Molecular dynamics simulations of class C beta-lactamase from Citrobacter freundii: insights into the base catalyst for acylation.
Herein, we present results from molecular dynamics (MD) simulations of the class C beta-lactamase from Citrobacter freundii and its Michaelis complex with aztreonam. Four different configurations of the active site were modeled in aqueous solution, and their relative stability was estimated by means of quantum mechanical energy calculations. For the free enzyme, the energetically most stable configurations present a neutral Lys67 residue or an anionic Tyr150 side chain. Our calculations predict that these two configurations are quite close in terms of free energy, the anionic Tyr150 state being favored by approximately 1 kcal/mol. In contrast, for the noncovalent complex formed between the C. freundii enzyme and aztreonam, the energetic analyses predict that the configuration with the neutral Lys67 residue is much more stable than the anionic Tyr150 one (approximately 20 kcal/mol). Moreover, the MD simulations reveal that the neutral Lys67 state results in a proper enzyme-aztreonam orientation for nucleophilic attack and in a very stable contact between the nucleophilic hydroxyl group of Ser64 and the neutral amino side chain of Lys67. Thus, both the computed free energies and the structural analyses support the assignation of Lys67 as the base catalyst for the acylation step in the native form of the C. freundii enzyme.
Díaz
Natalia
N
Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería, 8, 33006 Oviedo, Asturias, Spain. diazfnatalia@uniovi.es
Suárez
Dimas
D
Sordo
Tomás L
TL
D000215:Acylation; D001051:Apoenzymes / Q000737:chemistry / Q000378:metabolism; D001398:Aztreonam / Q000737:chemistry / Q000378:metabolism; D002384:Catalysis; D016971:Citrobacter freundii / Q000201:enzymology*; D020650:Combinatorial Chemistry Techniques; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D011789:Quantum Theory; D013816:Thermodynamics; D065093:beta-Lactamase Inhibitors; D001618:beta-Lactamases / Q000737:chemistry* / Q000145:classification* / Q000235:genetics
D001051:Apoenzymes; D004791:Enzyme Inhibitors; D065093:beta-Lactamase Inhibitors; D001618:beta-Lactamases; D001398:Aztreonam