Structure of the Complex of Bovine Pancreatic Phospholipase A₂ with a Transition-State Analogue

The 1.89 Å resolution structure of the complex of bovine pancreatic phospholipase A₂ (PLA2) with the transition-state analogue L-1-O-octyl-2-heptylphosphonyl-sn-glycero-3-phosphoethanolamine (TSA) has been determined. The crystal of the complex is trigonal, space group P3₁21, a = b = 46.58 and c = 102.91 Å and isomorphous to the native recombinant wild type (WT). The structure was refined to a final crystallographic R value of 18.0% including 957 protein atoms, 88 water molecules, one calcium ion and all 31 non-H atoms of the inhibitor at 1.89 Å resolution. In all, 7 726 reflections were used between 8.0 and 1.89 Å resolution. The inhibitor is deeply locked into the active-site cleft and coordinates to the calcium ion by displacing the two water molecules in the calcium pentagonal bipyramid by the anionic O atoms of the phosphate and phosphonate group. The hydroxyl group of Tyr69 hydrogen bonds to the second anionic O atom of the phosphate group while that of the phosphonate group replaces the third water, `catalytic' water, which forms a hydrogen bond to N^δ1 of His48. The fourth water which also shares N^δ1 of His48 is displaced by the steric hinderance of the inhibitor. The fifth conserved structural water is still present in the active site and forms a network of hydrogen bonds with the surrounding residues. The structure is compared with the other known TSA–PLA2 complexes.