1VPI

PHOSPHOLIPASE A2 INHIBITOR FROM VIPOXIN

Summary for 1VPI

• Entry DOI: 10.2210/pdb1vpi/pdb
• Descriptor: PHOSPHOLIPASE A2 INHIBITOR (2 entities in total)
• Functional Keywords: phospholipase a2 inhibitor, recognition, molecular evolution, neurotoxin
• Biological source: Vipera ammodytes (sand viper)
• Cellular location: Secreted: P04084
• Total number of polymer chains: 1
• Total formula weight: 13650.03

Authors

Devedjiev, Y.D.,Popov, A.N. (deposition date: 1996-12-17, release date: 1997-12-24, Last modification date: 2024-10-23)

Primary citation

Devedjiev, Y.,Popov, A.,Atanasov, B.,Bartunik, H.D.
X-ray structure at 1.76 A resolution of a polypeptide phospholipase A2 inhibitor.
J.Mol.Biol., 266:160-172, 1997

PubMed Abstract: The high resolution crystal structure of a natural PLA2 inhibitor has been determined by Patterson search methods. In the heterodimeric, neurotoxic complex, vipoxin, isolated from the venom of Bulgarian viper, PLA2 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 A 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 PLA2. The topology of the inhibitor represents the PLA2 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 PLA2 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 PLA2 in gland cells and other toxic PLA2 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 PLA2. Having a high spatial homology with the PLA2 family of enzymes but opposing their action, the inhibitor from vipoxin presents an example of a divergent evolution of an ancient PLA2. The presence of a space for binding calcium in the inhibitor is believed to be a rudiment and proof of a common origin with PLA2.

PubMed: 9054978
DOI: 10.1006/jmbi.1996.0778

Experimental method

X-RAY DIFFRACTION (1.76 Å)