Crystal structure of phospholipase A₂ from Indian cobra reveals a trimeric association

Phospholipase A₂ (PLA₂) from Indian cobra venom (Naja naja naja) was crystallized from ethanol in space group P4₃2₁2 in the presence of Ca²⁺. The x-ray crystal structure was determined to 2.3-Å resolution by molecular replacement techniques using a theoretical model constructed from homologous segments of the bovine pancreatic, porcine pancreatic, and rattlesnake venom crystal structures. The structure was refined to an R value of 0.174 for 17,542 reflections between 6.0- and 2.3-Å resolution (F > 2σ), including 148 water molecules. The 119-amino acid enzyme has an overall architecture strikingly similar to the other known PLA₂ structures with regions implicated in catalysis showing the greatest structural conservation. Unexpectedly, three monomers were found to occupy the asymmetric unit and are oriented with their catalytic sites facing the pseudo-threefold axis with ≈15% of the solvent accessible surface of each monomer buried in trimer contacts. The majority of the interactions at the subunit interfaces are made by residues unique to PLA₂ sequences from cobra and krait venoms. The possible relevance of this unique trimeric structure is considered.