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1tbk

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(New page: 200px<br /><applet load="1tbk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1tbk" /> '''NMR structure of the VS ribozyme stem-loop V...)
Current revision (09:25, 6 December 2023) (edit) (undo)
 
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[[Image:1tbk.gif|left|200px]]<br /><applet load="1tbk" size="450" color="white" frame="true" align="right" spinBox="true"
 
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'''NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.'''<br />
 
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==Overview==
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==NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.==
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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.
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<StructureSection load='1tbk' size='340' side='right'caption='[[1tbk]]' scene=''>
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== Structural highlights ==
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<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>
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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='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>
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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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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.
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==About this Structure==
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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>
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1TBK 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TBK 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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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=15766243 15766243]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1tbk" style="background-color:#fffaf0;"></div>
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[[Category: Campbell, D.O.]]
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[[Category: Legault, P.]]
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[[Category: u-turn; hairpin]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:58:24 2007''
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==See Also==
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Campbell DO]]
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[[Category: Legault P]]

Current revision

NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.

PDB ID 1tbk

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