Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis.
Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis.
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中华根霉天冬氨酸蛋白酶的 1.8 A 分辨率的结构和精修。
DOI：
10.1016/0022-2836(87)90411-6
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发表时间：
1987
影响因子：
5.6
通讯作者：
Davies,DR
中科院分区：
文献类型：
--
作者：
Suguna,K;Bott,RR;Padlan,EA;Subramanian,E;Sheriff,S;Cohen,GH;Davies,DR
根霉胃蛋白酶 (EC 3.4.23.6) 是一种来自中国根霉的天冬氨酸蛋白酶，其结构已被精炼至 1.8 Å 分辨率下的晶体学 R 因子为 0.143。已确定 2417 个蛋白质原子的位置，均方根 (r.m.s.) 误差为 0.12 Å。在最终模型中，均方根值键距的理想偏差为 0.010 Å，角距的理想偏差为 0.034 Å。在精炼过程中，已定位出一个钙离子和 373 个水分子，其中 17 个是内部水分子。活性天冬氨酸残基 Asp35 和 Asp218 与邻近残基和几个水分子参与类似的氢键相互作用。一个水分子位于催化天冬氨酸残基的两个羧基之间，处于紧密的氢键键合位置。这一改进对高度移动的“瓣”（突出于结合袋的β-发夹环区域）产生了明确的解释。当分子堆积在晶体中时，会形成大的溶剂通道，从而暴露结合袋并使其易于接近。分子间接触主要涉及溶剂分子和少量蛋白质原子。根霉胃蛋白酶的三维结构与其他天冬氨酸蛋白酶结构非常相似。与青霉蛋白酶结构的详细比较显示出惊人的相似性以及活性位点几何形状和分子堆积方面的细微差异。
The structure of rhizopuspepsin (EC 3.4.23.6), the aspartic proteinase fromRhizopus chinensis, has been refined to a crystallographicR-factor of 0.143 at 1.8 Å resolution. The positions of 2417 protein atoms have been determined with a root-mean-square (r.m.s.) error of 0.12 Å. In the final model, the r.m.s. deviation from ideality for bond distances is 0.010 Å, and for angle distances it is 0.034 Å. During the course of the refinement, a calcium ion and 373 water molecules, of which 17 are internal, have been located. The active aspartate residues, Asp35 and Asp218, are involved in similar hydrogen-bonding interactions with neighboring residues and with several water molecules. One water molecule is located between the two carboxyl groups of the catalytic aspartate residues in a tightly hydrogen-bonded position. The refinement resulted in an unambiguous interpretation of the highly mobile “flap”, a β-hairpin loop region that projects over the binding pocket. Large solvent channels are formed when the molecules pack in the crystal, exposing the binding pocket and making it easily accessible. Intermolecular contacts involve mainly solvent molecules and a few protein atoms. The three-dimensional structure of rhizopuspepsin closely resembles other aspartic proteinase structures. A detailed comparison with the structure of penicillopepsin showed striking similarities as well as subtle differences in the active site geometry and molecular packing.