Soisson S M, MacDougall-Shackleton B, Schleif R, Wolberger C
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA.
J Mol Biol. 1997 Oct 17;273(1):226-37. doi: 10.1006/jmbi.1997.1314.
The crystal structure of the sugar-binding and dimerization domain of the Escherichia coli gene regulatory protein, AraC, has been determined in complex with the competitive inhibitor D-fucose at pH 5.5 to a resolution of 1.6 A. An in-depth analysis shows that the structural basis for AraC carbohydrate specificity arises from the precise arrangement of hydrogen bond-forming protein side-chains around the bound sugar molecule. van der Waals interactions also contribute to the epimeric and anomeric selectivity of the protein. The methyl group of D-fucose is accommodated by small side-chain movements in the sugar-binding site that result in a slight distortion in the positioning of the amino-terminal arm. A comparison of this structure with the 1.5 A structure of AraC complexed with L-arabinose at neutral pH surprisingly revealed very small structural changes between the two complexes. Based on solution data, we suspect that the low pH used to crystallize the fucose complex affected the structure, and speculate about the nature of the changes between pH 5.5 and neutral pH and their implications for gene regulation by AraC. A comparison with the structurally unrelated E. coli periplasmic sugar-binding proteins reveals that conserved features of carbohydrate recognition are present, despite a complete lack of structural similarity between the two classes of proteins, suggesting convergent evolution of carbohydrate binding.
已确定大肠杆菌基因调控蛋白AraC的糖结合和二聚化结构域与竞争性抑制剂D-岩藻糖在pH 5.5时形成复合物的晶体结构，分辨率为1.6 Å。深入分析表明，AraC碳水化合物特异性的结构基础源于围绕结合糖分子形成氢键的蛋白质侧链的精确排列。范德华相互作用也有助于蛋白质的差向异构体和异头物选择性。D-岩藻糖的甲基通过糖结合位点中小的侧链移动得以容纳，这导致氨基末端臂的定位略有扭曲。将该结构与在中性pH下与L-阿拉伯糖复合的AraC的1.5 Å结构进行比较，令人惊讶地发现两种复合物之间的结构变化非常小。基于溶液数据，我们怀疑用于结晶岩藻糖复合物的低pH影响了结构，并推测了pH 5.5和中性pH之间变化的性质及其对AraC基因调控的影响。与结构不相关的大肠杆菌周质糖结合蛋白进行比较发现，尽管两类蛋白质之间完全缺乏结构相似性，但存在碳水化合物识别的保守特征，这表明碳水化合物结合的趋同进化。
