8HX1

Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobacterium smegmatis

8HX1 の概要

• エントリーDOI: 10.2210/pdb8hx1/pdb
• EMDBエントリー: 35071
• 分子名称: Putative starvation-induced DNA protecting protein/Ferritin and Dps (1 entity in total)
• 機能のキーワード: msdps2, cryo-em, dna binding protein
• 由来する生物種: Mycolicibacterium smegmatis MC2 155
• タンパク質・核酸の鎖数: 12
• 化学式量合計: 214258.36

構造登録者

Dutta, S.,Garg, P. (登録日: 2023-01-03, 公開日: 2024-07-10, 最終更新日: 2025-06-18)

主引用文献

Garg, P.,Satheesh, T.,Ganji, M.,Dutta, S.
Cryo-EM Reveals the Mechanism of DNA Compaction by Mycobacterium smegmatis Dps2.
J.Mol.Biol., 436:168806-168806, 2024

PubMed Abstract: DNA binding protein from starved cells (Dps) is a miniature ferritin complex, which plays a vital role in protecting bacterial DNA during starvation to maintain the integrity of bacteria under hostile conditions. Several approaches, including cryo-electron tomography, have been previously implemented by other research groups to decipher the structure of the Dps protein bound to DNA. However, none of the structures of the Dps-DNA complex was resolved to high resolution to identify the DNA binding residues. Like other bacteria, Mycobacterium smegmatis also expresses Dps2 (called MsDps2), which binds DNA to protect it under oxidative stress conditions. In this study, we implemented various biochemical and biophysical studies to characterize the DNA protein interactions of Dps2 protein from Mycobacterium smegmatis. We employed single-particle cryo-EM-based structural analysis of MsDps2-DNA complexes and identified that the region close to the N-terminus confers the DNA binding property. Based on cryo-EM data, we also pinpointed several arginine residues, proximal to the DNA binding region, responsible for DNA binding. We also performed mutations of these residues, which dramatically reduced the MsDps2-DNA interaction. In addition, we proposed a model that elucidates the mechanism of DNA compaction, which adapts a lattice-like structure. We performed single-molecule imaging of MsDps2-DNA interactions that corroborate well with our structural studies. Taken together, our results delineate the specific MsDps2 residues that play an important role in DNA binding and compaction, providing new insights into Mycobacterial DNA compaction mechanisms under stress conditions.

PubMed: 39349276
DOI: 10.1016/j.jmb.2024.168806

実験手法

ELECTRON MICROSCOPY (3.29 Å)