2ap0
From Proteopedia
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| - | [[Image:2ap0.gif|left|200px]]<br /><applet load="2ap0" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2ap0" /> | ||
| - | '''Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, 20 Lowest Energy Structures'''<br /> | ||
| - | == | + | ==Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, 20 Lowest Energy Structures== |
| + | <StructureSection load='2ap0' size='340' side='right'caption='[[2ap0]]' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2ap0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AP0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AP0 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CH:N3-PROTONATED+CYTIDINE-5-MONOPHOSPHATE'>CH</scene></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=2ap0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ap0 OCA], [https://pdbe.org/2ap0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ap0 RCSB], [https://www.ebi.ac.uk/pdbsum/2ap0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ap0 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
The helical junction region of a -1 frameshift stimulating hairpin-type mRNA pseudoknot from sugarcane yellow leaf virus (ScYLV) is characterized by a novel C27.(G7-C14) loop 2-stem 1 minor groove base triple, which is stacked on a C8+.(G12-C28) loop 1-stem 2 major groove base triple. Substitution of C27 with adenosine reduces frameshifting efficiency to a level just twofold above the slip-site alone. Here, we show that the global structure of the C27A ScYLV RNA is nearly indistinguishable from the wild-type counterpart, despite the fact that the helical junction region is altered and incorporates the anticipated isostructural A27.(G7-C14) minor groove base triple. This interaction mediates a 2.3-A displacement of C8+ driven by an A27 N6-C8+ O2 hydrogen bond as part of an A(n-1).C+.G-Cn base quadruple. The helical junction regions of the C27A ScYLV and the beet western yellows virus (BWYV) pseudoknots are essentially superimposable, the latter of which contains an analogous A25.(G7-C14) minor groove base triple. These results reveal that the global ground-state structure is not strongly correlated with frameshift stimulation and point to a reduced thermodynamic stability and/or enhanced kinetic lability that derives from an altered helical junction architecture in the C27A ScYLV RNA as a significant determinant for setting frameshifting efficiencies in plant luteoviral mRNA pseudoknots. | The helical junction region of a -1 frameshift stimulating hairpin-type mRNA pseudoknot from sugarcane yellow leaf virus (ScYLV) is characterized by a novel C27.(G7-C14) loop 2-stem 1 minor groove base triple, which is stacked on a C8+.(G12-C28) loop 1-stem 2 major groove base triple. Substitution of C27 with adenosine reduces frameshifting efficiency to a level just twofold above the slip-site alone. Here, we show that the global structure of the C27A ScYLV RNA is nearly indistinguishable from the wild-type counterpart, despite the fact that the helical junction region is altered and incorporates the anticipated isostructural A27.(G7-C14) minor groove base triple. This interaction mediates a 2.3-A displacement of C8+ driven by an A27 N6-C8+ O2 hydrogen bond as part of an A(n-1).C+.G-Cn base quadruple. The helical junction regions of the C27A ScYLV and the beet western yellows virus (BWYV) pseudoknots are essentially superimposable, the latter of which contains an analogous A25.(G7-C14) minor groove base triple. These results reveal that the global ground-state structure is not strongly correlated with frameshift stimulation and point to a reduced thermodynamic stability and/or enhanced kinetic lability that derives from an altered helical junction architecture in the C27A ScYLV RNA as a significant determinant for setting frameshifting efficiencies in plant luteoviral mRNA pseudoknots. | ||
| - | + | The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical.,Cornish PV, Stammler SN, Giedroc DP RNA. 2006 Nov;12(11):1959-69. Epub 2006 Sep 25. PMID:17000902<ref>PMID:17000902</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: | + | <div class="pdbe-citations 2ap0" style="background-color:#fffaf0;"></div> |
| - | [[Category: Cornish | + | == References == |
| - | [[Category: Giedroc | + | <references/> |
| - | + | __TOC__ | |
| - | + | </StructureSection> | |
| - | + | [[Category: Large Structures]] | |
| + | [[Category: Cornish PV]] | ||
| + | [[Category: Giedroc DP]] | ||
Current revision
Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, 20 Lowest Energy Structures
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