Mixed-function oxidation of E. coli glutamine synthetase is a site-specific reaction involving covalent modification of specific amino acid residues. It causes loss of a specific histidine residue which is thought to be at one of the metal binding sites. The modified enzyme is catalytically inactive. Oxidative modification causes enhanced susceptibility to proteolytic attack and several different types of proteases recognize the oxidatively modified enzyme. This specific covalent modification increases the rate of degradation of glutamine synthetase to about the same extent as major structural modifications such as relaxation, subunit dissociation and denaturation. Moreover, the oxidative modification is one that is likely to occur in vivo. Adenylylation, which causes reversible inactivation of glutamine synthetase, has no effect on rate of proteolysis. We propose that the degradation of E. coli glutamine synthetase occurs by a two-step process. Control of the degradation is likely to be at the first step, which is inactivation by mixed-function oxidation of the enzyme. Metabolic control of the degradation process and the link with the nutritional state of the cell could be achieved by substrate protection against oxidative modification. At present, the apparent energy requirement of the degradation process is unexplained. Although most of our studies have involved E. coli glutamine synthetase, there is evidence that oxidative modification may be a general mechanism by which proteins are marked for degradation. Many enzymes are inactivated by oxidative modification which can be catalyzed by a variety of mixed-function oxidase systems. Several different types of intracellular proteases in E. coli and mammalian cells preferentially degrade the oxidized form of glutamine synthetase. Oxidative modification of proteins can occur in vivo and may be involved in intracellular protein turnover. It has also been implicated in host defense mechanisms and in aging.