STRUCTURE OF A SNAKE-VENOM PHOSPHOLIPASE A(2) MODIFIED BY P-BROMO-PHENACYL-BROMIDE

The crystal structure of acidic phospholipase A(2) (APLA(2)) from Agki strodon halys pallas covalently modified by p-bromo-phenacyl-bromide ( pBPB) was determined to a resolution of 2.0 Angstrom by an isomorphous difference Fourier method with the native APLA(2) structure as an ini tial model and refined to a crystallographic R factor of 15.3%. The mo dified APLA(2) structure is remarkably similar to that of the native o ne. Least-squares superposition of C alpha atoms of native and modifie d APLA(2) results in a root-mean-square coordinate deviation of 0.243 Angstrom. The p-bromo-phenacyl group near the active site occupies a p osition similar to that in pBPB modified bovine pancreatic PLA(2). The inhibitor covalently bound to the ND1 atom of His48 fits well in the hydrophobic channel, forming extensive hydrophobic interactions with t he surrounding residues, especially with the side chains of Phe5 and C ys45 and the main chain of Gly30. However, the inhibitor does not chan ge the conformation of these residues except that Trp31 at the entranc e of the hydrophobic channel moves slightly toward the inhibitor. Comp ared with native APLA(2). the Ca2+-binding loop shows a little conform ational change and a cation, probably Na+, occupies in the position of Ca2+. The binding of pBPB to APLA(2) induce no other significant conf ormational changes in the enzyme molecule elsewhere. (C) 1998 Elsevier Science Ltd. All rights reserved.