Molecular basis of site-selective N2-guanosine methylation in human tRNAs
Abstract
N2-methylguanosine (m2G) and N2,N2-dimethylguanosine (m22G) are conserved tRNA modifications installed at distinct positions. In human cells, TRMT11-TRMT112 modifies G10, TRMT1 modifies G26, and TRMT1L modifies G27. How these enzymes select different guanosines within the common L-shaped tRNA scaffold remains unclear. Here we report cryo-EM structures of human TRMT1, TRMT1L and TRMT11-TRMT112 bound to their tRNA substrates. TRMT1 forms a homodimer that creates composite RNA-binding surfaces, with a TRMT1-specific C-terminal Linker anchoring the G26-containing region. Disruption of dimerization or truncation of the Linker impairs tRNA binding and catalysis. Structures of TRMT1 in apo, sinefungin-bound and SAM-reacted states show that G26 flipping precedes cofactor binding, whereas cofactor engagement induces closure of the L1 loop and organizes the catalytic pocket. TRMT1L preserves a closely related catalytic geometry despite substitutions of several active-site residues, but engages tRNATyr in a markedly different orientation. TRMT11-TRMT112 uses a distinct docking architecture in which the THUMP and methyltransferase domains of TRMT11 jointly position the tRNA. At the target site, Arg314 replaces the interaction of G10 with C25, while Tyr311 stabilizes the extruded G10 through aromatic stacking. Together, these structures reveal a general principle for site-selective N2-guanosine methylation: enzyme-specific global docking defines the target region, whereas local base remodeling and base extrusion enables catalytic selection.
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