Transcription initiation by the σ54 form of bacterial RNA polymerase requires hydrolysis of ATP by an enhancer binding protein (EBP). We present SAS-based solution structures of the ATPase domain of the EBP NtrC1 from Aquifex aeolicus in different nucleotide states. Structures of apo protein and that bound to AMPPNP or ADP-BeFx (ground-state mimics), ADP-AlFx (a transition-state mimic), or ADP (product) show substantial changes in the position of the GAFTGA loops that contact polymerase, particularly upon conversion from the apo state to the ADP-BeFx state, and from the ADP-AlFx state to the ADP state. Binding of the ATP analogs stabilizes the oligomeric form of the ATPase and its binding to σ54, with ADP-AlFx having the largest effect. These data indicate that ATP binding promotes a conformational change that stabilizes complexes between EBPs and σ54, while subsequent hydrolysis and phosphate release drive the conformational change needed to open the polymerase/promoter complex.
All Science Journal Classification (ASJC) codes
- Structural Biology
- Molecular Biology