Conformational modeling of substrate binding to endocellulase E2 from Thermomonospora fusca.

Molecular mechanics calculations have been used to place a cellotetraose substrate into the active site of the crystallographically determined structure of endocellulase E2 from Thermomonospora fusca. In the lowest energy model structure, the second residue of the substrate oligosaccharide is tilted away from the planar ribbon geometry of cellulose as it is in the X-ray structure of the E2cd-cellobiose co-crystal. This tilt is the result of the topology of the binding site, and results in several strong carbohydrate-protein hydrogen bonds. The tilting produces a twisting of the glycosidic linkage of the cleavage site between residues two and three. In the predicted enzyme-substrate complex both of the Asp residues believed to function in general acid and base roles in the previously proposed model for the mechanism are distant from the bond being cleaved. Molecular dynamics simulations of the complex were conducted, and while the putative catalytic Asp residues remained distant from the cleavage site, the proton of Tyr73 briefly came within van der Waals contact of the linkage oxygen.