Haloalkane dehalogenases: Structure of a Rhodococcus enzyme

The hydrolytic haloalkane dehalogenases are promising bioremediation and bi ocatalytic agents. Two:general classes of dehalogenases have been reported from Xanthobacter and Rhodococcus, While these enzymes share 30% amino acid sequence identity, they have significantly different substrate specificiti es and halide-binding properties. We report the 1.5 Angstrom resolution cry stal structure of the Rhodococcus dehalogenase at pH 5.5, pH 7.0, and pH 5. 5 in the presence of NaI, The Rhodococcus and Xanthobacter enzymes have sig nificant structural homology in the alpha/beta hydrolase core, but differ c onsiderably in the cap domain. Consistent with its broad specificity for pr imary, secondary, and cyclic haloalkanes, the Rhodococcus enzyme has a subs tantially larger active site cavity. Significantly, the Rhodococcus dehalog enase has a different catalytic triad topology than the Xanthobacter enzyme . In the Xanthobacter dehalogenase, the third carboxylate functionality in the triad is provided by D260, which is positioned on the loop between beta 7 and the penultimate helix. The carboxylate functionality in the Rhodococ cus catalytic tried is donated from E141, a model of the enzyme cocrystalli zed with sodium iodide shows two iodide binding sites; one that defines the normal substrate and product-binding site and a second within the active s ite region. In the substrate and product complexes, the halogen binds to th e Xanthobacter enzyme via hydrogen bonds with the (NH)-H-eta of both W125 a nd W175. The Rhodococcus enzyme does not have a tryptophan analogous to W17 5. Instead, bound halide is stabilized with hydrogen bonds to the (NH)-H-et a of W118 and to (NH)-H-delta of N52, It appears that when cocrystallized w ith NaI the Rhodococcus enzyme has a rare stable S-I covalent bond to S-y o f C187.