Bacterial type II toxin-antitoxin (TA) systems exhibit high specificity within each pair to ensure precise recognition of the toxin by its cognate antitoxin to inhibit toxicity of the free toxin. Despite high structural similarity among some TAs, crosstalk between noncognate TA pairs is rare. To determine how the Escherichia coli RelB antitoxin suppresses its cognate RelE toxin, we engineered C-terminal truncations of RelB and tested their functional effects on toxin suppression in E. coli. We find that removal of the long C-terminal α3 and connecting loop 4 of RelB prevents RelE suppression. Quantitative binding assays of RelE and RelB variants support a reduced affinity upon removal of the RelB C terminus. Disrupting these interactions between RelB and RelE also led to a significant decrease in transcriptional repression at the relBrelE DNA operator (relO), underscoring the requirement for RelE binding to RelB for optimal repression at DNA repressor elements. Comparison to other structurally homologous TA systems, such as E. coli DinJ-YafQ, reveals key differences in the molecular mechanisms of both toxin suppression and DNA repressor activity highlighting the diversity in TA regulation and function.