Vallee B L, Auld D S
Department of Pathology, Harvard Medical School, Boston, MA 02115.
Proc Natl Acad Sci U S A. 1990 Jan;87(1):220-4. doi: 10.1073/pnas.87.1.220.
The x-ray crystallographic structures of 12 zinc enzymes have been chosen as standards of reference to identify the ligands to the catalytic and structural zinc atoms of other members of their respective enzyme families. Universally, H2O is a ligand and critical component of the catalytically active zinc sites. In addition, three protein side chains bind to the catalytic zinc atom, whereas four protein ligands bind to the structural zinc atom. The geometry and coordination number of zinc can vary greatly to accommodate particular ligands. Zinc forms complexes with nitrogen and oxygen just as readily as with sulfur, and this is reflected in catalytic zinc sites having a binding frequency of His much greater than Glu greater than Asp = Cys, three of which bind to the metal atom. The systematic spacing between the ligands is striking. For all catalytic zinc sites except the coenzyme-dependent alcohol dehydrogenase, the first two ligands are separated by a "short-spacer" consisting of 1 to 3 amino acids. These ligands are separated from the third ligand by a "long spacer" of approximately 20 to approximately 120 amino acids. The spacer enables formation of a primary bidentate zinc complex, whereas the long spacer contributes flexibility to the coordination sphere, which can poise the zinc for catalysis as well as bring other catalytic and substrate binding groups into apposition with the active site. The H2O is activated by ionization, polarization, or poised for displacement. Collectively, the data imply that the preferred mechanistic pathway for activating the water--e.g., zinc hydroxide or Lewis acid catalysis--will be determined by the identity of the other three ligands and their spacing.
已选取12种锌酶的X射线晶体结构作为参考标准，以确定其各自酶家族中其他成员的催化锌原子和结构锌原子的配体。普遍而言，H₂O是催化活性锌位点的一种配体和关键成分。此外，三条蛋白质侧链与催化锌原子结合，而四条蛋白质配体与结构锌原子结合。锌的几何形状和配位数可因特定配体而有很大差异。锌与氮和氧形成配合物的难易程度与和硫形成配合物相当，这在催化锌位点中体现为His的结合频率远高于Glu，高于Asp = Cys，其中三个与金属原子结合。配体之间的系统间距很显著。对于除辅酶依赖性醇脱氢酶外的所有催化锌位点，前两个配体由1至3个氨基酸组成的“短间隔区”隔开。这些配体与第三个配体之间由约20至约120个氨基酸的“长间隔区”隔开。短间隔区有助于形成初级双齿锌配合物，而长间隔区为配位球提供灵活性，这既能使锌为催化做好准备，又能使其他催化和底物结合基团与活性位点并列。H₂O通过电离、极化或准备好被取代而被激活。总体而言，这些数据表明激活水的首选机制途径——例如氢氧化锌或路易斯酸催化——将由其他三个配体的身份及其间距决定。
