STRUCTURE OF ACTINIDIN, AFTER REFINEMENT AT 1.7-A RESOLUTION
STRUCTURE OF ACTINIDIN, AFTER REFINEMENT AT 1.7-A RESOLUTION
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DOI：
10.1016/0022-2836(80)90255-7
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发表时间：
1980-01-01
影响因子：
5.6
通讯作者：
BAKER, EN
中科院分区：
文献类型：
--
作者：
BAKER, EN
巯基蛋白酶猕猴桃蛋白酶在1.7埃下精制后的结构。决议，被描述。1666个原子中的大多数的位置以优于0.1埃的精度确定;只有2个残基（219和220）和第三个残基（87）的侧链不能被看到。此外，该模型包含272个溶剂分子，除了一个可能是铵离子外，其余都是水。原子B值给出了结构的不同部分的迁移率的良好指示。猕猴桃蛋白酶具有双结构域结构，其中一个结构域在其二级结构中主要是螺旋的，而另一个结构域围绕扭曲的β-螺旋结构构建。床单。螺旋中氢键的几何形状，β-结构和转折进行了分析。所有这些都是显著非线性的，角度为N.sbd.。cxa.H.cntdot.. cntdot.. cnt.O. apprx. 160度羰基从每个螺旋的轴向外倾斜，这种倾斜显然不受是否形成额外氢键的影响（例如，水或侧链原子）。每个结构域围绕非极性侧链的实质性核心折叠，但结构域之间的界面大多是极性的。该界面上的相互作用涉及8个埋水分子的网络，Glu 35，Glu 50，Lys 181和Lys 17的埋羧基和氨基，其他极性侧链和一些疏水基团。另一个内部带电的侧链，Glu 52的侧链，与一个埋在里面的溶剂分子相邻，可能是铵离子。描述了其他侧链环境。一个脯氨酸残基具有顺式构型。巯基被氧化，可能变成SO-2，其中一个氧原子清晰可见，但另一个氧原子则不太确定。活性位点的几何形状与Drenth等人提出的木瓜蛋白酶的机制是一致的。描述了272个溶剂分子的位置。最有序的水分子是那些在内部（总共17个），在表面口袋里，或在分子间接触区域。这些通常形成3或4个氢键，2个与质子受体结合，1或2个与质子供体结合。其他水分子在表面形成水桥，有时覆盖非极性基团的暴露边缘。分子间的接触涉及很少的蛋白质原子，但许多水分子。
The structure of the sulfydryl protease, actinidin, after refinement at 1.7 .ANG. resolution, is described. The positions of most of the 1666 atoms were determined with an accuracy better than 0.1 .ANG.; only 2 residues (219 and 220) and the side-chain of a 3rd (87) cannot be seen. In addition, the model contains 272 solvent molecules, all taken as water, except one which may be an ammonium ion. Atomic B values give a good indication of the mobility of different parts of the structure. Actinidin has a double domain structure, with one domain mostly helical in its secondary structure, and the other domain built around a twisted .beta.-sheet. The geometry of hydrogen bonds in helices, .beta.-structure and turns has been analysed. All are significantly non-linear, with the angle N.sbd..cxa.H.cntdot..cntdot..cntdot.O .apprx. 160.degree.. Carbonyl groups are tilted outwards from the axis of each helix, the tilting apparently unaffected by whether or not additional hydrogen bonds are made (e.g., to water or side-chain atoms). Each domain is folded round a substantial core of non-polar side-chains, but the interface between domains is mostly polar. Interactions across this interface involve a network of 8 buried water molecules, the buried carboxyl and amino groups of Glu35, Glu50, Lys181 and Lys17, other polar side-chains and a few hydrophobic groups. One other internal charged side-chain, that of Glu52, is adjacent to a buried solvent molecule, probably an ammonium ion. Other side-chain environments are described. One proline residue has a cis configuration. The sulfydryl group is oxidized, probably to SO-2, with one oxygen atom clearly visible but the other somewhat less certain. The active site geometry is otherwise compatible with the mechanism proposed by Drenth et al. for papain. The positions of the 272 solvent molecules are described. The best-ordered water molecules are those that are internal (total of 17), in surface pockets, or in the intermolecular contact regions. These generally form 3 or 4 hydrogen bonds, 2 to proton acceptors and 1 or 2 to proton donors. Other water molecules make water bridges on the surface, sometimes covering the exposed edges of non-polar groups. Intermolecular contacts involve few protein atoms, but many water molecules.