Wolfova Julie, Smatanova Ivana Kuta, Brynda Jiri, Mesters Jeroen R, Lapkouski Mikalai, Kuty Michal, Natalello Antonino, Chatterjee Neal, Chern Sy-Yeu, Ebbel Erin, Ricci Angela, Grandori Rita, Ettrich Rüdiger, Carey Jannette
Institute of Physical Biology, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic.
Biochim Biophys Acta. 2009 Sep;1794(9):1288-98. doi: 10.1016/j.bbapap.2009.08.001. Epub 2009 Aug 7.
Two previously reported holoprotein crystal forms of the flavodoxin-like E. coli protein WrbA, diffracting to 2.6 and 2.0 A resolution, and new crystals of WrbA apoprotein diffracting to 1.85 A, are refined and analysed comparatively through the lens of flavodoxin structures. The results indicate that differences between apo- and holoWrbA crystal structures are manifested on many levels of protein organization as well as in the FMN-binding sites. Evaluation of the influence of crystal contacts by comparison of lattice packing reveals the protein's global response to FMN binding. Structural changes upon cofactor binding are compared with the monomeric flavodoxins. Topologically non-equivalent residues undergo remarkably similar local structural changes upon FMN binding to WrbA or to flavodoxin, despite differences in multimeric organization and residue types at the binding sites. Analysis of the three crystal structures described here, together with flavodoxin structures, rationalizes functional similarities and differences of the WrbAs relative to flavodoxins, leading to a new understanding of the defining features of WrbAs. The results suggest that WrbAs are not a remote and unusual branch of the flavodoxin family as previously thought but rather a central member with unifying structural features.
之前报道过的两种类黄素氧还蛋白大肠杆菌蛋白WrbA的全蛋白晶体形式，衍射分辨率分别为2.6 Å和2.0 Å，以及新的WrbA脱辅基蛋白晶体，衍射分辨率为1.85 Å，通过黄素氧还蛋白结构的视角进行了精修和比较分析。结果表明，脱辅基和全蛋白WrbA晶体结构之间的差异在蛋白质组织的多个层面以及FMN结合位点都有体现。通过比较晶格堆积来评估晶体接触的影响，揭示了蛋白质对FMN结合的整体反应。将辅因子结合后的结构变化与单体黄素氧还蛋白进行了比较。尽管结合位点的多聚体组织和残基类型存在差异，但拓扑学上不等价的残基在FMN与WrbA或黄素氧还蛋白结合时会发生非常相似的局部结构变化。对这里描述的三种晶体结构以及黄素氧还蛋白结构进行分析，使WrbA相对于黄素氧还蛋白的功能异同合理化，从而对WrbA的定义特征有了新的认识。结果表明，WrbA并非如之前所认为的那样是黄素氧还蛋白家族中一个遥远且不寻常的分支，而是具有统一结构特征的核心成员。
