Nichols J C, Vyas N K, Quiocho F A, Matthews K S
Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251.
J Biol Chem. 1993 Aug 15;268(23):17602-12. doi: 10.2210/pdb1ltp/pdb.
Using primary sequence similarity to arabinose-binding protein, D-glucose/D-galactose-binding protein, and ribose-binding protein (Vyas, N. K., Vyas, M. N., and Quiocho, F. A. (1991) J. Biol. Chem. 266, 5226-5237; Mowbray, S. L., and Cole, L. B. (1992) J. Mol. Biol. 225, 155-175), the core domain (residues 62-323) of the bacterial regulatory protein lac repressor has been aligned to these sugar-binding proteins of known structure. Although the sequence identity is not striking, there is strong overall homology based on two separate matrix scoring systems (minimum base change per codon (MBC/C) and amino acid homology per residue (AAH/R)) (mean score: MBC/C < 1.25, AAH/R > 5.50; random sequences: MBC/C = 1.45, AAH/R = 4.46). Similarly, the predicted secondary structure of the repressor exhibits excellent agreement with the known secondary structures of the sugar-binding proteins. Using this primary sequence alignment, the tertiary structure of the core domain of the lac repressor has been modeled based on the known structures of the sugar-binding proteins as templates. While the structure deduced for the repressor is hypothetical, the model generated allows a comparison between the predicted tertiary arrangement and the wealth of genetic and chemical data elucidated for the repressor. Important residues involved in operator and sugar binding and in protein assembly have been identified using genetic methods, and placement of these residues in the model is consistent with their known function. This approach, therefore, provides a means to visualize the core domain of the lac repressor that allows interpretation of genetic and chemical data for specific residues and rational design of future experiments.
利用与阿拉伯糖结合蛋白、D - 葡萄糖/D - 半乳糖结合蛋白和核糖结合蛋白的一级序列相似性（维亚斯，N. K.，维亚斯，M. N.，和基奥乔，F. A.（1991）《生物化学杂志》266，5226 - 5237；莫布雷，S. L.，和科尔，L. B.（1992）《分子生物学杂志》225，155 - 175），细菌调节蛋白乳糖阻遏物的核心结构域（第62 - 323位氨基酸残基）已与这些已知结构的糖结合蛋白进行比对。尽管序列同一性并不显著，但基于两种独立的矩阵评分系统（每个密码子的最小碱基变化数（MBC/C）和每个残基的氨基酸同源性（AAH/R））存在很强的整体同源性（平均得分：MBC/C < 1.25，AAH/R > 5.50；随机序列：MBC/C = 1.45，AAH/R = 4.46）。同样，阻遏物的预测二级结构与糖结合蛋白的已知二级结构表现出极好的一致性。利用这种一级序列比对，以糖结合蛋白的已知结构为模板，对乳糖阻遏物核心结构域的三级结构进行了建模。虽然为阻遏物推导的结构是假设性的，但生成的模型允许对预测的三级排列与为阻遏物阐明的大量遗传和化学数据进行比较。利用遗传方法已鉴定出参与操纵子和糖结合以及蛋白质组装的重要残基，并且这些残基在模型中的位置与其已知功能一致。因此，这种方法提供了一种可视化乳糖阻遏物核心结构域的手段，有助于解释特定残基的遗传和化学数据，并为未来实验进行合理设计。
