5uz3: Difference between revisions

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==Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 10th position==
==Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 10th position==
<StructureSection load='5uz3' size='340' side='right'caption='[[5uz3]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
<StructureSection load='5uz3' size='340' side='right'caption='[[5uz3]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5uz3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UZ3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5uz3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UZ3 FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5uz1|5uz1]], [[5uz2|5uz2]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></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=5uz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uz3 OCA], [http://pdbe.org/5uz3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uz3 RCSB], [http://www.ebi.ac.uk/pdbsum/5uz3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uz3 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=5uz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uz3 OCA], [https://pdbe.org/5uz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uz3 RCSB], [https://www.ebi.ac.uk/pdbsum/5uz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uz3 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI--&gt;BII transition in the backbone 3' to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.
Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.,Gruber DR, Toner JJ, Miears HL, Shernyukov AV, Kiryutin AS, Lomzov AA, Endutkin AV, Grin IR, Petrova DV, Kupryushkin MS, Yurkovskaya AV, Johnson EC, Okon M, Bagryanskaya EG, Zharkov DO, Smirnov SL Nucleic Acids Res. 2018 Nov 16;46(20):10827-10839. doi: 10.1093/nar/gky893. PMID:30289469<ref>PMID:30289469</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5uz3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Endutkin, A V]]
[[Category: Synthetic construct]]
[[Category: Gruber, D R]]
[[Category: Endutkin AV]]
[[Category: Hoppins, J J]]
[[Category: Gruber DR]]
[[Category: Miears, H L]]
[[Category: Hoppins JJ]]
[[Category: Smirnov, S L]]
[[Category: Miears HL]]
[[Category: Zharkov, D O]]
[[Category: Smirnov SL]]
[[Category: 5-methylcytosine]]
[[Category: Zharkov DO]]
[[Category: 8-oxoguanine]]
[[Category: Cpg site]]
[[Category: Dna]]
[[Category: Drew-dickerson]]
[[Category: Epigenetic]]
[[Category: Methylated dna]]
[[Category: Modified dna]]
[[Category: Non-canonical]]

Latest revision as of 10:28, 1 May 2024

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 10th positionSolution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 10th position

Structural highlights

5uz3 is a 2 chain structure with sequence from Synthetic construct. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT
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