Dreusicke D, Karplus P A, Schulz G E
Institut für Organische Chemie und Biochemie der Universität, Freiburg i.Br., Federal Republic of Germany.
J Mol Biol. 1988 Jan 20;199(2):359-71. doi: 10.1016/0022-2836(88)90319-1.
The crystal structure of porcine cytosolic adenylate kinase has been established at 2.1 A resolution using a restrained least-squares refinement method. Based on 11,251 independent reflections of better than 10 A resolution, a final R-factor of 19.3% was obtained with a model obeying standard geometry within 0.026 A in bond lengths and 3.3 degrees in bond angles. In comparison with the previous structure at 3 A resolution, there is a significant improvement. The high resolution structure has been used to rationalize the strictly conserved residues in the adenylate kinase family. Among these is the glycine-rich loop, which forms a giant anion hole accommodating a sulfate ion which mimics a phosphoryl group of a substrate. Such a structure seems to occur in a large group of mononucleotide binding proteins. Moreover, a conserved cis-proline has been detected in the active center. A structural comparison with the complex between adenylate kinase from yeast and a substrate-analog at medium resolution indicates that this kinase performs appreciable mechanical movements during a catalytic cycle. The reported structure presumably represents an open form of the enzyme, similar to that in solution in the absence of substrates. However, since there are large intermolecular contacts in the crystal, some deviation from the solution structure has to be expected.
利用约束最小二乘法精修方法，已将猪胞质腺苷酸激酶的晶体结构解析到2.1埃的分辨率。基于11251个分辨率优于10埃的独立反射，获得了最终19.3%的R因子，所得模型的键长在0.026埃内、键角在3.3度内符合标准几何结构。与之前3埃分辨率的结构相比，有了显著改进。高分辨率结构已被用于阐释腺苷酸激酶家族中严格保守的残基。其中富含甘氨酸的环形成了一个巨大的阴离子孔，容纳一个模拟底物磷酸基团的硫酸根离子。这样的结构似乎存在于一大类单核苷酸结合蛋白中。此外，在活性中心检测到一个保守的顺式脯氨酸。与酵母腺苷酸激酶和一个底物类似物在中等分辨率下形成的复合物进行结构比较表明，该激酶在催化循环中会进行明显的机械运动。报道的结构可能代表了该酶的一种开放形式，类似于在无底物溶液中的形式。然而，由于晶体中有大量分子间接触，预计会与溶液结构存在一些偏差。
