Abstract
Haloalkane dehalogenases (EC 3.8.1.5) play an important role in hydrolytic degradation of halogenated compounds, resulting in a halide ion, a proton, and an alcohol. They are used in biocatalysis, bioremediation, and biosensing of environmental pollutants and also for molecular tagging in cell biology. The method of ancestral sequence reconstruction leads to prediction of sequences of ancestral enzymes allowing their experimental characterization. Based on the sequences of modern haloalkane dehalogenases from the subfamily II, the most common ancestor of thoroughly characterized enzymes LinB from Sphingobium japonicum UT26 and DmbA from Mycobacterium bovis 5033/66 was in silico predicted, recombinantly produced and structurally characterized. The ancestral enzyme AncLinB-DmbA was crystallized using the sitting-drop vapor-diffusion method, yielding rod-like crystals that diffracted X-rays to 1.5 Å resolution. Structural comparison of AncLinB-DmbA with their closely related descendants LinB and DmbA revealed some differences in overall structure and tunnel architecture. Newly prepared AncLinB-DmbA has the highest active site cavity volume and the biggest entrance radius on the main tunnel in comparison to descendant enzymes. Ancestral sequence reconstruction is a powerful technique to study molecular evolution and design robust proteins for enzyme technologies.
Highlights
Halogenated compounds are major components of herbicides, insecticides, fungicides, and other chemical agents that are widespread in industry and agriculture
Haloalkane dehalogenases (HLDs) are divided into three subfamilies, HLD-I, HLD-II, and HLD-III, according to the composition of their catalytic residues and the anatomy of the cap domain
The structural analysis of the reconstructed ancestral enzyme AncLinBDmbA was performed, and the crystal structure was compared with closely related descendants LinB and DmbA
Summary
Halogenated compounds are major components of herbicides, insecticides, fungicides, and other chemical agents that are widespread in industry and agriculture. Haloalkane dehalogenases (HLDs) (EC 3.8.1.5) are hydrolytic enzymes that cleave carbon-halogen bonds in a broad range of halogenated aliphatic compounds, resulting in a corresponding alcohol, a halide ion, and a proton [2,3,4]. The interest in these enzymes is growing because of their utilization in biocatalysis, bioremediation, biosensing, and molecular imaging [5]. The tertiary structure of HLDs is comprised of two domains: an α/β-hydrolase core domain and a helical cap domain. The catalytic residues in the HLD-I subfamily are D-H-D/W-W, while HLD-II members predominantly contain D-H-E/N-W and HLD-III members contain D-H-D/N-W [10,11]
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