3GS8

An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand

3GS8 の概要

• エントリーDOI: 10.2210/pdb3gs8/pdb
• 関連するPDBエントリー: 3GS1 3GS5
• 分子名称: RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'), RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'), RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'), ... (7 entities in total)
• 機能のキーワード: hairpin ribozyme, rna ribozyme, n1-deazaadenosine, rna
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 20504.54

構造登録者

Spitale, R.C.,Volpini, R.,Heller, M.G.,Krucinska, J.,Cristalli, G.,Wedekind, J.E. (登録日: 2009-03-26, 公開日: 2009-04-21, 最終更新日: 2024-02-21)

主引用文献

Spitale, R.C.,Volpini, R.,Heller, M.G.,Krucinska, J.,Cristalli, G.,Wedekind, J.E.
Identification of an imino group indispensable for cleavage by a small ribozyme.
J.Am.Chem.Soc., 131:6093-6095, 2009

PubMed Abstract: The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site. To define the requirements for chemical activity using a conservative modification, we synthesized and incorporated N1-deazaadenosine into the full-length ribozyme construct. This single-atom variant severely impairs activity, although the active-site fold remains intact in the accompanying crystal structures. The results demonstrate the essentiality of the imino moiety as well as the importance of its interaction with the substrate in the precatalytic and transition-state conformations. This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships.

PubMed: 19354216
DOI: 10.1021/ja900450h

実験手法

X-RAY DIFFRACTION (2.85 Å)