The hammerhead ribozyme
Researchers using the LS-CAT Sector 21 beamlines at the APS have proposed a mechanism for the hammerhead ribozyme.
The hammerhead ribozyme was the first of the small nucleolytic ribozymes to be described and the first to have its crystal structure determined. While these initial structures were found to be trapped in an inactive conformation, structures of the extended hammerhead ribozymes inhibited by placement of a deoxy- or methoxy- modification at the cleavage site were largely in agreement with solution biochemical experiments.
The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analog vanadate reveals significant rearrangements relative to the previously solved structures. The active site contracts, bringing G10.1 closer to the cleavage site, and repositioning a divalent metal ion such that it could, ul-timately, interact directly with the scissile phosphate.
This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second diva-lent ion is observed coordinated to the O6 of G12. This metal ion is well-placed to help tune the pKA of G12. Based on this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.
Aamir Mir and Barbara L. Golden, “Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analog,” Biochemistry, Just Accepted Manuscript, DOI: 10.1021/acs.biochem.5b01139, Published Online November 9, 2015.