Mg²⁺-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• TrmD is a bacteria-specific methyltransferase essential for synthesizing methylated m¹G37-tRNA.
• The role and structural location of Mg²⁺ in TrmD's catalytic mechanism were previously unknown.

Purpose of the Study:

• To determine the binding site and function of Mg²⁺ in TrmD's catalytic activity.
• To elucidate the mechanism by which Mg²⁺ facilitates methyl transfer.

Main Methods:

• Molecular dynamics (MD) simulations to identify the Mg²⁺ binding pocket.
• Experimental mutation studies to validate computational findings.
• Quantum mechanical (QM) calculations to assess methyl transfer feasibility.

Main Results:

• A Mg²⁺ binding pocket was identified in the TrmD active site, coordinated by aspartate and glutamate residues.
• Mg²⁺ binding induces a specific conformation in the methyl donor S-adenosylmethionine (SAM) and reorganizes the active site.
• QM calculations confirmed that methyl transfer is energetically favorable only with Mg²⁺ bound in the identified position.

Conclusions:

• Mg²⁺ is essential for TrmD catalysis by optimizing the active site geometry for methyl transfer.
• The findings provide a basis for developing novel antibacterial drugs targeting Mg²⁺ binding to TrmD.