2F88

Solution NMR structure of domain 5 from the Pyaiella littoralis (PL) group II intron

2F88 の概要

• エントリーDOI: 10.2210/pdb2f88/pdb
• 分子名称: D5-PL RNA RIBOZYME DOMAIN (1 entity in total)
• 機能のキーワード: rna hairpin, gnra tetraloop, internal bulge, mg metal binding site, rna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 11009.61

構造登録者

Dayie, K.T. (登録日: 2005-12-02, 公開日: 2006-02-28, 最終更新日: 2024-05-29)

主引用文献

Seetharaman, M.,Eldho, N.V.,Padgett, R.A.,Dayie, K.T.
Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA
Rna, 12:235-247, 2006

PubMed Abstract: Domain 5 (D5) is absolutely required for all catalytic functions of group II introns. Here we describe the solution NMR structure, electrostatic calculations, and detailed magnesium ion-binding surface of D5 RNA from the Pylaiella littoralis large ribosomal RNA intron (D5-PL). The overall structure consists of a hairpin capped by a GNRA tetraloop. The stem is divided into lower and upper helices of 8 and 5 bp, respectively, separated by an internal bulge. The D5-PL internal bulge nucleotides stack into the helical junction, resulting in a coupling between the bulge A25 and the closing base pair (G8-C27) of the lower helix. Comparison of the D5-PL structure to previously reported related structures indicates that our structure is most similar, in the helical regions, to the crystal structure of D5 from yeast Ai5gamma (D5-Ai5gamma) and the NMR structure of the U6 snRNA stem-loop region. Our structure differs in many respects from both the NMR and X-ray structures of D5-Ai5gamma in the bulge region. Electrostatic calculations and NMR chemical shift perturbation analyses reveal magnesium ion-binding sites in the tetraloop, internal bulge, and the AGC triad in the lower stem. Our results suggest that the structure, electrostatic environment, and the magnesium ion-binding sites within the tetraloop, bulge, and triad regions are conserved features of the splicing machinery of both the group II introns and the spliceosome that are likely key for catalytic function.

PubMed: 16428604
DOI: 10.1261/rna.2237806

実験手法

SOLUTION NMR