Fig. 3. The methyltransferase ribozyme employs general acid catalysis.

(a) A protonated cytidine is suggested in the active site for RNA-catalysed methyl group transfer. The mechanism involves the nucleophilic attack of the nitrogen lone pair (N¹ of A7) on the methyl carbon (at O⁶ of m⁶G). The guanine leaving group accepts a proton from cytidine C12⁺, resulting in a positive charge on m¹A and a standard G:C hydrogen bonding pattern in the product state. (b) Representative PAGE images of the kinetic assays from 3 independent experiments with split MTR1 at pH 6.0 and pH 7.5 under single-turnover conditions. (c) pH rate profile for split MTR1 (n = 2 or 3, individual data points for each buffer (different symbols for same pH indicate different buffers used; for details see methods section and source data). (d, e) Comparison of methyl transfer rates for split (d) and full-length (e) MTR1, reaction with m⁶G at pH 6.0 (red) and pH 7.5 (blue). Conditions in b-e) 5'-³²P-labeled R1, 10 μM MTR1, 100 μM m⁶G, 40 mM MgCl₂, 25°C.