2ap5

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(New page: 200px<br /><applet load="2ap5" size="350" color="white" frame="true" align="right" spinBox="true" caption="2ap5" /> '''Solution Structure of the C27A ScYLV P1-P2 F...)
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[[Image:2ap5.gif|left|200px]]<br /><applet load="2ap5" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2ap5" />
 
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'''Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, Average Structure'''<br />
 
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==Overview==
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==Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, Average Structure==
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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.
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<StructureSection load='2ap5' size='340' side='right'caption='[[2ap5]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2ap5]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AP5 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ap5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ap5 OCA], [https://pdbe.org/2ap5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ap5 RCSB], [https://www.ebi.ac.uk/pdbsum/2ap5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ap5 ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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2AP5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AP5 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17000902 17000902]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 2ap5" style="background-color:#fffaf0;"></div>
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[[Category: Cornish, P.V.]]
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== References ==
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[[Category: Giedroc, D.P.]]
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<references/>
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[[Category: rna pseudoknot; frameshifting]]
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__TOC__
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</StructureSection>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:07:09 2008''
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[[Category: Large Structures]]
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[[Category: Cornish PV]]
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[[Category: Giedroc DP]]

Current revision

Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, Average Structure

PDB ID 2ap5

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