1sy4
From Proteopedia
Refined solution structure of the S. cerevisiae U6 INTRAMOLECULAR STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR COUPLINGS (RDCS)
Overview
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.
About this Structure
This structure supersedes the now removed PDB entry 1nyz. Full crystallographic information is available from OCA.
Reference
Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification., Reiter NJ, Nikstad LJ, Allmann AM, Johnson RJ, Butcher SE, RNA. 2003 May;9(5):533-42. PMID:12702812 Page seeded by OCA on Sat May 3 09:16:12 2008
