The 3-D Structure and Reaction Mechanism in The Highly Organized supra-Molecule of Pyruvate Dehydrogenase Complex.

丙酮酸脱氢酶复合物是一种高度有序的多酶系统，由丙酮酸脱氢酶（E1）、二氢硫辛酰乙酰转移酶（E2）和硫辛酰胺脱氢酶（E3）三个组分酶的多个拷贝组成，特异、高效地催化不可逆的系列反应。根据不同的生物体，复合物可分为两类由不同对称性的E2组成的中心核心结构。一个在革兰氏阴性细菌中具有432对称性，另一个在革兰氏阳性细菌和真核生物中具有532对称性。从酵母中分离的E3组分的晶体结构被确定为后一种类型。发现有两种结晶习性不同的晶体。晶体结构用分子置换法求解。通过对电子密度图的平均化和平坦化，改善了初始相位。在非晶体学二重对称性约束下，用XPLOR对FRODO处理的分子模型的原子坐标进行了修正。虽然分子堆积方式不同，但分子结构相似。与谷胱甘肽还原酶的比较表明，虽然在C-末端结构域中观察到较大的原子偏差，但两个结构域之间的活性位点具有几乎相同的三维结构。这种相似性也在来自具有432对称性的不同生物体的E3中观察到。从目前的调查，它已被揭示，E3的三级结构基本上是相同的，即使在不同的架构之间的两种类型。这种结构上的高度保守性可能是酶的功能抑制作用。

The pyruvate dehydrogenase complex is one of the highly organized multienzyme system, consisting of multiple copies of three component enzymes, pyruvate dehydrogenase (E1), dihydrolipoyl acetyltransferase (E2), and lipoamide dehydrogenase (E3), which catalyses the irreversible serial reactios specifically and efficiently. The complexes are classified into two types of the central core structures composed of E2s with different symmetries depending on organisms. One has the 432 symmetry in Gram negative bacteria and the other the 532 symmetry in Gram positive bacteria and in eukaryotes. The cyustal structure of the isolated component of E3 from yeast was determined for the latter type. It has been found that there are two types of crystals which are different with each other in crystal habit. The crystal structures were solved by the molecular replacement method. The initial phases were improved by averaging and flattening of electron density map. The atomic coordinates of the molecular model constracted by FRODO were refined by XPLOR with a constrain of non-crystallographic 2-fold symmetry. Although the molecular packings are different, but the molecular structures are similar. Closer comparison with glutathion reductase indicated that although the large atomic deviations are observed in the C-terminal domain, the active site between the two domains has almost the same 3-D structure. This similarity is also observed in E3 from the different organisms with 432 symmetry. From the present investigation, it has been thus revealed that the tertiary structures of E3s are essentially the same even in the different architecture between the two types. It is noticed that such a strong conservation of the structure may be the functional restrain by the enzyme.