Homology modelling of the Lactococcus lactis leader peptidase NisP and its interaction with the precursor of the lantibiotic nisin

A model is presented for the 3-D structure of the catalytic domain of the putative leader peptidase NisP of Lactococcus lactis, and the interaction with its specific substrate, the precursor of the lantibiotic nisin. This homology model is based on the crystal structures of subtilisin BPN' and thermitase in complex with the inhibitor eglin. Predictions are made of the general protein fold, inserted loops, Ca2+ binding sites, aromatic interactions and electrostatic interactions of NisP. Cleavage of the leader peptide from precursor nisin by NisP is the last step in maturation of nisin. A detailed prediction of the substrate binding site attempts to explain the basis of specificity of NisP for precursor nisin. Specific acidic residues in the S1 sub site of the substrate binding region of NisP appear to be of particular importance for electrostatic interaction with the P1 Arg residue of precursor nisin after which cleavage occurs. The hydrophobic S4 subsite of NisP may also contribute to substrate binding as it does in subtilisins. Predictions of enzyme-substrate interaction were tested by protein engineering of precursor nisin and determining susceptibility of mutant precursors to cleavage by NisP. An unusual property of NisP predicted from this catalytic domain model is a surface patch near the substrate binding region which is extremely rich in aromatic residues. It may be involved in binding to the cell membrane or to hydrophobic membrane proteins, or it may serve as the recognition and binding region for the modified, hydrophobic C-terminal segment of precursor nisin. Similar predictions for the tertiary structure and substrate binding are made for the highly homologous protein EpiP, the putative leader peptidase for the lantibiotic epidermin from Staphylococcus epidermidis, but EpiP lacks the aromatic patch. Based on these models, protein engineering can be employed not only to test the predicted enzyme-substrate interactions, but also to design lantibiotic leader peptidases with a desired specificity.