1sy4
From Proteopedia
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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
1SY4 is a Protein complex structure of sequences from [1]. This structure superseeds 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
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