1SY4

Refined solution structure of the S. cerevisiae U6 INTRAMOLECULAR STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR COUPLINGS (RDCS)

「1NYZ」から置き換えられました

1SY4 の概要

• エントリーDOI: 10.2210/pdb1sy4/pdb
• 関連するPDBエントリー: 1LC6 1NC0 1NZ1 1SYZ
• 分子名称: U6 Intramolecular Stem-Loop RNA (1 entity in total)
• 機能のキーワード: rna, stem-loop (gnra-like tetraloop), a-c wobble pair, internal loop
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 7668.61

構造登録者

Reiter, N.J.,Nikstad, L.J.,Allman, A.M.,Johnson, R.J.,Butcher, S.E. (登録日: 2004-03-31, 公開日: 2004-04-06, 最終更新日: 2024-05-22)

主引用文献

Reiter, N.J.,Nikstad, L.J.,Allman, A.M.,Johnson, R.J.,Butcher, S.E.
Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.
RNA, 9:533-542, 2003

PubMed Abstract: Phosphorothioate-substitution experiments are often used to elucidate functionally important metal ion-binding sites on RNA. All previous experiments with S(P)-phosphorothioate-substituted RNAs have been done in the absence of structural information for this particular diastereomer. Yeast U6 RNA contains a metal ion-binding site that is essential for spliceosome function and includes the pro-S(P) oxygen 5' of U(80). S(P)-phosphorothioate substitution at this location creates spliceosomes dependent on thiophilic ions for the first step of splicing. We have determined the solution structure of the U(80) S(P)-phosphorothioate-substituted U6 intramolecular stem-loop (ISL), and also report the refined NMR structure of the unmodified U6 ISL. Both structures were determined with inclusion of (1)H-(13)C residual dipolar couplings. The precision of the structures with and without phosphorothioate (RMSD = 1.05 and 0.79 A, respectively) allows comparison of the local and long-range structural effect of the modification. We find that the U6-ISL structure is unperturbed by the phosphorothioate. Additionally, the thermodynamic stability of the U6 ISL is dependent on the protonation state of the A(79)-C(67) wobble pair and is not affected by the adjacent phosphorothioate. These results indicate that a single S(P)-phosphorothioate substitution can be structurally benign, and further validate the metal ion rescue experiments used to identify the essential metal-binding site(s) in the spliceosome.

PubMed: 12702812
DOI: 10.1261/rna.2199103

実験手法

SOLUTION NMR