Nisin is a cationic antimicrobial peptide produced by some lactic acid bacteria. However, expression of nisin resistance protein (NSR) could confer nisin resistance on some non-nisin-producing Lactococcus lactis. To deeply elucidate molecular mechanism underlying NSR-mediated nisin resistance, an NSR mutant with N-terminal 38 amino acid residues deleted (NSRΔ38) was overexpressed in Escherichia coli by fusion with GST. Purified NSRΔ38 was obtained through glutathione (GSH) affinity chromatography followed by cleavage of GST tag. Putative proteolytic activity of NSRΔ38 was determined in vitro against nisin. Antimicrobial activity analysis revealed that nisin lost its bactericidal activity after incubation with NSRΔ38. Further reversed-phase high performance liquid chromatography (RP-HPLC) analysis indicated that NSRΔ38 displayed proteolytic activity against nisin, thus inactivating the antimicrobial peptide. The current study paves the way for in-depth functional studies on NSR.