pKa, MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step.
The acylation step of the catalytic mechanism of beta-lactamases and penicillin-binding proteins (PBPs) has been studied with various approaches. The methods applied range from molecular dynamics (MD) simulations to multiple titration calculations using the Poisson-Boltzmann approach to quantum mechanical (QM) methods. The mechanism of class A beta-lactamases was investigated in the greatest detail. Most approaches support the critical role of Glu-166 and hydrolytic water in the acylation step of the enzymatic catalysis in class A beta-lactamases. The details of the catalytic mechanism have been revealed by the QM approach, which clearly pointed out the critical role of Glu-166 acting as a general base in the acylation step with preferred substrates. Lys-73 shuffles a proton abstracted by Glu-166 O(epsilon ) to the beta-lactam nitrogen through Ser-130 hydroxyl. This proton is transferred from O(gamma) of the catalytic Ser-70 through the bridging hydrolytic water to Glu-166 O(epsilon ). Then the hydrogen is simultaneously passed through S(N)2 inversion mechanism at Lys-73 N(zeta) to Ser-130 O(gamma), which loses its proton to the beta-lactam nitrogen. The protonation of beta-lactam nitrogen proceeds with an immediate ring opening and collapse of the first tetrahedral species into an acyl-enzyme intermediate. However, the studies that considered the effect of solvation lower the barrier for the pathway, which utilizes Lys-73 as a general base, thus creating a possibility of multiple mechanisms for the acylation step in the class A beta-lactamases. These findings help explain the exceptional efficiency of these enzymes. They emphasize an important role of Glu-166, Lys-73, and Ser-130 for enzymatic catalysis and shed light on details of the acylation step of class A beta-lactamase mechanism. The acylation step for class C beta-lactamases and six classes of PBPs were also considered with continuum solvent models and MD simulations.
Massova
Irina
I
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143-0446, USA. irina@gene.com
Kollman
Peter A
PA
D000215:Acylation; D001407:Bacillus / Q000737:chemistry; D001426:Bacterial Proteins; D002352:Carrier Proteins / Q000737:chemistry*; D003198:Computer Simulation; D016972:Enterobacter cloacae / Q000201:enzymology; D004926:Escherichia coli / Q000201:enzymology; D006602:Hexosyltransferases; D006868:Hydrolysis; D007700:Kinetics; D008958:Models, Molecular; D018716:Molecular Mimicry; D002267:Muramoylpentapeptide Carboxypeptidase / Q000737:chemistry*; D046915:Penicillin-Binding Proteins; D010458:Peptidyl Transferases; D011487:Protein Conformation; D011522:Protons; D011789:Quantum Theory; D012997:Solvents; D013211:Staphylococcus aureus / Q000737:chemistry; D013696:Temperature; D001618:beta-Lactamases / Q000737:chemistry*
D001426:Bacterial Proteins; D002352:Carrier Proteins; D046915:Penicillin-Binding Proteins; D011522:Protons; D012997:Solvents; D010458:Peptidyl Transferases; D006602:Hexosyltransferases; D002267:Muramoylpentapeptide Carboxypeptidase; D001618:beta-Lactamases