Ornithine decarboxylase (ODC) converts C5 ornithine into C4 putrescine, a monomer for polyamide synthesis. However, ODC also has minor activity towards cell metabolite C6 lysine and yields C5 cadaverine. The accumulation of cadaverine in the reaction solution causes increase in the operational cost of subsequent distillation process for putrescine purification. Here, to increase ODC substrate specificity toward ornithine over lysine, molecular modelling and protein network analysis, specifically k-clique community analysis, around the substrate tunnel were performed. This resulted in a mutant with two-fold increase in substrate specificity (ornithine versus lysine) without losing its original activity towards ornithine (kcat/KM  = 61.5 s−1  mM-1), compared to the native enzyme. When this mutant was used for putrescine synthesis, 31.6 g/L putrescine (based on 51.5 g/L ornithine) titer was achieved, while 0.007 g/L (based on 2.57 g/L lysine) cadaverine was produced. This corresponds to four-fold decrease in cadaverine yield compared to the native ODC.