X-ray structure at 1.76 angstrom resolution of a polypeptide phospholipase A(2) inhibitor

The high resolution crystal structure of a natural PLA(2) inhibitor has been determined by Patterson search methods. In the heterodimeric, neurotoxic complex, vipoxin, isolated from the venom of Bulgarian viper, PLA(2) inhibitor represents the non-toxic subunit. The model was refined to a crystallographic R-factor of 15.5% for data between 6 and 1.76 Angstrom resolution. The packing of the inhibitor in the crystal reveals close contacts between the molecules, which are symmetry-related by the 2-fold axes of the lattice. These pairs associate as a crystallographic dimer, stabilized by a set of interactions, including van der Waals contacts between residues from symmetry-related pairs, denoted as the recognition site and the recognition surface. Residues Ph3, Trp31 and Tyr119 represent the recognition site of inhibitor which possibly fits to the hydrophobic wall of the target PLA(2). The topology of the inhibitor represents the PLA(2) type of folding: three long helices and a beta-hairpin. Superposition of the structure of the inhibitor shows an almost complete overlap with different mammalian and viper PLA(2) in the backbone and in the position of the sidechains of the residues that belong to the active centre and the hydrophobic wall. A ''lock and key'' mechanism of recognition of its native PLA(2) in gland cells and other toxic PLA(2) in vitro has been suggested. The mechanism includes complementary ''head to tail'' interactions between the recognition site of the inhibitor and a recognition surface located on the hydrophobic wall of the target PLA(2). Having a high spatial homology with the PLA(2) family of enzymes but opposing their action, the inhibitor from vipoxin presents an example of a divergent evolution of an ancient PLA(2). The presence of a space for binding calcium in the inhibitor is believed to be a rudiment and proof of a common origin with PLA(2). (C) 1997 Academic Press Limited.