1ow9
From Proteopedia
(New page: 200px<br /><applet load="1ow9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ow9" /> '''NMR Structure of the Active Conformation of ...) |
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'''NMR Structure of the Active Conformation of the VS Ribozyme Cleavage Site'''<br /> | '''NMR Structure of the Active Conformation of the VS Ribozyme Cleavage Site'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Substrate cleavage by the Neurospora Varkud satellite (VS) ribozyme | + | Substrate cleavage by the Neurospora Varkud satellite (VS) ribozyme involves a structural change in the stem-loop I substrate from an inactive to an active conformation. We have determined the NMR solution structure of a mutant stem-loop I that mimics the active conformation of the cleavage site internal loop. This structure shares many similarities, but also significant differences, with the previously determined structures of the inactive internal loop. The active internal loop displays different base-pairing interactions and forms a novel RNA fold composed exclusively of sheared G-A base pairs. From chemical-shift mapping we identified two Mg2+ binding sites in the active internal loop. One of the Mg2+ binding sites forms in the active but not the inactive conformation of the internal loop and is likely important for catalysis. Using the structure comparison program mc-search, we identified the active internal loop fold in other RNA structures. In Thermus thermophilus 16S rRNA, this RNA fold is directly involved in a long-range tertiary interaction. An analogous tertiary interaction may form between the active internal loop of the substrate and the catalytic domain of the VS ribozyme. The combination of NMR and bioinformatic approaches presented here has identified a novel RNA fold and provides insights into the structural basis of catalytic function in the Neurospora VS ribozyme. |
==About this Structure== | ==About this Structure== | ||
| - | 1OW9 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:// | + | 1OW9 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=1OW9 OCA]. |
==Reference== | ==Reference== | ||
NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site., Hoffmann B, Mitchell GT, Gendron P, Major F, Andersen AA, Collins RA, Legault P, Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7003-8. Epub 2003 Jun 2. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12782785 12782785] | NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site., Hoffmann B, Mitchell GT, Gendron P, Major F, Andersen AA, Collins RA, Legault P, Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7003-8. Epub 2003 Jun 2. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12782785 12782785] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Andersen, A | + | [[Category: Andersen, A A.]] |
| - | [[Category: Collins, R | + | [[Category: Collins, R A.]] |
[[Category: Gendron, P.]] | [[Category: Gendron, P.]] | ||
[[Category: Hoffmann, B.]] | [[Category: Hoffmann, B.]] | ||
[[Category: Legault, P.]] | [[Category: Legault, P.]] | ||
[[Category: Major, F.]] | [[Category: Major, F.]] | ||
| - | [[Category: Mitchell, G | + | [[Category: Mitchell, G T.]] |
[[Category: cleavage site]] | [[Category: cleavage site]] | ||
[[Category: gnra tetraloop]] | [[Category: gnra tetraloop]] | ||
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[[Category: vs ribozyme]] | [[Category: vs ribozyme]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:22:25 2008'' |
Revision as of 12:22, 21 February 2008
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NMR Structure of the Active Conformation of the VS Ribozyme Cleavage Site
Overview
Substrate cleavage by the Neurospora Varkud satellite (VS) ribozyme involves a structural change in the stem-loop I substrate from an inactive to an active conformation. We have determined the NMR solution structure of a mutant stem-loop I that mimics the active conformation of the cleavage site internal loop. This structure shares many similarities, but also significant differences, with the previously determined structures of the inactive internal loop. The active internal loop displays different base-pairing interactions and forms a novel RNA fold composed exclusively of sheared G-A base pairs. From chemical-shift mapping we identified two Mg2+ binding sites in the active internal loop. One of the Mg2+ binding sites forms in the active but not the inactive conformation of the internal loop and is likely important for catalysis. Using the structure comparison program mc-search, we identified the active internal loop fold in other RNA structures. In Thermus thermophilus 16S rRNA, this RNA fold is directly involved in a long-range tertiary interaction. An analogous tertiary interaction may form between the active internal loop of the substrate and the catalytic domain of the VS ribozyme. The combination of NMR and bioinformatic approaches presented here has identified a novel RNA fold and provides insights into the structural basis of catalytic function in the Neurospora VS ribozyme.
About this Structure
1OW9 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site., Hoffmann B, Mitchell GT, Gendron P, Major F, Andersen AA, Collins RA, Legault P, Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7003-8. Epub 2003 Jun 2. PMID:12782785
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