1NZ1
Solution structure of the S. cerevisiae U6 Intramolecular stem-loop containing an SP phosphorothioate at nucleotide U80
Summary for 1NZ1
| Entry DOI | 10.2210/pdb1nz1/pdb |
| Related | 1LC6 1NC0 1NYZ |
| Descriptor | SP U6 Intramolecular Stem-Loop RNA (1 entity in total) |
| Functional Keywords | u6 rna, stem-loop, phosphorothioate, sp phosphorothioate, residual dipolar coupling, rdc, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 7684.68 |
| Authors | Reiter, N.J.,Nikstad, L.J.,Allman, A.M.,Johnson, R.J.,Butcher, S.E. (deposition date: 2003-02-14, release date: 2003-05-13, Last modification date: 2024-05-22) |
| Primary citation | 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 Cited by 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: 12702812DOI: 10.1261/rna.2199103 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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