Understanding the cooperative effects in the catalysis of homodimeric fluoroacetate dehalogenase

Fluoroacetate dehalogenases (FAcD), a homodimeric enzyme, catalyzes the conversion of fluoroacetic acid to glycolic acid (GoA). It has been proved that the enzyme has a half-of-the-site reactivity. Namely, its catalytic (C) subunit converts the first substrate to a covalent intermediate; then, the non-catalytic (NC) subunit binds a second substrate and promotes the conversion of the intermediate in the C subunit into the final product. After the release of the product, the C subunit becomes the NC subunit, and the previous NC subunit becomes the C subunit. To elucidate the detailed mechanism behind this cooperative catalysis, we have conducted microsecond-scale MD simulations along the reaction pathway. The simulations indicate that the substrate in the NC subunit induces W185 and Y141 adopting an open conformation in the C subunit. The opening of W185 (C) facilitates the entry of catalytic water, enhancing the catalytic activity for product formation, while the opening of Y141 (C) creates an unfavorable environment for product binding, promoting its release. An interaction network analysis reveals that the substrate in the NC subunit can induce conformational changes through a conserved water chain at the interface.