6R47
The structure of pistol ribozyme bound to magnesium
Summary for 6R47
| Entry DOI | 10.2210/pdb6r47/pdb |
| Descriptor | RNA (50-MER), RNA, MAGNESIUM ION, ... (4 entities in total) |
| Functional Keywords | rna, ribozyme, pseudoknot, magnesium |
| Biological source | Alistipes putredinis More |
| Total number of polymer chains | 2 |
| Total formula weight | 21106.84 |
| Authors | Lilley, D.M.J.,Wilson, T.M.,Liu, Y. (deposition date: 2019-03-22, release date: 2019-07-03, Last modification date: 2024-05-15) |
| Primary citation | Wilson, T.J.,Liu, Y.,Li, N.S.,Dai, Q.,Piccirilli, J.A.,Lilley, D.M.J. Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes. J.Am.Chem.Soc., 141:7865-7875, 2019 Cited by PubMed Abstract: Comparison of the secondary and three-dimensional structures of the hammerhead and pistol ribozymes reveals many close similarities, so in this work we have asked if they are mechanistically identical. We have determined a new crystal structure of the pistol ribozyme and have shown that G40 acts as general base in the cleavage reaction. The conformation in the active site ensures an in-line attack of the O2' nucleophile, and the conformation at the scissile phosphate and the position of the general base are closely similar to those in the hammerhead ribozyme. However, the two ribozymes differ in the nature of the general acid. 2'-Amino substitution experiments indicate that the general acid of the hammerhead ribozyme is the O2' of G8, while that of the pistol ribozyme is a hydrated metal ion. The two ribozymes are related but mechanistically distinct. PubMed: 31017785DOI: 10.1021/jacs.9b02141 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.1 Å) |
Structure validation
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