6u8x

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:58, 25 December 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='6u8x' size='340' side='right'caption='[[6u8x]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
<StructureSection load='6u8x' size='340' side='right'caption='[[6u8x]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6u8x]] 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=6U8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U8X FirstGlance]. <br>
+
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U8X 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]] 2.9506388&#8491;</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]] 2.9506388&#8491;</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='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=6u8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8x OCA], [https://pdbe.org/6u8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u8x RCSB], [https://www.ebi.ac.uk/pdbsum/6u8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8x ProSAT]</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=6u8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8x OCA], [https://pdbe.org/6u8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u8x RCSB], [https://www.ebi.ac.uk/pdbsum/6u8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8x 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
-
</div>
 
-
<div class="pdbe-citations 6u8x" style="background-color:#fffaf0;"></div>
 
==See Also==
==See Also==
*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]]
*[[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]]

Current revision

Crystal structure of DNMT3B-DNMT3L in complex with CpApG DNA

PDB ID 6u8x

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools