Catalytic Mechanism of Hyaluronate Lyase from <i>Spectrococcus pneumonia</i>: Quantum Mechanical/Molecular Mechanical and Density Functional Theory Studies

Abstract

Hyaluronate lyase from <i>Spectrococcus pneumonia</i> can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. The major functions of hyaluronan are to regulate water balance and osmotic pressure and act as an ion-exchange resin. It has been suggested in our previous molecular dynamics simulation that the binding of the substrate molecule could lead to the ionization of Y408 and protonation of H399. Followed by our recent molecular dynamics simulation of the enzyme–substrate complex, a unified proton abstraction and donation mechanism for this enzyme can be established using a combined quantum mechanical and molecular mechanical approach and density functional theory method. Y408 is shown to serve as the general base in the proton abstraction, while general acid is the next proton donation step. Overall, this reaction can be classified into <i>syn</i>-elimination reaction mechanism. The neutralization effects of C5 carboxylate group by several polar residues such as N349 and H399 were also examined. Finally, in combination of our previous molecular dynamics simulations, a complete catalytic cycle for the degradation of hyaluronan tetrasaccharide catalyzed by the hyaluronate lyase from <i>Spectrococcus pneumonia</i> is proposed