Abstract
The self-cleaving ribozyme of the hepatitis delta virus (HDV) is the only catalytic RNA known to be required for the viability of a human pathogen. We obtained crystals of a 72-nucleotide, self-cleaved form of the genomic HDV ribozyme that diffract X-rays to 2.3 Å resolution by engineering the RNA to bind a small, basic protein without affecting ribozyme activity. The co-crystal structure shows that the compact catalytic core comprises five helical segments connected as an intricate nested double pseudoknot. The 5′-hydroxyl leaving group resulting from the self-scission reaction is buried deep within an active-site cleft produced by juxtaposition of the helices and five strand-crossovers, and is surrounded by biochemically important backbone and base functional groups in a manner reminiscent of protein enzymes.
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Acknowledgements
We thank K. Nagai for U1A-RBD expression plasmids; C. Ogata and D. Cook for help at beamline X4A of the National Synchrotron Light Source (Brookhaven National Laboratory); the staff of the Cornell High Energy Synchrotron Source for support at beamlines A-1 and F-1; R. Batey, D.Battle, J. Kieft, A. Luptak and R. Rambo for help with synchrotron data collection and useful comments; P. Adams, M. Been, S. Bellon, C. Correll, R. Gaudet, D. Herschlag, J. Ippolito, P. Moore, L.Silvian, T. Steitz, S. Strobel, O. Uhlenbeck and D. Wilson for helpful discussions; and the staff of the Yale Center for Structural Biology for crystallographic and computational support. A.R.F. was a Fellow of the Jane Coffin Childs Memorial Fund for Medical Research. This work was supported in part by grants from the Jane Coffin Childs Memorial Fund for Medical Research, the Searle Scholars program, the NIH, and a Beckman Young Investigator award. J.A.D. is an assistant investigator of the Howard Hughes Medical Institute, a Searle scholar, and a Fellow of the David and Lucile Packard Foundation.
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Ferré-D'Amaré, A., Zhou, K. & Doudna, J. Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567–574 (1998). https://doi.org/10.1038/26912
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DOI: https://doi.org/10.1038/26912
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