Crystal structure of echicetin from Echis carinatus (Indian Saw-scaled viper) at 2.4 Å resolution

Abstract

Echicetin is a heterodimeric protein from the venom of the Indian saw-scaled viper, Echis carinatus. It binds to platelet glycoprotein Ib (GPIb) and thus inhibits platelet aggregation. It has two subunits, α and β, consisting of 131 and 123 amino acid residues, respectively. The two chains are linked with a disulphide bond. The level of amino acid sequence homology between two subunits is 50%. The protein was purified from the venom of E. carinatus and crystallized using ammonium sulphate as a precipitant. The crystal structure has been determined at 2.4 Å resolution and refined to an R-factor of 0.187. Overall dimensions of the heterodimer are ˜80 Å×35 Å×35 Å. The backbone folds of the two subunits are similar. The central portions of the polypeptide chains of a and β-subunits move into each other to form a tight dimeric association. The remaining portions of the chains of both subunits fold in a manner similar to those observed in the carbohydrate-binding domains of C-type lectins. In echicetin, the Ca²⁺-binding sites are not present, despite being topologically equivalent to other similar Ca²⁺-binding proteins of the superfamily. The residues Ser41, Glu43 and Glu47 in the calcium-binding proteins of the related family are conserved but the residues Glu126/120 are replaced by lysine at the corresponding sites in the α and β-subunits.