The N-terminal isochorismatase (ISC) domain of VibB (VibB-ISC) catalyzes the vinyl ether hydrolysis of isochorismate to 2,3-dihydro-2,3-dihydroxybenzoate and pyruvate. Structures of the ISC domain and its complex with isochorismate have been determined at 1.35 and 1.10 Å resolution, respectively. Two catalytic waters which were absent from previously reported homologous structures were observed adjacent to isochorismate and the catalytic residues (Asp35 and Lys118) in the VibB-ISC complex. Molecular-dynamics (MD) simulations starting with the structure of the VibB-ISC complex suggest that the catalytic waters contribute to the hydrolysis of the vinyl ether by participating in two reactions. Firstly, they may function as a general acid to protonate the Asp35 carboxylate prior to isochorismate protonation; secondly, one of the catalytic waters may be activated by the ionizable side chain of Asp35 to perform a nucleophilic attack on the intermediate carbocation/oxocarbonium ion. The positions of the waters are both significantly affected by the mutation of Asp35 and Lys118. The structural, biochemical and MD results reveal the residues that are involved in substrate binding and provide clues towards defining a possible mechanism.