Initial events in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus [corrected] pneumoniae: QM/MM simulation.

Abstract

Hyaluronate lyase from Spectrococcus pneumonia 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. In this work, we focus on the prerequisite issue of the enzymatic reaction, i.e., the initial reactive conformer. Based on the quantum mechanical and molecular mechanical molecular dynamic simulations and free energy profiles, a near attack conformer was obtained for the degradation of hyaluronan catalyzed by the hyaluronate lyase. Along with the substrate binding, the phenylhydroxyl hydrogen atom of Tyr408 will transfer to nearby His399 via a near barrierless transition state, which results in a negatively charged Tyr408 and positively charged His399. The Tyr408, rather than the previously proposed His399, was suggested to act as the general base for the subsequent β-elimination reaction. The His399 was suggested to have the function of neutralizing the C5-carboxyl group.

• Authors: Min Zheng, Hongling Zhang, Dingguo Xu
• Journal: The journal of physical chemistry. B (J Phys Chem B) Vol. 116 Issue 36 Pg. 11166-72 (Sep 13 2012) ISSN: 1520-5207 [Electronic] United States
• PMID: 22916709 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• Hyaluronic Acid
• Polysaccharide-Lyases
• hyaluronate lyase

Topics

• Binding Sites
• Catalysis
• Hyaluronic Acid (chemistry, metabolism)
• Molecular Dynamics Simulation
• Polysaccharide-Lyases (chemistry, metabolism)
• Protein Conformation
• Streptococcus pneumoniae (chemistry, enzymology)