7lmm: Difference between revisions
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==== | ==Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2== | ||
<StructureSection load='7lmm' size='340' side='right'caption='[[7lmm]]' scene=''> | <StructureSection load='7lmm' size='340' side='right'caption='[[7lmm]], [[Resolution|resolution]] 2.80Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[7lmm]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LMM FirstGlance]. <br> | ||
</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=7lmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lmm OCA], [https://pdbe.org/7lmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lmm RCSB], [https://www.ebi.ac.uk/pdbsum/7lmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lmm 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]] 2.798Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7lmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lmm OCA], [https://pdbe.org/7lmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lmm RCSB], [https://www.ebi.ac.uk/pdbsum/7lmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lmm ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/DNMT1_BOVIN DNMT1_BOVIN] Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B 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. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells. Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing. Promotes tumor growth.[UniProtKB:P13864][UniProtKB:P26358] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
DNA methylation and trimethylated histone H4 Lysine 20 (H4K20me3) constitute two important heterochromatin-enriched marks that frequently cooperate in silencing repetitive elements of the mammalian genome. However, it remains elusive how these two chromatin modifications crosstalk. Here, we report that DNA methyltransferase 1 (DNMT1) specifically 'recognizes' H4K20me3 via its first bromo-adjacent-homology domain (DNMT1(BAH1)). Engagement of DNMT1(BAH1)-H4K20me3 ensures heterochromatin targeting of DNMT1 and DNA methylation at LINE-1 retrotransposons, and cooperates with the previously reported readout of histone H3 tail modifications (i.e., H3K9me3 and H3 ubiquitylation) by the RFTS domain to allosterically regulate DNMT1's activity. Interplay between RFTS and BAH1 domains of DNMT1 profoundly impacts DNA methylation at both global and focal levels and genomic resistance to radiation-induced damage. Together, our study establishes a direct link between H4K20me3 and DNA methylation, providing a mechanism in which multivalent recognition of repressive histone modifications by DNMT1 ensures appropriate DNA methylation patterning and genomic stability. | |||
DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation.,Ren W, Fan H, Grimm SA, Kim JJ, Li L, Guo Y, Petell CJ, Tan XF, Zhang ZM, Coan JP, Yin J, Kim DI, Gao L, Cai L, Khudaverdyan N, Cetin B, Patel DJ, Wang Y, Cui Q, Strahl BD, Gozani O, Miller KM, O'Leary SE, Wade PA, Wang GG, Song J Nat Commun. 2021 May 3;12(1):2490. doi: 10.1038/s41467-021-22665-4. PMID:33941775<ref>PMID:33941775</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7lmm" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bos taurus]] | |||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Ren W]] | ||
[[Category: Song J]] | |||
Latest revision as of 18:53, 18 October 2023
Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2
Structural highlights
FunctionDNMT1_BOVIN Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B 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. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells. Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing. Promotes tumor growth.[UniProtKB:P13864][UniProtKB:P26358] Publication Abstract from PubMedDNA methylation and trimethylated histone H4 Lysine 20 (H4K20me3) constitute two important heterochromatin-enriched marks that frequently cooperate in silencing repetitive elements of the mammalian genome. However, it remains elusive how these two chromatin modifications crosstalk. Here, we report that DNA methyltransferase 1 (DNMT1) specifically 'recognizes' H4K20me3 via its first bromo-adjacent-homology domain (DNMT1(BAH1)). Engagement of DNMT1(BAH1)-H4K20me3 ensures heterochromatin targeting of DNMT1 and DNA methylation at LINE-1 retrotransposons, and cooperates with the previously reported readout of histone H3 tail modifications (i.e., H3K9me3 and H3 ubiquitylation) by the RFTS domain to allosterically regulate DNMT1's activity. Interplay between RFTS and BAH1 domains of DNMT1 profoundly impacts DNA methylation at both global and focal levels and genomic resistance to radiation-induced damage. Together, our study establishes a direct link between H4K20me3 and DNA methylation, providing a mechanism in which multivalent recognition of repressive histone modifications by DNMT1 ensures appropriate DNA methylation patterning and genomic stability. DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation.,Ren W, Fan H, Grimm SA, Kim JJ, Li L, Guo Y, Petell CJ, Tan XF, Zhang ZM, Coan JP, Yin J, Kim DI, Gao L, Cai L, Khudaverdyan N, Cetin B, Patel DJ, Wang Y, Cui Q, Strahl BD, Gozani O, Miller KM, O'Leary SE, Wade PA, Wang GG, Song J Nat Commun. 2021 May 3;12(1):2490. doi: 10.1038/s41467-021-22665-4. PMID:33941775[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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