1nz1
From Proteopedia
(New page: 200px<br /><applet load="1nz1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nz1" /> '''Solution structure of the S. cerevisiae U6 I...) |
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'''Solution structure of the S. cerevisiae U6 Intramolecular stem-loop containing an SP phosphorothioate at nucleotide U80'''<br /> | '''Solution structure of the S. cerevisiae U6 Intramolecular stem-loop containing an SP phosphorothioate at nucleotide U80'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Phosphorothioate-substitution experiments are often used to elucidate | + | 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== | ==About this Structure== | ||
| - | 1NZ1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1NZ1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZ1 OCA]. |
==Reference== | ==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12702812 12702812] | 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12702812 12702812] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Allman, A | + | [[Category: Allman, A M.]] |
| - | [[Category: Butcher, S | + | [[Category: Butcher, S E.]] |
| - | [[Category: Johnson, R | + | [[Category: Johnson, R J.]] |
| - | [[Category: Nikstad, L | + | [[Category: Nikstad, L J.]] |
| - | [[Category: Reiter, N | + | [[Category: Reiter, N J.]] |
[[Category: phosphorothioate]] | [[Category: phosphorothioate]] | ||
[[Category: rdc]] | [[Category: rdc]] | ||
| Line 24: | Line 24: | ||
[[Category: u6 rna]] | [[Category: u6 rna]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:11:34 2008'' |
Revision as of 12:11, 21 February 2008
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Solution structure of the S. cerevisiae U6 Intramolecular stem-loop containing an SP phosphorothioate at nucleotide U80
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
1NZ1 is a Protein complex structure of sequences from [1]. 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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