Analysis of metal ion dependence in glmS ribozyme self-cleavage and coenzyme binding

Abstract

The bacterial glmS ribozyme is mechanistically unique among both riboswitches and RNA catalysts. Its self-cleavage activity is the basis of riboswitch regulation of glucosamine-6-phosphate (GlcN6P) production, and catalysis requires GlcN6P as a coenzyme. Previous work has shown that the coenzyme amine of GlcN6P is essential for glmS ribozyme self-cleavage, as is its protonation state. Metal ions are also essential within the glmS ribozyme core for both structure and function of the ribozyme. Although metal ions do not directly promote catalysis, we show that metal ion identity and the varying physicochemical properties of metal ions have an impact on the rate of glmS ribozyme self-cleavage. Specifically, these studies demonstrate that metal ion identity influences the overall apparent pKa of ribozyme self-cleavage, and metal ion binding largely reflects phosphate oxygen affinity. Results suggest that metal ions take alternative roles in supporting the mechanism of catalysis. Metal ions are essential to RNA structure and function. This work provides evidence that metal ion properties dictate binding and influence differences in the overall apparent pKa of the coenzyme-dependent self-cleavage reaction. The results have implications regarding alternative roles for metal ions in catalysis and impact the design of antibiotic coenzymes. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.