Toxin-antitoxin (TA) systems are widespread genetic modules in the genomes of bacteria and archaea emerging as key players that modulate bacterial physiology. They consist of two parts, a toxic component that blocks an essential cellular process and an antitoxin that inhibits this toxic activity during normal growth. According to the nature of the antitoxin and the mode of inhibition, TA systems are subdivided into different types. Here, we describe the characterization of a type II-like TA system in Escherichia coli called EzeT. While in conventional type II systems the antitoxin is expressed in trans to form an inactive protein-protein complex, EzeT consists of two domains combining toxin and cis-acting antitoxin functionalities in a single polypeptide chain. We show that the C-terminal domain of EzeT is homologous to zeta toxins and is toxic in vivo. The lytic phenotype could be attributed to UDP-N-acetylglucosamine phosphorylation, so far only described for type II epsilon/zeta systems from Gram-positive streptococci. Presence of the N-terminal domain inhibits toxicity in vivo and strongly attenuates kinase activity. Autoinhibition by a cis-acting antitoxin as described here for EzeT-type TA systems can explain the occurrence of single or unusually large toxins, further expanding our understanding of the TA system network.