8YDC

Crystal structure of a hammerhead ribozyme with pseudoknot

8YDC の概要

• エントリーDOI: 10.2210/pdb8ydc/pdb
• 分子名称: ribozyme strand, DNA/RNA (5'-R(*AP*CP*AP*UP*GP*UP*CP*U)-D(P*C)-R(P*UP*GP*GP*GP*A)-3'), GUANOSINE-5'-TRIPHOSPHATE (3 entities in total)
• 機能のキーワード: catalysis, rna
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 23686.12

構造登録者

Liu, Y.,Zhan, X. (登録日: 2024-02-20, 公開日: 2024-08-21)

主引用文献

Zhan, X.,Wilson, T.J.,Li, Z.,Zhang, J.,Yang, Y.,Lilley, D.M.J.,Liu, Y.
The structure and catalytic mechanism of a pseudoknot-containing hammerhead ribozyme.
Nat Commun, 15:6628-6628, 2024

PubMed Abstract: We have determined the crystal structure of a pseudoknot (PK)-containing hammerhead ribozyme that closely resembles the pistol ribozyme, with essentially identical secondary structure and connectivity. The activity is more sensitive to deletion of the G8 2'OH than to the absence of magnesium ions, indicating that the catalytic mechanism is the same as the extended hammerhead, and distinct from the pistol ribozyme. Here we show that nucleophilic attack is almost perfectly in-line, and the G8 2'OH is well positioned to act as general acid, being directed towards the O5' leaving group, and 2.9 Å away from it. Despite the similarity in overall structure to the pistol ribozyme, the local structure close to the cleavage site differs, and the PK hammerhead retains its unique mechanistic identity and demonstrates enhanced activity over other hammerhead ribozymes under standard conditions.

PubMed: 39103372
DOI: 10.1038/s41467-024-50892-y

実験手法

X-RAY DIFFRACTION (2.89 Å)