6kdt - Revision history

OCA at 10:31, 22 November 2023

OCA — Wed, 22 Nov 2023 10:31:31 GMT

←Older revision		Revision as of 10:31, 22 November 2023
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	<StructureSection load='6kdt' size='340' side='right'caption='[[6kdt]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='6kdt' size='340' side='right'caption='[[6kdt]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kdt]] is a 4 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=6KDT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KDT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kdt]] is a 4 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=6KDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KDT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>~~, ~~<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]] 2.87Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DNMT3B ([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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6kdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kdt OCA], [https://pdbe.org/6kdt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kdt RCSB], [https://www.ebi.ac.uk/pdbsum/6kdt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kdt ProSAT]</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=6kdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kdt OCA], [~~http~~://pdbe.org/6kdt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kdt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kdt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kdt ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://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>	+	[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 ==		== Function ==
-	[~~[http~~://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> [[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/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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6kdt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kdt" 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: Chen, Y P]]	+	[[Category: Chen Y-P]]
-	[[Category: Lin, C C]]	+	[[Category: Lin C-C]]
-	[[Category: Shen, C K]]	+	[[Category: Shen C-K]]
-	[[Category: Yang, W Z]]	+	[[Category: Yang W-Z]]
-	[[Category: Yuan~~, H S]]~~	+	[[Category: Yuan HS]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Dna methyltransferase]]~~	+
-	~~[[Category: Dnmt3b]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:01, 22 April 2020

OCA — Wed, 22 Apr 2020 06:01:19 GMT

←Older revision		Revision as of 06:01, 22 April 2020
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	<StructureSection load='6kdt' size='340' side='right'caption='[[6kdt]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='6kdt' size='340' side='right'caption='[[6kdt]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kdt]] is a 4 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=6KDT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KDT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kdt]] is a 4 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=6KDT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KDT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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">DNMT3B ([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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DNMT3B ([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='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://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6kdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kdt OCA], [http://pdbe.org/6kdt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kdt RCSB], [http://www.ebi.ac.uk/pdbsum/6kdt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kdt ProSAT]</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=6kdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kdt OCA], [http://pdbe.org/6kdt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kdt RCSB], [http://www.ebi.ac.uk/pdbsum/6kdt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kdt ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 07:08, 4 March 2020

OCA — Wed, 04 Mar 2020 07:08:47 GMT

←Older revision		Revision as of 07:08, 4 March 2020
Line 3:		Line 3:
	<StructureSection load='6kdt' size='340' side='right'caption='[[6kdt]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='6kdt' size='340' side='right'caption='[[6kdt]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kdt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KDT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kdt]] is a 4 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=6KDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KDT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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">DNMT3B ([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='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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6kdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kdt OCA], [http://pdbe.org/6kdt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kdt RCSB], [http://www.ebi.ac.uk/pdbsum/6kdt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kdt 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=6kdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kdt OCA], [http://pdbe.org/6kdt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kdt RCSB], [http://www.ebi.ac.uk/pdbsum/6kdt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kdt ProSAT]</span></td></tr>
Line 12:		Line 13:
	== Function ==		== Function ==
	[[http://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> [[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>		[[http://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> [[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 methyltransferases are primary enzymes for cytosine methylation at CpG sites of epigenetic gene regulation in mammals. De novo methyltransferases DNMT3A and DNMT3B create DNA methylation patterns during development, but how they differentially implement genomic DNA methylation patterns is poorly understood. Here, we report crystal structures of the catalytic domain of human DNMT3B-3L complex, noncovalently bound with and without DNA of different sequences. Human DNMT3B uses two flexible loops to enclose DNA and employs its catalytic loop to flip out the cytosine base. As opposed to DNMT3A, DNMT3B specifically recognizes DNA with CpGpG sites via residues Asn779 and Lys777 in its more stable and well-ordered target recognition domain loop to facilitate processive methylation of tandemly repeated CpG sites. We also identify a proton wire water channel for the final deprotonation step, revealing the complete working mechanism for cytosine methylation by DNMT3B and providing the structural basis for DNMT3B mutation-induced hypomethylation in immunodeficiency, centromere instability and facial anomalies syndrome.
		+
		+	Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.,Lin CC, Chen YP, Yang WZ, Shen JCK, Yuan HS Nucleic Acids Res. 2020 Feb 21. pii: 5742902. doi: 10.1093/nar/gkaa111. PMID:32083663<ref>PMID:32083663</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kdt" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chen, Y P]]		[[Category: Chen, Y P]]

OCA at 06:20, 19 February 2020

OCA — Wed, 19 Feb 2020 06:20:44 GMT

←Older revision		Revision as of 06:20, 19 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kdt ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of human DNMT3B (Q772R)-DNMT3L complex==
-		+	<StructureSection load='6kdt' size='340' side='right'caption='[[6kdt]], [[Resolution\|resolution]] 2.87Å' scene=''>
-	~~Authors~~: ~~Lin, C~~.-C.~~, Chen, Y~~.-P., ~~Yang~~, W.-Z., ~~Shen, C~~.-K., ~~Yuan~~, H.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6kdt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KDT FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~human DNMT3B~~ (~~Q772R~~)~~-DNMT3L complex~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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>
-	[[Category: ~~Lin, C.-C~~]]	+	<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=6kdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kdt OCA], [http://pdbe.org/6kdt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kdt RCSB], [http://www.ebi.ac.uk/pdbsum/6kdt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kdt ProSAT]</span></td></tr>
-	[[Category: Chen, Y.-P]]	+	</table>
-	[[Category: ~~Yuan~~, ~~H.S~~]]	+	== Disease ==
-	[[Category: Shen, C.-K]]	+	[[http://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>
-	[[Category: Yang, W.-Z]]	+	== Function ==
		+	[[http://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> [[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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen, Y P]]
		+	[[Category: Lin, C C]]
		+	[[Category: Shen, C K]]
		+	[[Category: Yang, W Z]]
		+	[[Category: Yuan, H S]]
		+	[[Category: Complex]]
		+	[[Category: Dna methyltransferase]]
		+	[[Category: Dnmt3b]]
		+	[[Category: Transferase]]

OCA at 04:12, 24 July 2019

OCA — Wed, 24 Jul 2019 04:12:13 GMT

←Older revision		Revision as of 04:12, 24 July 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Lin, C.-C., Chen, Y.-P., Yang, W.-Z., Shen, C.-K., Yuan, H.S.		Authors: Lin, C.-C., Chen, Y.-P., Yang, W.-Z., Shen, C.-K., Yuan, H.S.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Lin, C.-C]]		[[Category: Lin, C.-C]]
-	[[Category: Shen, C.-K]]
	[[Category: Chen, Y.-P]]		[[Category: Chen, Y.-P]]
	[[Category: Yuan, H.S]]		[[Category: Yuan, H.S]]
		+	[[Category: Shen, C.-K]]
	[[Category: Yang, W.-Z]]		[[Category: Yang, W.-Z]]

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

OCA — Wed, 10 Jul 2019 04:01:05 GMT

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

←Older revision

Revision as of 04:01, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kdt is ON HOLD Authors: Lin, C.-C., Chen, Y.-P., Yang, W.-Z., Shen, C.-K., Yuan, H.S. Description: Crystal structure of human DNMT3B (Q772R)-DNMT3...

OCA — Wed, 10 Jul 2019 04:01:03 GMT

New page: '''Unreleased structure''' The entry 6kdt is ON HOLD Authors: Lin, C.-C., Chen, Y.-P., Yang, W.-Z., Shen, C.-K., Yuan, H.S. Description: Crystal structure of human DNMT3B (Q772R)-DNMT3...

New page

'''Unreleased structure'''

The entry 6kdt is ON HOLD

Authors: Lin, C.-C., Chen, Y.-P., Yang, W.-Z., Shen, C.-K., Yuan, H.S.

Description: Crystal structure of human DNMT3B (Q772R)-DNMT3L complex
[[Category: Unreleased Structures]]
[[Category: Lin, C.-C]]
[[Category: Shen, C.-K]]
[[Category: Chen, Y.-P]]
[[Category: Yuan, H.S]]
[[Category: Yang, W.-Z]]