Interfacial catalysis: The mechanism of phospholipase A₂

A chemical description of the action of phospholipase A₂ (PLA₂) Can now be inferred with confidence from three high-resolution x-ray crystal structures. The first is the structure of the PLA₂ from the venom of the Chinese cobra (Naja naja atra) in a complex with a phosphonate transition-state analogue. This enzyme is typical of a large, well-studied homologous family of PLA₂s. The second is a similar complex with the evolutionarily distant bee-venom PLA₂. The third structure is the uninhibited PLA₂ from Chinese cobra venom. Despite the different molecular architectures of the cobra and bee-venom PLA₂s, the transition-state analogue interacts in a nearly identical way with the catalytic machinery of both enzymes. The disposition of the fatty-acid side chains suggests a common access route of the substrate from its position in the lipid aggregate to its productive interaction with the active site. Comparison of the cobra-venom complex with the uninhibited enzyme indicates that optimal binding and catalysis at the lipid-water interface is due to facilitated substrate diffusion from the interfacial binding surface to the catalytic site rather than an allosteric change in the enzyme's structure. However, a second bound calcium ion changes its position upon the binding of the transition-state analogue, suggesting a mechanism for augmenting the critical electrophile.