Lu G G, Lindqvist Y, Schneider G
Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.
Proteins. 1992 Feb;12(2):117-27. doi: 10.1002/prot.340120205.
A macroscopic approach has been employed to calculate the electrostatic potential field of nonactivated ribulose-1,5-bisphosphate carboxylase and of some complexes of the enzyme with activator and substrate. The overall electrostatic field of the L2-type enzyme from the photosynthetic bacterium Rhodospirillum rubrum shows that the core of the dimer, consisting of the two C-terminal domains, has a predominantly positive potential. These domains provide the binding sites for the negatively charged phosphate groups of the substrate. The two N-terminal domains have mainly negative potential. At the active site situated between the C-terminal domain of one subunit and the N-terminal domain of the second subunit, a large potential gradient at the substrate binding site is found. This might be important for polarization of chemical bonds of the substrate and the movement of protons during catalysis. The immediate surroundings of the activator lysine, K191, provide a positive potential area which might cause the pK value for this residue to be lowered. This observation suggests that the electrostatic field at the active site is responsible for the specific carbamylation of the epsilon-amino group of this lysine side chain during activation. Activation causes a shift in the electrostatic potential at the position of K166 to more positive values, which is reflected in the unusually low pK of K166 in the activated enzyme species. The overall shape of the electrostatic potential field in the L2 building block of the L8S8-type Rubisco from spinach is, despite only 30% amino acid homology for the L-chains, strikingly similar to that of the L2-type Rubisco from Rhodospirillum rubrum. A significant difference between the two species is that the potential is in general more positive in the higher plant Rubisco. In particular, the second phosphate binding site has a considerably more positive potential, which might be responsible for the higher affinity for the substrate of L8S8-type enzymes. The higher potential at this site might be due to two remote histidine residues, which are conserved in the plant enzymes.
已采用宏观方法来计算未活化的核酮糖-1,5-二磷酸羧化酶以及该酶与激活剂和底物的某些复合物的静电势场。来自光合细菌红螺菌的L2型酶的整体静电场表明，由两个C末端结构域组成的二聚体核心主要具有正电势。这些结构域为底物带负电荷的磷酸基团提供结合位点。两个N末端结构域主要具有负电势。在一个亚基的C末端结构域和第二个亚基的N末端结构域之间的活性位点处，发现底物结合位点存在较大的电势梯度。这可能对底物化学键的极化以及催化过程中质子的移动很重要。激活剂赖氨酸K191的紧邻环境提供了一个正电势区域，这可能导致该残基的pK值降低。这一观察结果表明，活性位点处的静电场负责激活过程中该赖氨酸侧链ε-氨基的特异性氨甲酰化。激活导致K166位置的静电势向更正的值移动，这反映在活化酶物种中K166异常低的pK值上。尽管菠菜的L8S8型Rubisco的L2结构单元中的静电势场的整体形状与红螺菌L2型Rubisco的静电势场的整体形状仅30%的氨基酸同源性，但却惊人地相似。这两个物种之间的一个显著差异是，高等植物Rubisco中的电势总体上更正。特别是，第二个磷酸结合位点具有明显更正的电势，这可能是L8S8型酶对底物具有更高亲和力的原因。该位点较高的电势可能归因于两个在植物酶中保守的远距离组氨酸残基。
