Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis
The determination of the protonation state of enzyme active sites may be crucial for the investigation of their mechanism of action. In the bizinc beta-lactamase family of enzymes, no consensus has been reached on the protonation state of a fully conserved amino acid present in the active site, Asp120. To address this issue, we carry out here density functional theory (DFT) calculations on large models (based on Bacteroides fragilis X-ray structure) which include the metal coordination polyhedron and groups interacting with it. Our calculations suggest that Asp120 is ionized. The relevance of this finding for site-directed mutagenesis experiments on the 120 position and on the mechanism of action is discussed.
Keywords: Aspartic Acid/*chemistry ; Bacteroides fragilis/*enzymology ; Binding Sites ; Catalysis ; Computational Biology ; Models ; Molecular ; Molecular Conformation ; Mutagenesis ; Site-Directed ; Protons ; beta-Lactamases/*chemistry/genetics
International School for Advanced Studies, SISSA and INFM-DEmocritos MOdeling Center for Research in aTOmistic Simulation, via Beirut 2-4, 34014 Trieste, Italy.
Record created on 2008-04-28, modified on 2016-08-08