ATP Ground- and Transition States of Bacterial Enhancer Binding AAA+ ATPases Support Complex Formation with Their Target Protein, σ54

• DOI: 10.1016/j.str.2007.02.007
• Publication Date: 2007-04-18T11:33:10Z
• Authors: Baoyu Chen; Michaeleen Doucleff; David E. Wemmer; Sacha De Carlo; Hector H. Huang; Eva Nogales; Timothy R. Hoover; Elena Kondrashkina; Liang Guo; B. Tracy Nixon
• Keywords: Adenosine Triphosphatases; 0303 health sciences; 03 medical and health sciences; Adenosine Triphosphate; Enhancer Elements, Genetic; Bacteria; X-Ray Diffraction; Structural Biology; Scattering, Small Angle; Molecular Biology; RNA Polymerase Sigma 54

Transcription initiation by the sigma54 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-BeF(x) (ground-state mimics), ADP-AlF(x) (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-BeF(x) state, and from the ADP-AlF(x) state to the ADP state. Binding of the ATP analogs stabilizes the oligomeric form of the ATPase and its binding to sigma54, with ADP-AlF(x) having the largest effect. These data indicate that ATP binding promotes a conformational change that stabilizes complexes between EBPs and sigma54, while subsequent hydrolysis and phosphate release drive the conformational change needed to open the polymerase/promoter complex.