5K7E

The structure of pistol ribozyme, soaked with Mn2+

5K7E の概要

• エントリーDOI: 10.2210/pdb5k7e/pdb
• 関連するPDBエントリー: 5K7C 5K7D
• 分子名称: RNA 47-MER, DNA/RNA 11-MER, MANGANESE (II) ION, ... (4 entities in total)
• 機能のキーワード: ribozyme, rna structure, pistol, rna-dna complex, rna/dna
• 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: 18720.99

構造登録者

Ren, A.,Patel, D. (登録日: 2016-05-26, 公開日: 2016-07-13, 最終更新日: 2023-09-27)

主引用文献

Ren, A.,Vusurovic, N.,Gebetsberger, J.,Gao, P.,Juen, M.,Kreutz, C.,Micura, R.,Patel, D.J.
Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage.
Nat.Chem.Biol., 12:702-708, 2016

PubMed Abstract: The field of small self-cleaving nucleolytic ribozymes has been invigorated by the recent discovery of the twister, twister-sister, pistol and hatchet ribozymes. We report the crystal structure of a pistol ribozyme termed env25, which adopts a compact tertiary architecture stabilized by an embedded pseudoknot fold. The G-U cleavage site adopts a splayed-apart conformation with in-line alignment of the modeled 2'-O of G for attack on the adjacent to-be-cleaved P-O5' bond. Highly conserved residues G40 (N1 position) and A32 (N3 and 2'-OH positions) are aligned to act as a general base and a general acid, respectively, to accelerate cleavage chemistry, with their roles confirmed by cleavage assays on variants, and an increased pKa of 4.7 for A32. Our structure of the pistol ribozyme defined how the overall and local topologies dictate the in-line alignment at the G-U cleavage site, with cleavage assays on variants revealing key residues that participate in acid-base-catalyzed cleavage chemistry.

PubMed: 27398999
DOI: 10.1038/nchembio.2125

実験手法

X-RAY DIFFRACTION (3.27 Å)