5ciu: Difference between revisions

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-'''Unreleased structure'''
-The entry 5ciu is ON HOLD
+==Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain==
+<StructureSection load='5ciu' size='340' side='right'caption='[[5ciu]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5ciu]] 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=5CIU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CIU FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.24&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</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=5ciu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ciu OCA], [https://pdbe.org/5ciu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ciu RCSB], [https://www.ebi.ac.uk/pdbsum/5ciu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ciu ProSAT]</span></td></tr>
+</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 ==
+DNA methylation is an important epigenetic modification involved in chromatin organization and gene expression. The function of DNA methylation depends on cell context and is correlated with histone modification patterns. In particular, trimethylation of Lys36 on histone H3 tail (H3K36me3) is associated with DNA methylation and elongation phase of transcription. PWWP domains of the de novo DNA methyltransferases DNMT3A and DNMT3B read this epigenetic mark to guide DNA methylation. Here we report the first crystal structure of the DNMT3B PWWP domain-H3K36me3 complex. Based on this structure, we propose a model of the DNMT3A PWWP domain-H3K36me3 complex and build a model of DNMT3A (PWWP-ADD-CD) in a nucleosomal context. The trimethylated side chain of Lys36 (H3K36me3) is inserted into an aromatic cage similar to the "Royal" superfamily domains known to bind methylated histones. A key interaction between trimethylated Lys36 and a conserved water molecule stabilized by Ser270 explains the lack of affinity of mutated DNMT3B (S270P) for the H3K36me3 epigenetic mark in the ICF (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome. The model of the DNMT3A-DNMT3L heterotetramer in complex with a dinucleosome highlights the mechanism for recognition of nucleosome by DNMT3s and explains the periodicity of de novo DNA methylation.
-Authors: RONDELET, G., DAL MASO, T., WILLEMS, L., WOUTERS, J.
+Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B.,Rondelet G, Dal Maso T, Willems L, Wouters J J Struct Biol. 2016 Jun;194(3):357-67. doi: 10.1016/j.jsb.2016.03.013. Epub 2016 , Mar 15. PMID:26993463<ref>PMID:26993463</ref>
-Description: Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Wouters, J]]
+<div class="pdbe-citations 5ciu" style="background-color:#fffaf0;"></div>
-[[Category: Willems, L]]
-[[Category: Rondelet, G]]
+==See Also==
-[[Category: Dal Maso, T]]
+*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: DAL MASO T]]
+[[Category: Rondelet G]]
+[[Category: Willems L]]
+[[Category: Wouters J]]