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A conserved element that stabilizes the group II intron active site
Olga Fedorova1, Anna Marie Pyle
1Howard Hughes Medical Institute at Yale, Yale University, New Haven, Connecticut 06520, USA.
RNA (New York, N.Y.)
|April 29, 2008
Summary
The domain 3 internal loop (D3IL) in group II introns interacts with other active site elements, stabilizing the catalytic structure. This research identifies key tertiary interaction partners for the conserved D3IL.
Area of Science:
- Molecular Biology
- Biochemistry
- RNA catalysis
Background:
- Group II introns are ribozymes with complex structures.
- The domain 3 internal loop (D3IL) is crucial for catalytic activity.
- Tertiary interaction partners of the D3IL were previously unknown.
Purpose of the Study:
- To identify the molecular interaction partners of the conserved domain 3 internal loop (D3IL) in group II introns.
- To elucidate the role of these interactions in active site architecture and catalytic function.
Main Methods:
- Site-directed photo-cross-linking.
- Nucleotide analog interference suppression (NAIS).
Main Results:
- The D3IL interacts with the epsilon-epsilon' duplex near the 5'-splice site in domain 1.
- Evidence suggests the D3IL also interacts with the domain 5 bulge.
- These interactions form a network supporting catalytic motif interactions.
Conclusions:
- The D3IL is a key component in a complex network of tertiary interactions within the group II intron active site.
- These interactions stabilize the active site, enhancing intron catalytic reactivity.
- Domain 3 acts as a catalytic effector through active site stabilization.
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