]	+	[[Category: Anteneh, H]]
-	[[Category: Song J]]	+	[[Category: Song, J]]
		+	[[Category: Aml]]
		+	[[Category: Dna methylation]]
		+	[[Category: Epigenetic]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-dna complex]]

OCA at 07:04, 15 April 2020

OCA — Wed, 15 Apr 2020 07:04:20 GMT

←Older revision		Revision as of 07:04, 15 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6w8j ~~is ON HOLD~~	+	==Structure of DNMT3A (R882H) in complex with CAG DNA==
-		+	<StructureSection load='6w8j' size='340' side='right'caption='[[6w8j]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W8J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W8J FirstGlance]. <br>
-	~~Description~~:	+	</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=6w8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w8j OCA], [http://pdbe.org/6w8j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w8j RCSB], [http://www.ebi.ac.uk/pdbsum/6w8j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w8j ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Anteneh H]]
		+	[[Category: Song J]]

OCA: Protected "6w8j" [edit=sysop:move=sysop]

OCA — Wed, 01 Apr 2020 07:27:37 GMT

Protected "6w8j" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:27, 1 April 2020

OCA: New page: '''Unreleased structure''' The entry 6w8j is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Apr 2020 07:27:36 GMT

New page: '''Unreleased structure''' The entry 6w8j is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6w8j is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]