3B58

Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and a 2',5'-Phosphodiester Linkage at the Active Site

3B58 の概要

• エントリーDOI: 10.2210/pdb3b58/pdb
• 関連するPDBエントリー: 2P7F 3B5A 3B5F 3B5S 3B91 3BBI 3BBK 3BBM
• 分子名称: Loop A Substrate strand, 29-mer Loop A and Loop B Ribozyme strand, Loop B S-turn strand, ... (6 entities in total)
• 機能のキーワード: hairpin ribozyme; 2', 5' phosphodiester, rna
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 20241.32

構造登録者

MacElrevey, C.,Krucinska, J.,Wedekind, J.E. (登録日: 2007-10-25, 公開日: 2008-08-12, 最終更新日: 2023-08-30)

主引用文献

MacElrevey, C.,Salter, J.D.,Krucinska, J.,Wedekind, J.E.
Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.
Rna, 14:1600-1616, 2008

PubMed Abstract: The hairpin ribozyme requires functional groups from Ade38 to achieve efficient bond cleavage or ligation. To identify molecular features that contribute to catalysis, structures of position 38 base variants 2,6-diaminopurine (DAP), 2-aminopurine (AP), cytosine (Cyt), and guanine (Gua) were determined between 2.2 and 2.8 A resolution. For each variant, two substrate modifications were compared: (1) a 2'-O-methyl-substituent at Ade-1 was used in lieu of the nucleophile to mimic the precatalytic state, and (2) a 3'-deoxy-2',5'-phosphodiester linkage between Ade-1 and Gua+1 was used to mimic a reaction-intermediate conformation. While the global fold of each variant remained intact, the results revealed the importance of Ade38 N1 and N6 groups. Absence of N6 resulting from AP38 coincided with failure to localize the precatalytic scissile phosphate. Cyt38 severely impaired catalysis in a prior study, and its structures here indicated an anti base conformation that sequesters the imino moiety from the scissile bond. Gua38 was shown to be even more deleterious to activity. Although the precatalytic structure was nominally affected, the reaction-intermediate conformation indicated a severe electrostatic clash between the Gua38 keto oxygen and the pro-Rp oxygen of the scissile bond. Overall, position 38 modifications solved in the presence of 2'-OMe Ade-1 deviated from in-line geometry, whereas variants with a 2',5' linkage exhibited S-turn destabilization, as well as base conformational changes from syn to anti. These findings demonstrate the importance of the Ade38 Watson-Crick face in attaining a reaction-intermediate state and the sensitivity of the RNA fold to restructuring when electrostatic and shape features fail to complement.

PubMed: 18596253
DOI: 10.1261/rna.1055308

実験手法

X-RAY DIFFRACTION (2.65 Å)