Crystal structure of a novel phospholipase A2 from crude venom of Indian cobra sub-species Naja naja sagittifera at 1.48 angstoms resolution.

Secretory phospholipase A2s (PLA2s), the structurally-homologous enzymes share a common qualitative catalytic site, but differ greatly in their pharmacological properties and toxicities. There has been a recognizable pattern of mutations in the primary sequence of PLA2s that alter their catalytic properties significantly. In the present study, the amino acid sequence and the three-dimensional structure of a new isoform of PLA2 from crude venom of Indian cobra sub-species Naja naja sagittifera (N.n.s.) has been determined by X-ray crystallography. The crystal structure has revealed several novel features of PLA2 folding and function. It contains 913 protein atoms and one each of Ca2+, phosphate and acetate ions with 142 solvent water molecules. A Ca2+ ion is present in the calcium-binding loop and forms a seven-fold coordination with a distorted pentagonal bipyramidal geometry. One of the coordination linkages is with the acetate ion, instead of the conserved water molecule. The presence of Lys at position 31 has a stabilizing effect on the loop Tyr 25-Cys 29 by interacting with carbonyl oxygen atoms of Tyr 25, Gly 26 and Cys 29. In turn, it lends stability to the Ca(2+)-binding loop as well. Another unique feature of the PLA2 structure is the formation of an intrastrand hydrogen bond, involving Ogamma of Thr 73 and Oepsilon2 of Glu 71, thus helping the beta-wing to act as a sharp arrow for insertion into other molecules. Yet another important feature of this PLA2 pertains to the conformation of its C-terminal segment, which is stabilized by a unique hydrogen bond through carbonyl oxygen of Lys 116 and Ndelta2 of Asn 120. This structural feature may be useful in the molecular recognition of the PLA2 through C-terminal segment.