ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins, including some antitoxins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner. Endogenous substrates include the regulatory proteins RcsA and SulA, the transcriptional activator SoxS, UmuD and at least type II antitoxins CcdA, HipB and MazE (PubMed:8022284, PubMed:16460757, PubMed:22720069, PubMed:24375411). Its overproduction specifically inhibits translation through at least two different pathways, one of them being the YoeB-YefM toxin-antitoxin system (PubMed:15009896). Hydrolysis of proteins in presence of ATP. Contains an allosteric site (distinct from its active site), whose occupancy by an unfolded polypeptide leads to enzyme activation. Homohexamer. Organized in a ring with a central cavity. ATP binding and hydrolysis do not affect the oligomeric state of the enzyme. By accumulation of abnormal proteins, such as at high temperatures. Under stress conditions. When both lon and ycgE are disrupted levels of OmpF decrease, leading to lower drug susceptibility, with a greater effect at 26 degrees than at 37 degrees Celsius. The mechanism is not yet understood (PubMed:19721064). Decreased persister cell formation upon antibiotic challenge due probably due to increased levels of MazF toxin (PubMed:24375411). Both its proteolytic and protein-activated ATPase activities are stimulated by DNA, especially single-stranded DNA. Both high- and low-affinity ATPase sites are present in the homooligomer. Optimal peptidase activity requires ATP binding and hydrolysis at both sites, but ATP hydrolysis is not stoichiometrically linked to peptide hydrolysis. Belongs to the peptidase S16 family. Extended N-terminus.