Crystal structure analysis of phospholipase A2 from trimeresurus flavoviridis (Habu snake) venom at 1.5 A resolution

The crystal structure of dimeric phospholipase A2 (PLA2) from the venom of Habu snake, Trimeresurus flavoviridis, has been determined by the molecular replacement method, and has been refined at 1.5 A resolution to an R-factor of 0.175. In the crystal, T. flavoviridis PLA2 forms a dimer using two 14 kDa subunits related by a pseudo 2-fold axis. Along the axis, the dimer has a narrow channel passing through it. Although no calcium ion is present in the calcium binding site, the peptide-chain folding of the subunits, the conformation of the catalytic residues, and the hydrogen-bonding network around the active sites are almost identical to those of the group I/II monomeric or dimeric PLA2s. The catalytic residues in both subunits are buried in the interior of the dimer and are inaccessible to substrate from the bulk solvent. In addition, the subunits of the dimer interact with each other at the hydrophobic region of the molecular surface where the entrance to the active site opens and where PLA2 is presumed to interact with the phospholipid of the substrate. Therefore, it is inferred that dimerization of T. flavoviridis PLA2 is the result of free-energy minimization by excluding the hydrophobic molecular surface from the aqueous solvent, rather than being required for the enzymatic function.