QM/MM Reveals Coordination Shift behind Early Lanthanide Preference in Methanol Dehydrogenase XoxF

Abstract

Lanthanides serve as essential catalytic cofactors in methanol dehydrogenase (MDH), yet the structural and energetic basis for the biological preference for early lanthanides (La–Gd) remains poorly understood. Here, we present a systematic Quantum-Mechanics/Molecular-Mechanics (QM/MM) study of the full Ln series (La–Lu) using the ωB97X-D4rev exchange-correlation functional. Structurally, we identify a substrate-dependent coordination switch: in the Michaelis–Menten complex, the biologically relevant light Ln (La–Gd) maintains a 10-coordinate geometry, whereas a discrete transition to a 9-coordinate state occurs from Tb onward, driven by the shift of the essential Asp301 from bidentate to monodentate coordination mode. Notably, this shift is absent in the substrate-free enzyme, indicating that substrate binding enforces the steric crowding that disfavors heavier metals. Energetic analysis reveals that within the biologically relevant window (La–Gd), substrate affinity is mostly uniform, while enzyme binding affinity exhibits a clear and steady preference for the lighter metals. These results demonstrate that biological lanthanide selection in MDH arises from a combination of higher binding affinity for early lanthanides and their ability to preserve a catalytically competent 10-coordinate geometry, rather than from differential substrate binding. Taken together, our findings provide a structural and energetic framework for understanding the coordination properties of the lanthanide series in the active site of the MDH and may guide further QM/MM studies on the reaction mechanism of this enzyme as well as the engineering of lanthanide-dependent biocatalysts.