1sy4: Difference between revisions

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[[Image:1sy4.gif|left|200px]]
{{Seed}}
[[Image:1sy4.png|left|200px]]


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{{STRUCTURE_1sy4|  PDB=1sy4  |  SCENE=  }}  
{{STRUCTURE_1sy4|  PDB=1sy4  |  SCENE=  }}  


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




==Overview==
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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.
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{{ABSTRACT_PUBMED_12702812}}


==About this Structure==
==About this Structure==
This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1nyz 1nyz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SY4 OCA].  
This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1nyz 1nyz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SY4 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://www.ncbi.nlm.nih.gov/pubmed/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://www.ncbi.nlm.nih.gov/pubmed/12702812 12702812]
Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure., Huppler A, Nikstad LJ, Allmann AM, Brow DA, Butcher SE, Nat Struct Biol. 2002 Jun;9(6):431-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11992125 11992125]
[[Category: Allman, A M.]]
[[Category: Allman, A M.]]
[[Category: Butcher, S E.]]
[[Category: Butcher, S E.]]
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[[Category: Internal loop]]
[[Category: Internal loop]]
[[Category: Rna]]
[[Category: Rna]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 09:16:12 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 01:02:12 2008''
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