Structure of an acidic phospholipase A₂ from Indian saw-scaled viper (Echis carinatus) at 2.6 Å resolution reveals a novel intermolecular interaction

Abstract

The crystal structure of an acidic phospholipase A₂ from the venom of Echis carinatus (saw-scaled viper; scPLA₂) has been determined at 2.6 Å resolution and refined to a crystallographic R factor of 0.192. Although the overall structure of scPLA₂ is essentially similar to those of other group II acidic PLA₂s from different species, it shows unique features in several parts. Particularly noteworthy is the C-terminal part, which folds differently to those of other group II PLA₂s. This part is considered to be responsible for inhibition of the platelet-aggregation activity. The calcium-binding loop is tightly organized with sevenfold coordination. Another striking feature of scPLA₂ is the involvement of Asn79 O^δ1 of a symmetry-related molecule in a coordination linkage with Ca²⁺ of the calcium-binding loop. This is the first observation of an internal metal ion participating in an intermolecular interaction. The -wing of a molecule is deeply inserted into the hydrophobic channel of another molecule and forms several intermolecular interactions. This results in the formation of an infinite chain of molecules. These chains are stacked in an antiparallel arrangement in the crystals.