2RPT

Structure of the CC mismatch from the thymidylate synthase binding site 1 hairpin and analysis of its interaction with paromomycin

2RPT の概要

• エントリーDOI: 10.2210/pdb2rpt/pdb
• 分子名称: RNA (5'-R(*GP*GP*CP*CP*CP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*CP*GP*GP*CP*C)-3') (1 entity in total)
• 機能のキーワード: nmr spectroscopy, rna structure, paromomycin, aminoglycoside-rna interaction, rna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 6450.94

構造登録者

Tavares, T.J.,Johnson, P.E. (登録日: 2008-08-23, 公開日: 2009-08-25, 最終更新日: 2024-05-29)

主引用文献

Tavares, T.J.,Beribisky, A.V.,Johnson, P.E.
Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin
Rna, 15:911-922, 2009

PubMed Abstract: The structure of a cytosine-cytosine (CC) mismatch-containing RNA molecule derived from a hairpin structure in the thymidylate synthase mRNA that binds the aminoglycoside paromomycin with high affinity was determined using nuclear magnetic resonance (NMR) spectroscopy. The cytosines in the mismatch form a noncanonical base pair where both cytosines are uncharged and stack within the stem of the RNA structure. Binding to paromomycin was analyzed using isothermal titration calorimetry (ITC) to demonstrate the necessity of the CC mismatch and to determine the affinity dissociation constant of this RNA to paromomycin to be 0.5 +/- 0.3 microM. The CC mismatch, and the neighboring GC base pairs experienced the highest degree of chemical shift changes in their H6 and H5 resonances indicating that paromomycin binds in the major groove at the CC mismatch site. In comparing the structure of CC mismatch RNA with a fully Watson-Crick GC base paired stem, the CC mismatch is shown to confer a widening of the major groove. This widening, combined with the dynamic nature of the CC mismatch, enables binding of paromomycin to this RNA molecule.

PubMed: 19329536
DOI: 10.1261/rna.1514909

実験手法

SOLUTION NMR