Structure of the RNA polymerase core-binding domain of sigma(54) reveals a likely conformational fracture point.
Transcription initiation by bacterial sigma(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 sigma(70) factor have been determined, little is known about the structure of the sigma(54) variant. We report here the structure of an Aquifex aeolicus sigma(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 sigma(54) in the polymerase complex.
Hong
Eunmi
E
Department of Chemistry, University of California, Berkeley, 94720-1460, USA.
Doucleff
Michaeleen
M
Wemmer
David E
DE
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D017124:Conserved Sequence; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017434:Protein Structure, Tertiary; D051877:RNA Polymerase Sigma 54 / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D055672:Static Electricity
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54