The crystal structure of recombinant murine liver cytosolic epoxide hydrolase has been determined at 2.8 Å resolution. The structure of this dimeric enzyme reveals a catalytic site in the C-terminal domain ("catalytic domain") partially similar to that of haloalkane dehalogenase. The binding of nanomolar affinity inhibitors confirm this as the active site involved in the hydrolysis of carcinogenic and mutagenic epoxide substrates of both natural and man-made origin, as well as endogenous lipid epoxides. A structure-based mechanism is proposed that illuminates the unique chemical strategy for the activation of epoxide substrates for hydrolysis and detoxification. Surprisingly, an "inactive" active site is found in the N-terminal domain ("vestigial domain") similar to that of another enzyme of halocarbon metabolism, haloacid dehalogenase. Although the vestigial domain does not participate in catalysis, it does play a critical structural role by stabilizing the dimer in a novel domain-swapped architecture. Despite inconclusively weak sequence identities among these three enzymes, the resemblance of the epoxide hydrolase catalytic and vestigial domains with haloalkane dehalogenase and haloacid dehalogenase, respectively, indicates common ancestral origins in the evolution of xenobiotic metabolism. Accordingly, a structure-based evolutionary sequence leading from primitive monomers to the current-day domain-swapped dimer is postulated.
