Crystal structure of a novel phospholipase A2 from Naja naja sagittifera with a strong anticoagulant activity

This is the first PLA₂ crystal structure from group I that shows a strong anticoagulant property. The monomeric PLA₂ was purified from the venom of Naja naja sagittifera (Indian cobra). Its amino acid sequence has been determined using cDNA technique. The amino acid sequence of sPLA₂ contains three positively charged and two negatively charged residues in the segment 54–71 (numbering scheme of sPLA₂) thus giving this region an overall cationic amphiphilic surface. This suggested the presence of an anticoagulant activity in sPLA₂. The enzyme was crystallized using hanging drop vapour diffusion method in the presence of calcium chloride. The crystals belong to space group P4₁ with cell dimensions of a=b=42.0 Å, c=65.9 Å. The X-ray crystal structure was determined at 1.8 Å resolution using molecular replacement method and refined to an R value of 0.179 for 10,023 reflections. The overall scaffolding of sPLA₂ is essentially similar to those observed for other group I PLA₂s. However, the conformations of various surface loops were found to be significantly different. The most significant observation pertains to the anticoagulant loop in which both the acidic residues are engaged in intramolecular interactions whereas all the three basic residues are free to interact with other molecules. This makes the sPLA₂ a potentially strong anticoagulating molecule.