Campbell Elizabeth A, Kamath Shreya, Rajashankar Kanagalaghatta R, Wu Mengyu, Darst Seth A
Laboratory for Molecular Biophysics, The Rockefeller University, New York, NY 10065.
Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439.
Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1805-E1814. doi: 10.1073/pnas.1619464114. Epub 2017 Feb 21.
The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σ, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σ fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σ The structure allowed us to build and refine an improved σ-holoenzyme model based on previously published 3.8-Å resolution X-ray data. The improved σ-holoenzyme model reveals a conserved interdomain interface within σ that, when disrupted by mutations, leads to transcription activity without activator intervention (so-called bypass mutants). Thus, the structure and stability of this interdomain interface are crucial for the role of σ in blocking transcription activity and in maintaining the activator sensitivity of σ.
细菌的σ因子赋予RNA聚合酶（RNAP）启动子特异性。一种替代σ因子σ，在其结构和功能机制上独具特色，形成转录无活性的启动子复合物，需要由专门的AAA ATP酶激活。我们报告了一个与同源启动子DNA结合的σ片段的3.4埃分辨率X射线晶体结构，揭示了σ识别启动子的分子细节。该结构使我们能够基于先前发表的3.8埃分辨率X射线数据构建并完善一个改进的σ全酶模型。改进后的σ全酶模型揭示了σ内一个保守的结构域间界面，当该界面因突变而被破坏时，会导致在没有激活剂干预的情况下产生转录活性（所谓的旁路突变体）。因此，这个结构域间界面的结构和稳定性对于σ在阻断转录活性以及维持σ对激活剂的敏感性方面所起的作用至关重要。
