4QJD

Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution

4QJD の概要

• エントリーDOI: 10.2210/pdb4qjd/pdb
• 関連するPDBエントリー: 4QJH
• 分子名称: Twister RNA sequence, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: self-cleaving ribozyme, 2' deoxy subsitution, nucleotide 5 (u), rna
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 94649.30

構造登録者

Eiler, D.R.,Wang, J.,Steitz, T.A. (登録日: 2014-06-03, 公開日: 2014-09-03, 最終更新日: 2023-09-20)

主引用文献

Eiler, D.,Wang, J.,Steitz, T.A.
Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme.
Proc.Natl.Acad.Sci.USA, 111:13028-13033, 2014

PubMed Abstract: Twister is a recently discovered RNA motif that is estimated to have one of the fastest known catalytic rates of any naturally occurring small self-cleaving ribozyme. We determined the 4.1-Å resolution crystal structure of a twister sequence from an organism that has not been cultured in isolation, and it shows an ordered scissile phosphate and nucleotide 5' to the cleavage site. A second crystal structure of twister from Orzyza sativa determined at 3.1-Å resolution exhibits a disordered scissile phosphate and nucleotide 5' to the cleavage site. The core of twister is stabilized by base pairing, a large network of stacking interactions, and two pseudoknots. We observe three nucleotides that appear to mediate catalysis: a guanosine that we propose deprotonates the 2'-hydroxyl of the nucleotide 5' to the cleavage site and a conserved adenosine. We suggest the adenosine neutralizes the negative charge on a nonbridging phosphate oxygen atom at the cleavage site. The active site also positions the labile linkage for in-line nucleophilic attack, and thus twister appears to simultaneously use three strategies proposed for small self-cleaving ribozymes. The twister crystal structures (i) show its global structure, (ii) demonstrate the significance of the double pseudoknot fold, (iii) provide a possible hypothesis for enhanced catalysis, and (iv) illuminate the roles of all 10 highly conserved nucleotides of twister that participate in the formation of its small and stable catalytic pocket.

PubMed: 25157168
DOI: 10.1073/pnas.1414571111

実験手法

X-RAY DIFFRACTION (3.1 Å)