1tbk
From Proteopedia
(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...) |
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| - | [[Image:1tbk.gif|left|200px]]<br /><applet load="1tbk" size=" | + | [[Image:1tbk.gif|left|200px]]<br /><applet load="1tbk" size="350" 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 /> | '''NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.'''<br /> | ||
==Overview== | ==Overview== | ||
| - | An important step in the substrate recognition of the Neurospora Varkud | + | 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== | ==About this Structure== | ||
| - | 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:// | + | 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1TBK OCA]. |
==Reference== | ==Reference== | ||
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] | 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] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Campbell, D | + | [[Category: Campbell, D O.]] |
[[Category: Legault, P.]] | [[Category: Legault, P.]] | ||
[[Category: u-turn; hairpin]] | [[Category: u-turn; hairpin]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:11:51 2008'' |
Revision as of 13:11, 21 February 2008
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NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.
Overview
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
1TBK is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Feb 21 15:11:51 2008
