Investigating protein-protein interfaces in bacterial transcription complexes: a fragmentation approach.

Transcription initiation by sigma(54)-RNA polymerase (RNAP) relies explicitly on a transient interaction with a complex molecular machine belonging to the AAA+ (ATPases associated with various cellular activities) superfamily. Members of the AAA+ superfamily convert chemical energy derived from NTP hydrolysis to a mechanical force used to remodel their target substrate. Recently Bordes and colleagues,1 using a protein fragmentation approach, identified a unique sequence within sigma(54)-dependent transcriptional activators that constitutes a sigma(54)-binding interface. This interface is not static, but subject to nucleotide-dependent movement which may represent a common mechanism for controlling output that has been adopted by other AAA+ proteins.