In order to understand roles of E168 and Y170 residues in loop-segment (N166-V177) of nylon-6 byproduct-degrading enzymes, we determined substrate-binding structures of E168Q and Y170F mutants using molecular dynamics simulation with in silico mutations. We found that movement of the loop-segment plays key roles not only in allowing the substrate to be bound by induced fit mechanism but also in forming water-exclusive environment. Fluctuations of the loop-segment in the mutant enzymes caused a room near the catalytic site, where water molecules can access. We propose that the water located exclusivity at the catalytic site is a major factor of its activity. (C) 2011 Elsevier B.V. All rights reserved.