Sekar K, Sekharudu C, Tsai M D, Sundaralingam M
Biological Macromolecular Structure Center, Departments of Chemistry and Biochemistry and the Ohio State Biochemistry Program, 100 West 18th Avenue, The Ohio State University, Columbus, OH 43210, USA.
Acta Crystallogr D Biol Crystallogr. 1998 May 1;54(Pt 3):342-6. doi: 10.1107/s0907444997012493.
The trigonal crystal structure of the recombinant bovine pancreatic phospholipase A2 has been re-refined at a slightly higher resolution (1.72 A). The crystals are trigonal, space group P3121, unit-cell parameters a = b = 46.78 and c = 102.89 A and are isomorphous to the previous structure. The structure was refined to a final crystallographic R value of 19.5% (Rfree = 28.4%) using 10 531 reflections. A total of 106 solvent molecules were included in the refinement compared with the earlier refinement which contains only 85 water molecules and 8 925 reflections at 1.8 A resolution. The root-mean-square deviation from the ideal bond lengths and bond angles is considerably better in the present refinement. The active site is extended ( approximately 14 A) from Ala1 to the calcium. The three catalytic residues (Asp99, His48 and the catalytic water) are connected by the conserved structural water and the N-terminal Ala1 on one side, and by the calcium through an equatorial water on the other. The water molecules play a role in the activity of the enzyme PLA2. The Ala1 end of the extended active site performs the activation of the phospholid membranes while the opposite end performs the hydrolysis of the monomeric phospholids.
重组牛胰磷脂酶A2的三角晶体结构已在稍高分辨率（1.72 Å）下重新精修。晶体为三角晶系，空间群P3121，晶胞参数a = b = 46.78 Å，c = 102.89 Å，与先前结构同晶。该结构使用10531个反射精修至最终晶体学R值为19.5%（Rfree = 28.4%）。与早期精修相比，此次精修纳入了总共106个溶剂分子，早期精修在1.8 Å分辨率下仅包含85个水分子和8925个反射。此次精修中，与理想键长和键角的均方根偏差明显更好。活性位点从Ala1延伸至钙（约14 Å）。三个催化残基（Asp99、His48和催化水）在一侧通过保守结构水与N端Ala1相连，在另一侧通过赤道水与钙相连。水分子在磷脂酶A2的活性中起作用。延伸活性位点的Ala1端对磷脂膜进行激活，而另一端对单体磷脂进行水解。
