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We analyzed processing of precursor tRNAs carrying a single 2′-deoxy, 2′-OCH 3 , or locked nucleic acid (LNA) modification at G+1 by  Escherichia coli  RNase P RNA in the absence and presence of its protein cofactor. The extra methyl or methylene group caused a substrate binding defect, which was rescued at higher divalent metal ion (M 2+ ) concentrations (more efficiently with Mn 2+  than Mg 2+ ), and had a minor effect on cleavage chemistry at saturating M 2+  concentrations. The 2′-OCH 3  and LNA modification at G+1 resulted in higher metal ion cooperativity for substrate binding to RNase P RNA without affecting cleavage site selection. This indicates disruption of an M 2+  binding site in enzyme-substrate complexes, which is compensated for by occupation of alternative M 2+  binding sites of lower affinity. The 2′-deoxy modification at G+1 caused at most a two-fold decrease in the cleavage rate; this mild defect relative to 2′-OCH 3  and LNA at G+1 indicates that the defect caused by the latter two is steric in nature. We propose that the 2′-hydroxyl at G+1 in the substrate is in the immediate vicinity of the M 2+  cluster at the phosphates of A67 to U69 in helix P4 of  E. coli  RNase P RNA.

biological chemistry

A 2′-methyl or 2′-methylene group at G+1 in precursor tRNA interferes with Mg 2+  binding at the enzyme-substrate interface in E-S complexes of  E. coli  RNase P