7YHP

CryoEM structure of Arabidopsis ROS1 in complex with 5mC-dsDNA at 3.1 Angstroms resolution

Summary for 7YHP

• Entry DOI: 10.2210/pdb7yhp/pdb
• EMDB information: 33835
• Descriptor: Sex-determining region Y protein,REPRESSOR OF SILENCING 1,DNA glycosylase/AP lyase ROS1, DNA (40-MER), IRON/SULFUR CLUSTER, ... (4 entities in total)
• Functional Keywords: ros1, dna glycosylase, dna demethylation, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 111242.35

Authors

Du, X.,Du, J. (deposition date: 2022-07-14, release date: 2022-11-30, Last modification date: 2024-07-03)

Primary citation

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

Experimental method

ELECTRON MICROSCOPY (3.1 Å)