7YHO

CryoEM structure of Arabidopsis ROS1 in complex with TG mismatch dsDNA at 3.3 Angstroms resolution

7YHO の概要

• エントリーDOI: 10.2210/pdb7yho/pdb
• EMDBエントリー: 33832
• 分子名称: Sex-determining region Y protein,DNA glycosylase/AP lyase ROS1, DNA (40-MER), IRON/SULFUR CLUSTER, ... (4 entities in total)
• 機能のキーワード: ros1, dna glycosylase, dna demethylation, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 111252.35

構造登録者

Du, X.,Du, J. (登録日: 2022-07-14, 公開日: 2022-11-30, 最終更新日: 2024-07-03)

主引用文献

Du, X.,Yang, Z.,Xie, G.,Wang, C.,Zhang, L.,Yan, K.,Yang, M.,Li, S.,Zhu, J.K.,Du, J.
Molecular basis of the plant ROS1-mediated active DNA demethylation.
Nat.Plants, 9:271-279, 2023

PubMed Abstract: Active DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly excise 5-methyl-cytosine (5mC), representing an efficient DNA demethylation pathway distinct from that of animals. Here, we report the cryo-electron microscopy structures of an Arabidopsis ROS1 catalytic fragment in complex with substrate DNA, mismatch DNA and reaction intermediate, respectively. The substrate 5mC is flipped-out from the DNA duplex and subsequently recognized by the ROS1 base-binding pocket through hydrophobic and hydrogen-bonding interactions towards the 5-methyl group and Watson-Crick edge respectively, while the different protonation states of the bases determine the substrate preference for 5mC over T:G mismatch. Together with the structure of the reaction intermediate complex, our structural and biochemical studies revealed the molecular basis for substrate specificity, as well as the reaction mechanism underlying 5mC demethylation by the ROS1/DME family of plant-specific DNA demethylases.

PubMed: 36624257
DOI: 10.1038/s41477-022-01322-8

実験手法

ELECTRON MICROSCOPY (3.3 Å)