5DUN

The crystal structure of OMe substituted twister ribozyme

5DUN の概要

• エントリーDOI: 10.2210/pdb5dun/pdb
• 分子名称: RNA (54-MER), MAGNESIUM ION, POTASSIUM ION, ... (4 entities in total)
• 機能のキーワード: ome, twister, rna, ribozyme
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 17639.93

構造登録者

Ren, A.,Patel, D.J.,Micura, R.,Rajashankar, K.R. (登録日: 2015-09-19, 公開日: 2015-10-28, 最終更新日: 2023-09-27)

主引用文献

Kosutic, M.,Neuner, S.,Ren, A.,Flur, S.,Wunderlich, C.,Mairhofer, E.,Vusurovic, N.,Seikowski, J.,Breuker, K.,Hobartner, C.,Patel, D.J.,Kreutz, C.,Micura, R.
A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class.
Angew.Chem.Int.Ed.Engl., 54:15128-15133, 2015

PubMed Abstract: Nucleolytic ribozymes catalyze site-specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild-type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine-6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pKa value of 5.1 was determined for a (13) C2-labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pKa of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine-6 in the catalytic mechanism besides the previously identified invariant guanine-48 and a Mg(2+) ion, both of which are directly coordinated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn(2+) or Cd(2+) accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 Å X-ray structure of a 2'-OCH3 -U5 modified twister ribozyme.

PubMed: 26473980
DOI: 10.1002/anie.201506601

実験手法

X-RAY DIFFRACTION (2.64 Å)