1d0u
From Proteopedia
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| - | [[Image:1d0u.gif|left|200px]]<br /><applet load="1d0u" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1d0u" /> | ||
| - | '''SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN'''<br /> | ||
| - | == | + | ==SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN== |
| + | <StructureSection load='1d0u' size='340' side='right'caption='[[1d0u]]' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1d0u]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D0U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D0U FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d0u OCA], [https://pdbe.org/1d0u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d0u RCSB], [https://www.ebi.ac.uk/pdbsum/1d0u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d0u ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
Phosphorothioate substitution-interference experiments, routinely used to stereospecifically identify phosphoryl oxygen sites that participate in RNA-ligand binding and RNA-directed catalysis, rest in their interpretation on the untested assumption that substitution does not alter the conformation of the modified molecule from its biologically active state. Using NMR spectroscopy, we have tested this assumption by determining the structural effect of stereospecific phosphorothioate substitution at five positions in an RNA hairpin containing the binding site for bacteriophage MS2 capsid protein. At most sites, substitution has little or no effect, causing minor perturbations in the phosphate backbone and increasing the stacking among nucleotides in the hairpin loop. At one site, however, phosphorothioate substitution causes an unpaired adenine necessary for formation of the capsid protein-RNA complex to loop out of the RNA helix into the major groove. These results indicate that phosphorothioate substitution can substantially alter the conformation of RNA at positions of irregular secondary structure, complicating the use of substitution-interference experiments to study RNA structure and function. | Phosphorothioate substitution-interference experiments, routinely used to stereospecifically identify phosphoryl oxygen sites that participate in RNA-ligand binding and RNA-directed catalysis, rest in their interpretation on the untested assumption that substitution does not alter the conformation of the modified molecule from its biologically active state. Using NMR spectroscopy, we have tested this assumption by determining the structural effect of stereospecific phosphorothioate substitution at five positions in an RNA hairpin containing the binding site for bacteriophage MS2 capsid protein. At most sites, substitution has little or no effect, causing minor perturbations in the phosphate backbone and increasing the stacking among nucleotides in the hairpin loop. At one site, however, phosphorothioate substitution causes an unpaired adenine necessary for formation of the capsid protein-RNA complex to loop out of the RNA helix into the major groove. These results indicate that phosphorothioate substitution can substantially alter the conformation of RNA at positions of irregular secondary structure, complicating the use of substitution-interference experiments to study RNA structure and function. | ||
| - | + | Phosphorothioate substitution can substantially alter RNA conformation.,Smith JS, Nikonowicz EP Biochemistry. 2000 May 16;39(19):5642-52. PMID:10801314<ref>PMID:10801314</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 1d0u" style="background-color:#fffaf0;"></div> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | [[Category: | + | __TOC__ |
| - | [[Category: | + | </StructureSection> |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | + | [[Category: Nikonowicz EP]] | |
| - | + | [[Category: Smith JS]] | |
Current revision
SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN
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