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. Author manuscript; available in PMC: 2012 Aug 1.
Published in final edited form as: Q Rev Biophys. 2010 Sep 8;43(4):423–447. doi: 10.1017/S0033583510000144

Figure 8.

Figure 8

Hypothetical catalytic mechanisms of the glmS ribozyme (Klein & Ferré-D’Amaré, 2006). (a) GlcN6P deprotonates the 2′-OH nucleophile through a proton relay employing two tightly bound water molecules, functioning as a general base catalyst. The resulting ammonium form of GlcN6P functions to stabilize the transition state electrostatically and also donates a proton to the 5′-oxo leaving group, functioning as a general acid catalyst. (b) The N1 imine of G40 functions as a general base catalyst. GlcN6P, in its ammonium form, functions as an electrostatic and general-acid catalyst. The ribozyme is inactive in the absence of GlcN6P or if a G40A mutation is made. The degree of impairment of the ribozyme indicated in parentheses is therefore an estimate based on the in vitro cleavage rate.