Structure of the RNA Polymerase Core-Binding Domain of σ 54 Reveals a Likely Conformational Fracture Point

Abstract

Transcription initiation by bacterial σ 54-RNA polymerase requires a conformational change of the holopolymerase–DNA complex, driven by an enhancer-binding protein. Although structures of the core polymerase and the more common σ 70 factor have been determined, little is known about the structure of the σ 54 variant. We report here the structure of an Aquifex aeolicus σ 54 domain (residues 69–198), which binds core RNA polymerase. The structure is composed of two distinct subdomains held together by a small, conserved hydrophobic interface that appears to act as a fracture point in the structure. The N-terminal, four-helical subdomain has a negative surface and conserved residues that likely contact the core polymerase, while the C-terminal, three-helical bundle has a strongly positive patch that could contact DNA. Sequence conservation indicates that these structural features are conserved and are important for the role of σ 54 in the polymerase complex.