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General acid catalysis by the hepatitis delta virus ribozyme
Subha R Das1, Joseph A Piccirilli
1Howard Hughes Medical Institute, Department of Biochemistry & Molecular Biology, University of Chicago, 5841 S. Maryland Avenue, MC1028, Chicago, Illinois 60637, USA.
Nature Chemical Biology
|January 13, 2006
Summary
This study demonstrates that a cytosine nucleobase in the hepatitis delta virus ribozyme acts as a general acid catalyst. This finding supports the role of RNA nucleobases in catalysis, similar to protein enzymes.
Area of Science:
- Biochemistry
- Molecular Biology
- RNA Catalysis
Background:
- RNA enzymes (ribozymes) may utilize nucleobases as catalysts.
- Establishing nucleobase-mediated general acid-base catalysis in ribozymes has been challenging.
Purpose of the Study:
- To investigate the catalytic role of a specific cytosine residue in the hepatitis delta virus ribozyme.
- To unambiguously link nucleobase protonation to catalytic activity.
Main Methods:
- Utilized a hyperactivated RNA substrate with a 5'-phosphorothiolate modification.
- Examined the effects of cytosine mutations and pH variations on ribozyme activity.
Main Results:
- The modified substrate mitigated the impact of cytosine mutations and pH changes.
- Protonation of the cytosine nucleobase was directly linked to stabilizing the leaving group.
Conclusions:
- The active-site cytosine residue functions as a general acid catalyst.
- This catalysis involves proton transfer to the leaving group via the N3-imino nitrogen.
- RNA nucleobases can play catalytic roles analogous to histidine in protein enzymes.