Jasmonic acid (JA) is a plant volatile that acts as an important cellular regulator mediating diverse developmental processes and defense responses. Not only the attacked plant but also neighboring plants are affected, becoming more attractive to herbivore predators and less susceptible to invaders. The three-dimensional (3D) model of methyl jasmonate esterase (MJE), which is only responsible for methyl jasmonate (MeJA)-cleaving activity, is constructed based on the crystal structure of salicylic acid-binding protein 2 (SABP2, PDB code 1XKL) by using InsightII/Homology module, and further refined using unrestrained dynamics simulations. With the aid of understanding the molecular interactions between the natural substrate: MeJA and MJE, a 3D model of the complex MeJA-MJE is developed by molecular docking program, and the result may be helpful to explain the experimental realization and the new mutant designs as well. The results indicate that the general 3D organization of MJE is a typical alpha/beta hydrolase superfamily and comprises a central, parallel or mixes beta sheet surrounded by alpha helices. The catalytic residues always constitute a highly conserved triad: Ser83, Asp211, His240, which is consistent with experimental observation. In addition, the key binding-site residues of Thr107 and Leu214 play an important role in the catalysis of MJE. One important finding is that the identification of the key binding site residues of Ser83, which plays an important role in the catalysis of MJE and this is in consistent with experimental observation. The inhibitor phenylmethanesulfonyl fluoride is docked to MJE. Our results also show that His240 and His82 are important in inhibition and it may be helpful for the future inhibitor study. (c) 2005 Elsevier Ltd. All rights reserved.