Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: Implications for the mechanism of acid-base catalysis

Acta Crystallographica Section D: Biological Crystallography

Volumn 70, Issue 9, 2014, Pages 2256-2263

  Schultz, Eric P ^a   Vasquez, Ernesto E ^a   Scott, William G ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

acid base catalysis; hammerhead ribozyme; RNA cleavage

Indexed keywords

ACID; ALKALI; HAMMERHEAD RIBOZYME; PURINE DERIVATIVE; RIBOZYME;

CATALYSIS; CHEMISTRY; CONFORMATION; CRYSTALLOGRAPHY; HYDROGEN BOND; KINETICS; MOLECULAR MODEL;

ACIDS; ALKALIES; CATALYSIS; CRYSTALLOGRAPHY; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PURINES; RNA, CATALYTIC;

EID: 84907015996     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S1399004714010608     Document Type: Article

References (20)

1. Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352-367.
2. Anderson, M., Schultz, E. P., Martick, M. & Scott, W. G. (2013). J. Mol. Biol. 425, 3790-3798.
3. Battye, T. G. G., Kontogiannis, L., Johnson, O., Powell, H. R. & Leslie, A. G. W. (2011). Acta Cryst. D67, 271-281.
4. Chi, Y.-I., Martick, M., Lares, M., Kim, R., Scott, W. G. & Kim, S.-H. (2008). PLoS Biol. 6, e234.
5. Cuchillo, C. M., Nogués, M. V. & Raines, R. T. (2011). Biochemistry, 50, 7835-7841.
6. DeLano, W. L. (2002). PyMOL. http://www.pymol.org.
7. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
8. Fedor, M. J. (2009). Annu. Rev. Biophys. 38, 271-299.
9. Forster, A. C. & Symons, R. H. (1987). Cell, 50, 9-16.
10. Han, J. & Burke, J. M. (2005). Biochemistry, 44, 7864-7870.
11. Martick, M., Lee, T.-S., York, D. M. & Scott,W. G. (2008). Chem. Biol. 15, 332-342.
12. Martick, M. & Scott, W. G. (2006). Cell, 126, 309-320.
13. Painter, J. & Merritt, E. A. (2006a). Acta Cryst. D62, 439-450.
14. Painter, J. & Merritt, E. A. (2006b). J. Appl. Cryst. 39, 109-111.
15. Prody, G. A., Bakos, J. T., Buzayan, J. M., Schneider, I. R. & Bruening, G. (1986). Science, 231, 1577-1580.
16. Scott, W. G. (1999). Curr. Opin. Chem. Biol. 3, 705-709.
17. Stage-Zimmermann, T. K. & Uhlenbeck, O. C. (1998). RNA, 4, 875-889.
18. Uhlenbeck, O. C. (1987). Nature (London), 328, 596-600.
19. Wang, S., Karbstein, K., Peracchi, A., Beigelman, L. & Herschlag, D. (1999). Biochemistry, 38, 14363-14378.
20. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.