New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.

Abstract

The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.

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Citation

Published Version (Please cite this version)

10.1093/nar/gku992

Publication Info

Kapral, Gary J, Swati Jain, Jonas Noeske, Jennifer A Doudna, David C Richardson and Jane S Richardson (2014). New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Nucleic Acids Res, 42(20). pp. 12833–12846. 10.1093/nar/gku992 Retrieved from https://hdl.handle.net/10161/10808.

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Scholars@Duke

Richardson

David C. Richardson

Professor Emeritus of Biochemistry

Protein structure, folding, and design; 3D computer graphics; x-ray crystallography.

Richardson

Jane Shelby Richardson

James B. Duke Distinguished Professor of Medicine

3D structure of macromolecules; molecular graphics; protein folding and design; all-atom contacts; x-ray crystallography; structure validation.


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