8VN4

Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 1200s

8VN4 の概要

• エントリーDOI: 10.2210/pdb8vn4/pdb
• 分子名称: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3'), DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3'), Intron-encoded endonuclease I-PpoI, ... (8 entities in total)
• 機能のキーワード: intron encoded homing endonuclease i-ppoi, hydrolase, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Physarum polycephalum; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 48961.24

構造登録者

Chang, C.,Gao, Y. (登録日: 2024-01-13, 公開日: 2024-07-10, 最終更新日: 2025-01-29)

主引用文献

Chang, C.,Zhou, G.,Gao, Y.
Observing one-divalent-metal-ion-dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo.
Elife, 13:-, 2024

PubMed Abstract: Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.

PubMed: 39141555
DOI: 10.7554/eLife.99960

実験手法

X-RAY DIFFRACTION (1.75 Å)