ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, sigma54.
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.
Chen
Baoyu
B
Integrative Biosciences Graduate Degree Program, Chemical Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Doucleff
Michaeleen
M
Wemmer
David E
DE
De Carlo
Sacha
S
Huang
Hector H
HH
Nogales
Eva
E
Hoover
Timothy R
TR
Kondrashkina
Elena
E
Guo
Liang
L
Nixon
B Tracy
BT
D000251:Adenosine Triphosphatases / Q000502:physiology*; D000255:Adenosine Triphosphate / Q000378:metabolism*; D001419:Bacteria / Q000201:enzymology*; D004742:Enhancer Elements, Genetic; D051877:RNA Polymerase Sigma 54 / Q000378:metabolism*; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
D000255:Adenosine Triphosphate; D051877:RNA Polymerase Sigma 54; D000251:Adenosine Triphosphatases