Solution structure of domain 1.1 of the σ factor from is preformed for binding to the RNA polymerase core.

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 in complex with RNAP and from 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 We found that 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 σ1.1. Moreover, modeling studies suggested that σ1.1 requires minimal conformational changes for accommodating RNAP in the DNA channel, whereas σ1.1 must be rearranged to fit therein. Thus, the mesophilic species and share the same σ1.1 fold, whereas the fold of σ1.1 from the thermophile is distinctly different. Finally, we describe an intriguing similarity between σ1.1 and δ, an RNAP-associated protein in , 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.