5KTJ

Crystal structure of Pistol, a class of self-cleaving ribozyme

5KTJ の概要

• エントリーDOI: 10.2210/pdb5ktj/pdb
• 分子名称: Pistol (50-MER), RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*GP*UP*CP*CP*AP*A)-3'), SAMARIUM (III) ION, ... (6 entities in total)
• 機能のキーワード: ribozyme, self-cleavage, internal transesterification, rna
• 由来する生物種: metagenome; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 45679.44

構造登録者

Nguyen, L.A.,Wang, J.,Steitz, T.A. (登録日: 2016-07-11, 公開日: 2016-10-05, 最終更新日: 2024-03-06)

主引用文献

Nguyen, L.A.,Wang, J.,Steitz, T.A.
Crystal structure of Pistol, a class of self-cleaving ribozyme.
Proc. Natl. Acad. Sci. U.S.A., 114:1021-1026, 2017

PubMed Abstract: Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2'-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5' leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.

PubMed: 28096403
DOI: 10.1073/pnas.1611191114

実験手法

X-RAY DIFFRACTION (2.97 Å)