Nucleotide-dependent conformational changes in the sigma54-dependent activator DctD

Activators of sigma(54)-RNA polymerase holoenzyme couple ATP hydrolysis to formation of an open promoter complex. DctD(Delta1-142), a truncated and constitutively active form of the sigma(54)-dependent activator DctD from Sinorhizobium meliloti, displayed an altered DNase I footprint at its binding site located upstream of the dctA promoter in the presence of ATP. The altered footprint was not observed for a mutant protein with a substitution at or near the putative arginine finger, a conserved arginine residue thought to contact the nucleotide. These data suggest that structural changes in DctD(Delta1-142) during ATP hydrolysis can be detected by alterations in the DNase I footprint of the protein and may be communicated by interactions between bound nucleotide and the arginine finger. In addition, kinetic data for changes in fluorescence energy transfer upon binding of 2'(3')-O-(N-methylanthraniloyl)-ATP (Mant-ATP) to DctD(Delta1-142) and DctD suggested that these proteins undergo multiple conformational changes following ATP binding.