Sekar K, Kumar A, Liu X, Tsai M D, Gelb M H, Sundaralingam M
Biological Macromolecular Structure Center, Departments of Chemistry and Biochemistry, 100 West 18th Avenue, The Ohio State University, Columbus, OH 43210-1185, USA.
Acta Crystallogr D Biol Crystallogr. 1998 May 1;54(Pt 3):334-41. doi: 10.1107/s090744499701247x.
The 1.89 A 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 A 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 A resolution. In all, 7 726 reflections [F>2sigma(F)] were used between 8.0 and 1.89 A 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 Ndelta1 of His48. The fourth water which also shares Ndelta1 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 to the other known TSA-PLA2 complexes.
已确定牛胰磷脂酶A2（PLA2）与过渡态类似物L-1-O-辛基-2-庚基磷酰基-sn-甘油-3-磷酸乙醇胺（TSA）复合物的分辨率为1.89 Å的结构。该复合物晶体为三方晶系，空间群P3121，a = b = 46.58 Å，c = 102.91 Å，与天然重组野生型（WT）同晶型。该结构在1.89 Å分辨率下精修至最终晶体学R值为18.0%，包括957个蛋白质原子、88个水分子、一个钙离子以及抑制剂的所有31个非氢原子。在8.0至1.89 Å分辨率之间总共使用了7726个反射[F>2σ(F)]。抑制剂深深地锁在活性位点裂隙中，并通过磷酸酯和膦酸酯基团的阴离子O原子取代钙五角双锥中的两个水分子与钙离子配位。Tyr69的羟基与磷酸酯基团的第二个阴离子O原子形成氢键，而膦酸酯基团的羟基取代了与His48的Nδ1形成氢键的第三个水分子，即“催化”水。也与His48的Nδ1共享的第四个水分子被抑制剂的空间位阻所取代。第五个保守结构水仍存在于活性位点，并与周围残基形成氢键网络。将该结构与其他已知的TSA-PLA2复合物进行了比较。
