We have used protein footprinting [Heyduk, E., & Heyduk, T. (1994) Biochemistry 33, 9643] to detect and map ligand-induced conformational changes in cAMP receptor protein (CRP). The binding of cAMP to CRP dramatically increases the specific DNA binding activity of the protein and, as has been previously shown, induces conformational changes in the protein. Protein footprinting experiments with the free CRP, the CRP-cAMP complex, and the CRP-cGMP complex were analyzed quantitatively. Binding of cAMP produced measurable differences in the susceptibility of CRP to the cleavage by Fe-EDTA. Almost all of these changes occurred in the C-terminal domain (DNA binding domain) of the protein. Additional changes were observed at the ends of the C alpha-helix, which is involved in intersubunit contacts in the CRP dimer, and in the hinge peptide, connecting N-terminal and C-terminal domains of the protein. The boundaries of the regions in the C-terminal domain, which exhibited changes in susceptibility to Fe-EDTA cleavage, almost exactly corresponded to D, E, and F alpha-helices which are involved directly in the recognition of DNA. The F alpha-helix, which provides all base-specific contacts in the CRP-DNA complex, became hypersensitive to Fe-EDTA-mediated cleavage, whereas the solvent exposure of D and E alpha-helices was decreased upon binding of cAMP. These results suggest that a significant part of cAMP-induced conformational change in CRP involves a movement of secondary structure elements in the C-terminal domain of the protein so that the recognition F alpha-helix becomes exposed to the solvent. In contrast to cAMP, binding of cGMP produced insignificant changes in susceptibility to Fe-EDTA-mediated cleavage. This is consistent with the inability of cGMP to induce functional conformational changes in CRP. The protein footprinting technique appears to be sufficiently sensitive for detection and mapping of ligand-induced conformational changes in proteins.