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[[Image:1tbk.gif|left|200px]]
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{{STRUCTURE_1tbk|  PDB=1tbk  |  SCENE=  }}
'''NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.'''


==NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.==
<StructureSection load='1tbk' size='340' side='right'caption='[[1tbk]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1tbk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TBK 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=1tbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tbk OCA], [https://pdbe.org/1tbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tbk RCSB], [https://www.ebi.ac.uk/pdbsum/1tbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tbk ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.


==Overview==
Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping.,Campbell DO, Legault P Biochemistry. 2005 Mar 22;44(11):4157-70. PMID:15766243<ref>PMID:15766243</ref>
An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TBK OCA].
</div>
<div class="pdbe-citations 1tbk" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping., Campbell DO, Legault P, Biochemistry. 2005 Mar 22;44(11):4157-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15766243 15766243]
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
[[Category: Campbell, D O.]]
== References ==
[[Category: Legault, P.]]
<references/>
[[Category: Hairpin]]
__TOC__
[[Category: U-turn]]
</StructureSection>
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 09:46:10 2008''
[[Category: Large Structures]]
[[Category: Campbell DO]]
[[Category: Legault P]]
Retrieved from "https://proteopedia.org/1tbk"