Kamphuis I G, Drenth J, Baker E N
J Mol Biol. 1985 Mar 20;182(2):317-29. doi: 10.1016/0022-2836(85)90348-1.
An accurate three-dimensional structure is known for papain (1.65 A resolution) and actinidin (1.7 A). A detailed comparison of these two structures was performed to determine the effect of amino acid changes on the conformation. It appeared that, despite only 48% identity in their amino acid sequence, different crystallization conditions and different X-ray data collection techniques, their structures are surprisingly similar with a root-mean-square difference of 0.40 A between 76% of the main-chain atoms (differences less than 3 sigma). Insertions and deletions cause larger differences but they alter the conformation over a very limited range of two to three residues only. Conformations of identical side-chains are generally retained to the same extent as the main-chain conformation. If they do change, this is due to a modified local environment. Several examples are described. Spatial positions of hydrogen bonds are conserved to a greater extent than are the specific groups involved. The greatest structural similarity is found for the active site residues of papain and actinidin, for the internal water molecules and for the main-chain conformation of residues in alpha-helices and anti-parallel beta-sheet structure. This was reflected also in the similarity of the temperature factors. It suggests that the secondary structural elements form the skeleton of the molecule and that their interaction is the main factor in directing the fold of the polypeptide chain. Therefore, substitution of residues in the skeleton will, in general, have the most drastic effect on the conformation of the protein molecule. In papain and actinidin, some main-chain-side-chain hydrogen bonds are also strongly conserved and these may determine the folding of non-repetitive parts of the structure. Furthermore, we included primary structure information for three homologous thiol proteases: stem bromelain, and the cathepsins B and H. By combining the three-dimensional structural information for papain and actinidin with sequence homologies and identities, we conclude that the overall folding pattern of the polypeptide chain is grossly the same in all five proteases, and that they utilize the same catalytic mechanism.
木瓜蛋白酶（分辨率为1.65埃）和猕猴桃蛋白酶（分辨率为1.7埃）的精确三维结构已为人所知。对这两种结构进行了详细比较，以确定氨基酸变化对构象的影响。结果显示，尽管它们的氨基酸序列仅有48%的一致性，且结晶条件不同、X射线数据收集技术也不同，但它们的结构却惊人地相似，76%的主链原子之间的均方根差异为0.40埃（差异小于3倍标准差）。插入和缺失会导致较大差异，但它们仅在两到三个残基的非常有限范围内改变构象。相同侧链的构象通常与主链构象保持相同程度的保留。如果它们确实发生变化，这是由于局部环境的改变。文中描述了几个例子。氢键的空间位置比所涉及的特定基团在更大程度上得以保留。木瓜蛋白酶和猕猴桃蛋白酶的活性位点残基、内部水分子以及α螺旋和反平行β折叠结构中残基的主链构象具有最大的结构相似性。这也反映在温度因子的相似性上。这表明二级结构元件构成了分子的骨架，并且它们之间的相互作用是指导多肽链折叠的主要因素。因此，一般来说，骨架中残基的取代对蛋白质分子的构象影响最为剧烈。在木瓜蛋白酶和猕猴桃蛋白酶中，一些主链-侧链氢键也高度保守，这些氢键可能决定了结构中非重复部分的折叠。此外，我们纳入了三种同源硫醇蛋白酶的一级结构信息：茎菠萝蛋白酶以及组织蛋白酶B和H。通过将木瓜蛋白酶和猕猴桃蛋白酶的三维结构信息与序列同源性和一致性相结合，我们得出结论，所有这五种蛋白酶中多肽链的整体折叠模式大致相同，并且它们利用相同的催化机制。
