Molecular insights into catalytic specificity of α-L-rhamnosidase from Bacteroides thetaiotaomicron by molecular docking and dynamics

Recently, a kind of α-L-rhamnosidase from Bacteroides thetaiotaomicron (BtRha) was characterized and studied for the hydrolysis of natural substrates. In order to investigate catalytic specificity of BtRha, three natural substrates, epimedin C, naringin, and hesperidin, were selected for molecular docking and dynamics simulation. The results revealed that there are two sets of catalytic residues participating in hydrolysis reaction: one set is composed of Arg37 and Glu39 while the other composed of Asp335 and Glu595. This study gained insight into the dynamic catalytic mechanism of BtRha for the first time, providing valuable clues for the rational design of individual α-L-rhamnosidase.