Dynamic characterization and substrate binding of cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase-an enzyme used in bioremediation.

In recent years, techniques involving the use oforganisms to remove or neutralize pollutants from contaminatedsites have attracted great attention. The aim of bioremediationis to use naturally occurring organisms to degradedangerous substances to less toxic or non toxic molecules.The gram-negative bacterium Pandoraea pnomenusa strainB-356 (Pp) has been found to be able to transform a persistentclass of organic pollutant compounds, namely the biphenyland polychlorinated biphenyls (PCBs). A key enzyme in thePCB catabolic pathway is NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (BphB), for whichthe crystal structure from Pp has been crystallized in apo-,NAD-bound and biphenyldiol-/NAD-bound forms. The substratebinding loop structure has not been completely resolvedto date in the former two bound states. Here we report theresults of the first extensive molecular dynamics simulationson the three different states of PpBphB. This allowed an indepth characterization of the mechanism of ligand uptake andbinding, including unraveling of the gating mechanism. Oursimulations give a deep insight into several dynamic featuresof the enzyme that were not captured by crystal structure