Structure and Mechanism of the glmS Ribozyme

Abstract

The self-cleaving glmS ribozyme is a mechanistically unique functional RNA among both riboswitches and RNA catalysts as its catalytic activity provides the basis of genetic regulation and depends upon glucosamine-6-phosphate (GlcN6P) as a coenzyme. A substantial body of biochemical and biophysical data relating the structure and function of the glmS ribozyme has been amassed, in our laboratory and others, in a relatively short period of time since its discovery. However, a precise and comprehensive mechanistic understanding of coenzyme function in glmS ribozyme self-cleavage has not been elaborated. Careful consideration of the available biochemical and biophysical data relating the structure and function of the glmS ribozyme necessitates that general acid and general base catalysis in a coenzyme-dependent active site mechanism of RNA cleavage are inherently interdependent. We propose a comprehensive mechanistic model wherein the coenzyme, GlcN6P, functions both as the initial general base catalyst and consequent general acid catalyst within a proton-relay thus fulfilling the apparent biochemical requirements for activity. This analysis in combination with other considerations regarding the effects of coenzyme binding on riboswitch structure and function suggests that the development of glmS ribozyme agonists as prospective antibiotic compounds must satisfy strict chemical requirements for binding and activity.