Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus
Structure and dynamics of substrate binding (cefotaxime) to the catalytic pocket of the mononuclear zinc-beta-lactamase from Bacillus cereus are investigated by molecular dynamics simulations. The calculations, which are based on the hydrogen-bond pattern recently proposed by Dal Peraro et al. (J Biol Inorg Chem 2002; 7:704-712), are carried out for both the free and the complexed enzyme. In the resting state, active site pattern and temperature B-factors are in agreement with crystallographic data. In the complexed form, cefotaxime is accommodated into a stable orientation in the catalytic pocket within the nanosecond timescale, interacting with the enzyme zinc-bound hydroxide and the surrounding loops. The beta-lactam ring remains stable and very close to the hydroxide nucleophile agent, giving a stable representation of the productive enzyme-substrate complex.
Keywords: Bacillus cereus/*enzymology ; Binding Sites ; Catalysis ; Cefotaxime/chemistry/*metabolism ; Computer Simulation ; Electrostatics ; Hydrogen Bonding ; Metalloproteins/*chemistry/*metabolism ; Models ; Molecular ; Motion ; Protein Binding ; Substrate Specificity ; Temperature ; Zinc/metabolism ; beta-Lactamases/*chemistry/*metabolism
International School for Advanced Studies, SISSA and INFM-DEMOCRITOS, Trieste, Italy.
Record created on 2008-04-28, modified on 2016-08-08