1sy4: Difference between revisions

<StructureSection load='1sy4' size='340' side='right'caption='[[1sy4]]' scene=''>

<table><tr><td colspan='2'>[[1sy4]] is a 1 chain structure. 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]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SY4 FirstGlance]. <br>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sy4 OCA], [https://pdbe.org/1sy4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sy4 RCSB], [https://www.ebi.ac.uk/pdbsum/1sy4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sy4 ProSAT]</span></td></tr>

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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.

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<ref>PMID:12702812</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

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<div class="pdbe-citations 1sy4" style="background-color:#fffaf0;"></div>

<references/>

[[Category: Large Structures]]

[[Category: Allman AM]]

[[Category: Butcher SE]]

[[Category: Johnson RJ]]

[[Category: Nikstad LJ]]

[[Category: Reiter NJ]]