2O7O

Crystal structure analysis of TetR(D) complex with doxycycline

2O7O の概要

• エントリーDOI: 10.2210/pdb2o7o/pdb
• 関連するPDBエントリー: 2TCT
• 分子名称: Tetracycline repressor protein class D, MAGNESIUM ION, SULFATE ION, ... (6 entities in total)
• 機能のキーワード: helix-turn-helix, metal coordination, transcription regulator
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23924.04

構造登録者

Aleksandrov, A.,Proft, J.,Hinrichs, W. (登録日: 2006-12-11, 公開日: 2007-05-15, 最終更新日: 2023-10-25)

主引用文献

Aleksandrov, A.,Proft, J.,Hinrichs, W.,Simonson, T.
Protonation Patterns in Tetracycline:Tet Repressor Recognition: Simulations and Experiments
Chembiochem, 8:675-685, 2007

PubMed Abstract: Resistance to the antibiotic tetracycline (Tc) is regulated by its binding as a Tc:Mg2+ complex to the Tet Repressor protein (TetR). Tc:TetR recognition is a complex problem, with the protein and ligand each having several possible conformations and protonation states, which are difficult to elucidate by experiment alone. We used a combination of free-energy simulations and crystallographic analysis to investigate the electrostatic interactions between protein and ligand and the possible role of induced fit in Tc binding. Tc in solution was described quantum mechanically, while Tc:TetR interactions were described by a recent, high-quality molecular-mechanics model. The orientations of the amide and imidazole groups were determined experimentally by a careful analysis of Debye-Waller factors in alternate crystallographic models. The agreement with experiment for these orientations suggested that the simulations and their more detailed, thermodynamic predictions were reliable. We found that the ligand prefers an extended, zwitterionic state both in solution and in complexation with the protein. Tc is thus preorganized for binding, while the protein combines lock-and-key behavior for regions close to the ligand's amide, enolate, and ammonium groups, with an induced fit for regions close to the Mg2+ ion. These insights and the modeling techniques employed should be of interest for engineering improved TetR ligands and improved TetR proteins for gene regulation, as well as for drug design.

PubMed: 17361981
DOI: 10.1002/cbic.200600535

実験手法

X-RAY DIFFRACTION (1.89 Å)