Solution structure of domain 1.1 of the σA factor from Bacillus subtilis is preformed for binding to the RNA polymerase core
| Autor: | Libor Krásný, Lukáš Žídek, Ivan Barvík, Petr Padrta, Milan Zachrdla, Alžbeta Rabatinová, Hana Šanderová |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
biology Cell Biology Bacillus subtilis 010402 general chemistry biology.organism_classification 01 natural sciences Biochemistry 0104 chemical sciences enzymes and coenzymes (carbohydrates) 03 medical and health sciences chemistry.chemical_compound 030104 developmental biology Protein structure chemistry Sigma factor RNA polymerase Thermotoga maritima biology.protein bacteria Binding site Molecular Biology Polymerase DNA |
| Zdroj: | Journal of Biological Chemistry. 292:11610-11617 |
| ISSN: | 0021-9258 |
| DOI: | 10.1074/jbc.m117.784074 |
| Popis: | Bacterial RNA polymerase (RNAP) requires σ factors to recognize promoter sequences. Domain 1.1 of primary σ factors (σ1.1) prevents their binding to promoter DNA in the absence of RNAP, and when in complex with RNAP, it occupies the DNA-binding channel of RNAP. Currently, two 3D structures of σ1.1 are available: from Escherichia coli in complex with RNAP and from T. maritima solved free in solution. However, these two structures significantly differ, and it is unclear whether this difference is due to an altered conformation upon RNAP binding or to differences in intrinsic properties between the proteins from these two distantly related species. Here, we report the solution structure of σ1.1 from the Gram-positive bacterium Bacillus subtilis We found that B. subtilis σ1.1 is highly compact because of additional stabilization not present in σ1.1 from the other two species and that it is more similar to E. coli σ1.1. Moreover, modeling studies suggested that B. subtilis σ1.1 requires minimal conformational changes for accommodating RNAP in the DNA channel, whereas T. maritima σ1.1 must be rearranged to fit therein. Thus, the mesophilic species B. subtilis and E. coli share the same σ1.1 fold, whereas the fold of σ1.1 from the thermophile T. maritima is distinctly different. Finally, we describe an intriguing similarity between σ1.1 and δ, an RNAP-associated protein in B. subtilis, bearing implications for the so-far unknown binding site of δ on RNAP. In conclusion, our results shed light on the conformational changes of σ1.1 required for its accommodation within bacterial RNAP. |
| Databáze: | OpenAIRE |
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