Pediocin PA-1 is a well-known Class IIa bacteriocin which shows strong inhibitory effect against Listeria monocytogenes. In this work, in order to improve the antimicrobial activity, eight single- site mutants and six combination mutants on nine interesting sites in the C-terminal region of pediocin PA-1 were constructed and expressed in Escherichia coli heterologously. Ten mutants demonstrated enhancement activity when performed the agar diffusion test to the indicator strain L. monocytogenes. The substitution of glycine in position 29 to alanine showed the most distinct increase of antimicrobial activity which clarified that 29G acted as a significant role as to guide the pediocin PA-1 molecule to dip into receptor membrane. Combination mutants of sites 29G to 32A illustrated that a hydrophobic tip of the hairpin-like structure and a smaller bundle of the α-helix domain facilitate the penetrating of pediocin PA-1 into a hydrophobic domain of the membrane-embedded subunits of the mannose-phosphotransferase system (MPTs).