Structural features of a snake venom thrombin-like enzyme: thrombin and trypsin on a single catalytic platform?

The Lachesis muta thrombin-like enzyme (LM-TL) is a single chain serine pro tease that shares 38% sequence identity with the serine protease domain of thrombin and also displays similar fibrinogen-clotting activity. In additio n, the 228 amino acid residue LM-TL is 52% identical to trypsin, and cleave s chromogenic substrates with similar specificity. Herein we report a three -dimensional (3D) model validated experimentally for LM-TL based on these t wo homologous proteins of known 3D structure. Spatial modeling of LM-TL rev eals a serine protease with a chymotrypsin fold presenting a hydrophobic po cket on its surface, involved in substrate recognition, and an important 90 's loop, involved in restricting the LM-TL catalytic site cleft. Docking an alysis showed that LM-TL would not form a stable complex with basic pancrea tic trypsin inhibitor and wild-type ecotin since its 90's loop would restri ct the access to the catalytic site. LM-TL formed acceptable interactions w ith fibrinopeptide A and a variant of ecotin: ecotin-TSRR/R in which both t he primary and secondary binding sites are mutated Val81Thr, Thr83Ser, Met8 4Arg, Met85Arg and Asp70Arg. Furthermore, analysis of the primary structure s of LM-TL and of the seven snake venom thrombin-like enzymes (SVTLEs) fami ly reveals a subgroup formed by LM-TL, crotalase, and bilineobin, both clos ely related to thrombin. Therefore, LM-TL provides an initial point to comp are SVTLEs with their counterparts, e.g. the mammalian serine proteases, an d a basis for the localization of important residues within the little know n SVTLEs family. (C) 2001 Elsevier Science B.V. All rights reserved.