Lysine carboxylation in proteins: OXA-10 β-lactamase

An increasing number of proteins are being shown to have an N-carboxylated lysine in their structures, a posttranslational modification of proteins that proceeds without the intervention of a specific enzyme. The role of the carboxylated lysine in these proteins is typically structural (hydro- gen bonding or metal coordination). However, car- boxylated lysines in the active sites of OXA-10 and OXA-1 -lactamases and the sensor domain of BlaR signal-transducer protein serve in proton transfer events required for the functions of these proteins. These examples demonstrate the utility of this un- usual amino acid in acid-base chemistry, in expan- sion of function beyond those of the 20 standard amino acids. In this study, the ONIOM quantum- mechanical/molecular-mechanical (QM/MM) method is used to study the carboxylation of lysine in the OXA-10 -lactamase. Lys-70 and the active site of the OXA-10 -lactamase were treated with B3LYP/6- 31G(d,p) density functional calculations and the remainder of the enzyme with the AMBER molecu- lar mechanics force field. The barriers for unas- sisted carboxylation of neutral lysine by carbon dioxide or bicarbonate are high. However, when the reaction with CO2 is catalyzed by a molecule of water in the active site, it is exothermic by about 13 kcal/mol, with a barrier of approximately 14 kcal/ mol. The calculations show that the carboxylation and decarboxylation of Lys-70 are likely to be accom- panied by deprotonation and protonation of the carbamate, respectively. The analysis may also be relevant for other proteins with carboxylated lysines, a feature that may be more common in nature than previously appreciated. Proteins 2005;