Identification by Mn ²⁺ rescue of two residues essential for the proton transfer of tRNase Z catalysis

Abstract

Thermotoga maritima tRNase Z cleaves pre-tRNAs containing the ₇₄CCA ₇₆ sequence precisely after the A ₇₆ residue to create the mature 3′ termini. Its crystal structure has revealed a four-layer αβ/βα sandwich fold that is typically found in the metallo-β-lactamase superfamily. The well-conserved six histidine and two aspartate residues together with metal ions are assumed to form the tRNase Z catalytic center. Here, we examined tRNase Z variants containing single amino acid substitutions in the catalytic center for pre-tRNA cleavage. Cleavage by each variant in the presence of Mg ²⁺ was hardly detected, although it is bound to pre-tRNA. Surprisingly, however, Mn ²⁺ ions restored the lost Mg ²⁺-dependent activity with two exceptions of the Asp52Ala and His222Ala substitutions, which abolished the activity almost completely. These results provide a piece of evidence that Asp-52 and His-222 directly contribute the proton transfer for the catalysis.