Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted...

Area of Science:

• Structural Biology
• Molecular Biology
• Biochemistry

Background:

• The SpoU and tRNA methyltransferase D (TrmD) family of methyltransferases (MTases) possesses a unique deep trefoil knot architecture conserved across all domains of life.
• In bacteria, TrmD is essential for catalyzing the N(1)-methylguanosine (m(1)G) modification at position 37 of transfer RNAs (tRNAs) containing the (36)GG(37) sequence.
• This m(1)G37 modification on tRNA is crucial for proper ribosomal function, specifically preventing +1 frameshift errors during translation.

Purpose of the Study:

• To elucidate the structural mechanism by which TrmD binds its substrate tRNA in an AdoMet-dependent manner.
• To understand the role of the conserved trefoil knot and TrmD-specific regions in substrate recognition and catalysis.

Main Methods:

• X-ray crystallography was employed to determine the structure of the TrmD homodimer.
• The crystal structure was obtained in complex with a substrate tRNA and an analog of S-adenosyl-l-methionine (AdoMet).

Main Results:

• The crystal structure revealed how TrmD binds the substrate tRNA through an AdoMet-dependent mechanism.
• The conserved trefoil knot center accommodates the adenosine moiety of AdoMet through conformational changes (loosening/retightening).
• TrmD-specific regions interact with the methionine moiety of AdoMet, facilitating global tRNA binding and specific recognition of G37 and G36.

Conclusions:

• The study provides a detailed structural understanding of TrmD-mediated tRNA m(1)G37 modification.
• The findings highlight the intricate interplay between the trefoil knot, TrmD-specific regions, AdoMet, and tRNA for precise substrate binding and catalysis.
• This mechanism ensures the synthesis of correctly modified m(1)G37-tRNA, vital for translational fidelity.