7L4C

Crystal structure of the DRM2-CTT DNA complex

7L4C の概要

• エントリーDOI: 10.2210/pdb7l4c/pdb
• 分子名称: DNA (cytosine-5)-methyltransferase DRM2, DNA (5'-D(*TP*AP*AP*AP*TP*TP*AP*AP*GP*AP*TP*TP*AP*AP*TP*AP*AP*T)-3'), DNA (5'-D(*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49)P*TP*TP*AP*AP*TP*TP*TP*A)-3'), ... (6 entities in total)
• 機能のキーワード: dna methyltransferase, complex, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• 由来する生物種: Arabidopsis thaliana (Mouse-ear cress); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 51770.97

構造登録者

Fang, J.,Song, J. (登録日: 2020-12-18, 公開日: 2021-08-04, 最終更新日: 2024-11-06)

主引用文献

Fang, J.,Leichter, S.M.,Jiang, J.,Biswal, M.,Lu, J.,Zhang, Z.M.,Ren, W.,Zhai, J.,Cui, Q.,Zhong, X.,Song, J.
Substrate deformation regulates DRM2-mediated DNA methylation in plants.
Sci Adv, 7:-, 2021

PubMed Abstract: DNA methylation is a major epigenetic mechanism critical for gene expression and genome stability. In plants, domains rearranged methyltransferase 2 (DRM2) preferentially mediates CHH (H = C, T, or A) methylation, a substrate specificity distinct from that of mammalian DNA methyltransferases. However, the underlying mechanism is unknown. Here, we report structure-function characterization of DRM2-mediated methylation. An arginine finger from the catalytic loop intercalates into the nontarget strand of DNA through the minor groove, inducing large DNA deformation that affects the substrate preference of DRM2. The target recognition domain stabilizes the enlarged major groove via shape complementarity rather than base-specific interactions, permitting substrate diversity. The engineered DRM2 C397R mutation introduces base-specific contacts with the +2-flanking guanine, thereby shifting the substrate specificity of DRM2 toward CHG DNA. Together, this study uncovers DNA deformation as a mechanism in regulating the specificity of DRM2 toward diverse CHH substrates and illustrates methylome complexity in plants.

PubMed: 34078593
DOI: 10.1126/sciadv.abd9224

実験手法

X-RAY DIFFRACTION (2.11 Å)