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首页> 美国卫生研究院文献>Protein Science : A Publication of the Protein Society >A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition.
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A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition.

机译：一种基于二级结构预测和折叠识别的细菌增强子结合蛋白中央结构域的拟议结构。

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摘要

The expression of genes transcribed by the RNA polymerase with the alternative sigma factor sigma 54 (E sigma 54) is absolutely dependent on activator proteins that bind to enhancer-like sites, located far upstream from the promoter. These unique prokaryotic proteins, known as enhancer-binding proteins (EBP), mediate open promoter complex formation in a reaction dependent on NTP hydrolysis. The best characterized proteins of this family of regulators are NtrC and NifA, which activate genes required for ammonia assimilation and nitrogen fixation, respectively. In a recent IRBM course (@ontiers of protein structure prediction," IRBM, Pomezia, Italy, 1995; see web site http://www.mrc-cpe.cam.uk/irbm-course95/), one of us (J.O.) participated in the elaboration of the proposal that the Central domain of the EBPs might adopt the classical mononucleotide-binding fold. This suggestion was based on the results of a new protein fold recognition algorithm (Map) and in the mapping of correlated mutations calculated for the sequence family on the same mononucleotide-binding fold topology. In this work, we present new data that support the previous conclusion. The results from a number of different secondary structure prediction programs suggest that the Central domain could adopt an alpha/beta topology. The fold recognition programs ProFIT 0.9, 3D PROFILE combined with secondary structure prediction, and 123D suggest a mononucleotide-binding fold topology for the Central domain amino acid sequence. Finally, and most importantly, three of five reported residue alterations that impair the Central domain. ATPase activity of the E sigma 54 activators are mapped to polypeptide regions that might be playing equivalent roles as those involved in nucleotide-binding in the mononucleotide-binding proteins. Furthermore, the known residue substitution that alter the function of the E sigma 54 activators, leaving intact the Central domain ATPase activity, are mapped on region proposed to play an equivalent role as the effector region of the GTPase superfamily.
机译：RNA聚合酶以替代的sigma因子sigma 54（E sigma 54）转录的基因的表达绝对依赖于激活蛋白，该蛋白与位于启动子上游的增强子样位点结合。这些独特的原核蛋白，称为增强子结合蛋白（EBP），在依赖NTP水解的反应中介导开放启动子复合物的形成。该调节因子家族中最有特色的蛋白是NtrC和NifA，它们分别激活氨同化和固氮所需的基因。在我们最近的一门IRBM课程中（@ontiers的蛋白质结构预测，” IRBM，意大利波梅齐亚，1995年；请参阅网站http://www.mrc-cpe.cam.uk/irbm-course95/），我们中的一个人（JO ）参与了EBP的中央结构域可能采用经典的单核苷酸结合折叠的提议的拟订，该提议基于新的蛋白质折叠识别算法（Map）的结果以及针对在同一单核苷酸结合折叠拓扑上的序列家族。在这项工作中，我们提供了支持先前结论的新数据。许多不同的二级结构预测程序的结果表明，中央结构域可以采用α/β拓扑。折叠识别程序ProFIT 0.9、3D PROFILE结合二级结构预测和123D提出了中央结构域氨基酸序列的单核苷酸结合折叠拓扑，最后，最重要的是，五分之三报告了r损害中央域的残留物改变。 E sigma 54激活剂的ATPase活性被定位到多肽区域，该区域可能起与单核苷酸结合蛋白中核苷酸结合相关的作用。此外，已知的可改变E sigma 54激活子功能而保留完整的中央结构域ATPase活性的残基取代被定位在拟与GTPase超家族的效应子区域起同等作用的区域。

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