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==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> | |||
The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical., Cornish PV, Stammler SN, Giedroc DP | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2ap0" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Cornish PV]] | |||
[[Category: Giedroc DP]] | |||
Latest revision as of 16:32, 13 December 2023
Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, 20 Lowest Energy Structures
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