Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes

TY - JOUR

T1 - Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes

AU - Wilson, Timothy J.

AU - Liu, Yijin

AU - Li, Nan-Sheng

AU - Dai, Qing

AU - Piccirilli, Joseph A.

AU - Lilley, David M. J.

N1 - We thank Saira Ashraf for expert RNA synthesis, and acknowledge financial support from Cancer Research UK (program grant A18604 to D.M.J.L) and the U.S. National Institutes of Health (GM131568 to J.A.P.). We thank Diamond light source for synchrotron time and the Wellcome Trust for the in-house diffractometer.

PY - 2019/5/15

Y1 - 2019/5/15

N2 - 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.

AB - 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.

KW - RNA catalysis

KW - general acid-base catalysis

KW - metal ions

KW - atomic mutagenesis

KW - X-ray crystallography

UR - https://www.scopus.com/pages/publications/85065769604

U2 - 10.1021/jacs.9b02141

DO - 10.1021/jacs.9b02141

M3 - Article

C2 - 31017785

SN - 0002-7863

VL - 141

SP - 7865

EP - 7875

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

IS - 19

ER -