Evidence-based docking of the urease activation complex

1Ureases require accessory proteins for their activation and proper function. In Klebsiella aerogenes, UreD, UreF, UreG, and UreE are sequentially complexed to UreABC as required for its activation. Until now, only low-resolution structures are available for this activation complex. To circumvent such limitation, our work intends to provide an atomic-level model for the (UreABC–UreDFG)3 complex from K. aerogenes, by employing comparative modeling associated to sequential macromolecular dockings, validated through small-angle X-ray scattering profiles and comparison with results from cross-linking, mutagenesis, and pull-down experiments. Additionally, normal mode analyses of the obtained complex supported the characterization of the elevated flexibility of both UreD–UreF dimer and (UreABC–UreDFG)3 oligomer, explaining the previously observed diffuse binding of UreD to the apoenzyme. The model shown here is the first atomic-level depiction of this complex, a required step for the unraveling of the urease activation process. 1Both authors share senior authorship. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:61 脲酶（Urease）的激活与正常功能依赖于辅助蛋白。在产气克雷伯菌（Klebsiella aerogenes）中，UreD、UreF、UreG与UreE会按顺序结合至UreABC，以完成其激活过程。截至目前，该激活复合物仅获得过低分辨率结构。为突破这一局限，本研究通过结合比较建模与顺序大分子对接技术，构建产气克雷伯菌（K. aerogenes）来源的(UreABC–UreDFG)₃复合物的原子级模型，并通过小角X射线散射（small-angle X-ray scattering）图谱、交联实验、诱变实验与下拉实验结果对该模型进行验证。此外，对所获复合物进行的简正模式分析证实，UreD–UreF二聚体与(UreABC–UreDFG)₃寡聚体均具有较高的柔性，这解释了此前观测到的UreD与脱辅基酶（apoenzyme）弥散结合现象。本研究展示的模型是该复合物首个原子级可视化描述，为阐明脲酶激活过程提供了必要基础。1 两位作者为共同通讯作者。交互式三维动态补全模型（animated Interactive 3D Complement, I3DC）可在Proteopedia数据库的http://proteopedia.org/w/Journal:JBSD:6 页面获取。