Fujinaga M, Chernaia M M, Tarasova N I, Mosimann S C, James M N
Department of Biochemistry, University of Alberta, Edmonton, Canada.
Protein Sci. 1995 May;4(5):960-72. doi: 10.1002/pro.5560040516.
The three-dimensional crystal structure of human pepsin and that of its complex with pepstatin have been solved by X-ray crystallographic methods. The native pepsin structure has been refined with data collected to 2.2 A resolution to an R-factor of 19.7%. The pepsin:pepstatin structure has been refined with data to 2.0 A resolution to an R-factor of 18.5%. The hydrogen bonding interactions and the conformation adopted by pepstatin are very similar to those found in complexes of pepstatin with other aspartic proteinases. The enzyme undergoes a conformational change upon inhibitor binding to enclose the inhibitor more tightly. The analysis of the binding sites indicates that they form an extended tube without distinct binding pockets. By comparing the residues on the binding surface with those of the other human aspartic proteinases, it has been possible to rationalize some of the experimental data concerning the different specificities. At the S1 site, valine at position 120 in renin instead of isoleucine, as in the other enzymes, allows for binding of larger hydrophobic residues. The possibility of multiple conformations for the P2 residue makes the analysis of the S2 site difficult. However, it is possible to see that the specific interactions that renin makes with histidine at P2 would not be possible in the case of the other enzymes. At the S3 site, the smaller volume that is accessible in pepsin compared to the other enzymes is consistent with its preference for smaller residues at the P3 position.
人胃蛋白酶及其与胃蛋白酶抑制剂复合物的三维晶体结构已通过X射线晶体学方法解析。天然胃蛋白酶结构已根据收集到的分辨率为2.2埃的数据进行精修，R因子为19.7%。胃蛋白酶-胃蛋白酶抑制剂结构已根据分辨率为2.0埃的数据进行精修，R因子为18.5%。胃蛋白酶抑制剂的氢键相互作用和构象与在胃蛋白酶抑制剂与其他天冬氨酸蛋白酶复合物中发现的非常相似。酶在与抑制剂结合时会发生构象变化，从而更紧密地包裹抑制剂。结合位点分析表明，它们形成一个没有明显结合口袋的延伸管。通过将结合表面上的残基与其他人天冬氨酸蛋白酶的残基进行比较，已能够合理解释一些关于不同特异性的实验数据。在S1位点，肾素中第120位的缬氨酸而非其他酶中的异亮氨酸，使得更大的疏水残基能够结合。P2残基存在多种构象的可能性使得对S2位点的分析变得困难。然而，可以看出，肾素与P2位组氨酸的特异性相互作用在其他酶的情况下是不可能的。在S3位点，与其他酶相比，胃蛋白酶中可利用的体积较小，这与其对P3位置较小残基的偏好一致。
