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Zinc Metallo-β-Lactamase from Bacteroides fragilis:  A Quantum Chemical Study on Model Systems of the Active Site

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journal contribution
posted on 18.04.2000, 00:00 by Natalia Díaz, Dimas Suárez, Kenneth M. Merz
Quantum chemical optimizations of the small model systems ([Zn(NH3)3(H2O)]2+, [Zn(NH3)3(OH)]+, [Zn(NH3)(SH) (HCOO)(OH)]-1(H2O) and [Zn(NH3)(SH)(HCOO)(H2O)] (H2O)) were performed at different levels of quantum mechanical theory (HF/6-31G*, B3LYP/6-31G*, and MP2/6-31G*) to characterize the Zn−ligand bonds for the Zn1 and Zn2 binding sites of metallo-β-lactamases. The nature of the zinc coordination environment was further studied by considering larger mononuclear complexes at the B3LYP/6-31G*//HF/6-31G* level of theory ([Zn(Me-Im)3(H2O)]2+, [Zn(Me-Im)(SCH3)(CH3COO)(H2O)](H2O), etc.). The structure and properties of a series of binuclear model compounds showing an hydroxy-mediated Zn1···Zn2 interaction were also analyzed at the same level of theory. One of the binuclear models with a global charge of +2, reproduces the main structural features of the Bacteroides fragilis active site as determined by X-ray crystallography. The proposed β-lactamase model has a monoprotonated state characterized by a strong H-bond interaction between a zinc-shared water molecule and a Zn2-bound Asp carboxylic group. The theoretical results are discussed in the context of experimental kinetic and structural data on the B. fragilis active site, resulting in insights into the nature of the zinc−ligand interactions, the location of the mechanistically relevant water molecules, and the actual protonation state of the active site. By combining the present results with previous theoretical and experimental work, mechanistic details for the mode of action of zinc β-lactamases are discussed.