The Escherichia coli ATP-dependent protease Lon degrades ribosomal S2 protein in the presence of inorganic polyphosphate (polyP). In this study, the process of the degradation was investigated in detail. During the degradation, 68 peptides with various sizes (4-29 residues) were produced in a processive fashion. Cleavage occurred at 45 sites, whose P-1 and P-3 positions were dominantly occupied by hydrophobic residues. These cleavage sites were located preferentially at the regions with rigid secondary structures and the P, residues of the major cleavage sites appeared to be concealed from the surface of the substrate molecule. Furthermore, polyP changed not only the substrate preference but also the oligomeric structure of the enzyme. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.