Koike Ryotaro, Amemiya Takayuki, Ota Motonori, Kidera Akinori
Global Scientific Information and Computing Center, Tokyo Institute of Technology, O-okayama, Tokyo 152-8550, Japan.
J Mol Biol. 2008 Jun 6;379(3):397-401. doi: 10.1016/j.jmb.2008.04.019. Epub 2008 Apr 11.
Overall structural changes of enzymes in response to ligand binding were investigated by database analysis of 62 non-redundant enzymes whose ligand-unbound and ligand-bound forms were available in the Protein Data Bank. The results of analysis indicate that transferases often undergo large rigid-body domain motions upon ligand binding, while other enzymes, most typically, hydrolases, change their structures to a small extent. It was also found that the solvent accessibility of the substrate molecule was low in transferases but high in hydrolases. These differences are explained by the enzymatic reaction mechanisms. The transferase reaction requires the catalytic groups to be insulated from the water environment, and thus transferases bury the ligand molecule inside the protein by closing the cleft. On the other hand, the hydrolase reaction involves the surrounding water molecules and occurs at the protein surface, requiring only a small structural change.
通过对62种非冗余酶进行数据库分析，研究了酶响应配体结合时的整体结构变化，这些酶的未结合配体形式和结合配体形式可在蛋白质数据库中获取。分析结果表明，转移酶在配体结合时通常会发生较大的刚体结构域运动，而其他酶，最典型的是水解酶，其结构变化较小。还发现，转移酶中底物分子的溶剂可及性较低，而水解酶中则较高。这些差异可以通过酶促反应机制来解释。转移酶反应要求催化基团与水环境隔离，因此转移酶通过闭合裂隙将配体分子埋在蛋白质内部。另一方面，水解酶反应涉及周围的水分子，发生在蛋白质表面，只需要很小的结构变化。
