The physical and the functional organization of the upstream cis-acting sequence that controls at a distance the transcriptional activity of Pu and Ps, the two sigma 54-dependent promoters of the TOL (toluene/xylene biodegradation) operons of Pseudomonas putida, have been determined. DNase I and hydroxyl radical footprinting of the promoters with the purified and pre-activated enhancer-binding protein XylR clearly indicated the presence of two distinct binding sites (proximal and distal) that were occupied independently and did not share an evident sequence similarity. However, alignment of the sequence on the basis of the cleavage protection patterns, along with those produced on Po, a third XylR-responsive promoter of a phenol degradation operon, generated a consensus sequence 5'-TTGATCAATTGATCAA-3' having greater similarity to the proximal than to the distal boxes. To verify that this consensus was the sequence recognized by XylR, we footprinted in vitro a synthetic site, the results indicating that it was strongly bound by the activator with the predicted pattern of interactions. The mode of protection indicated that XylR recognized the sequence as a palindrome and not as a tandem repeat, interacting with it on one side of the DNA helix. In vivo experiments involving directed deletions through the entire 5' region of the Pu promoter confirmed that the proximal XylR-binding sequence suffices for promoter activity. In vivo data also suggested that XylR binding to the upstream sequences promoted the assembly of the oligomeric form of the activator that is competent for transcription initiation.