Substrate Epoxidation Catalyzed by the Nonheme Iron Dioxygenase Dapdiamide Biosynthesis Enzyme C. Why Is the Substrate Tethered?

In this work a computational study shows the differences in binding and catalysis of a nonheme iron oxygenase with tethered versus nontethered substrate. The tethered substrate is positioned in an ideal orientation near the active site, while the nontethered substrate shows more dynamics and is not positioned well for double bond epoxidation.

Abstract

Enzymes usually react with a free substrate, although some examples have appeared in the literature of enzymes that utilize a substrate tethered to a protein carrier. However, it is not clear what advantage the tethering has, and therefore a computational study was performed. In particular, we report here the first computational study on the nonheme iron dioxygenase involved in the epoxidation reaction during the dapdiamide biosynthesis (DdaC) and investigate tethered and nontethered substrates. Molecular dynamics (MD) simulations show that the protein carrier applies pressure onto the surface of the protein and influences the fold and active site description and leads to differences in substrate-oxidant interactions. Quantum chemical calculations give much lower epoxidation barriers for the activation of the tethered substrate by 7 kcal mol⁻¹ over the nontethered substrate and highlight the advantage of a tethered substrate in catalysis.

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