Inhibition of a ribosome-inactivating ribonuclease: the crystal structure of the cytotoxic domain of colicin E3 in complex with its immunity protein

Background: The cytotoxicity of most ribonuclease E colicins towards Escher ichia coli arises from their ability to specifically cleave between bases 1 493 and 1494 of 16S ribosomal RNA. This activity is carried by the C-termin al domain of the colicin, an activity which if left unneutralised would lea d to destruction of the producing cell. To combat this the host E. coli cel l produces an inhibitor protein, the immunity protein, which forms a comple x with the ribonuclease domain effectively suppressing its activity. Results: We have solved the crystal structure of the cytotoxic domain of th e ribonuclease colicin E3 in complex with its immunity protein, lm3. The st ructure of the ribonuclease domain, the first of its class, reveals a highl y twisted central beta-sheet elaborated with a short N-terminal helix, the residues of which form a well-packed interface with the immunity protein. Conclusions: The structure of the ribonuclease domain of colicin E3 is nove l and forms an interface with its inhibitor which is significantly differen t in character to that reported for the DNase colicin complexes with their immunity proteins. The structure also gives insight into the mode of action of this class of enzymatic colicins by allowing the identification of pote ntially catalytic residues. This in turn reveals that the inhibitor does no t bind at the active site but rather at an adjacent site, leaving the catal ytic centre exposed in a fashion similar to that observed for the DNase col icins. Thus, E. coli appears to have evolved similar methods for ensuring e fficient inhibition of the potentially destructive effects of the two class es of enzymatic colicins.