AbstractThe results of a DFT theoretical investigation on the catalytic mechanism of the QC enzyme are presented. A rather large model‐system is used. It includes the most important residues that are believed to play a key‐role in the catalysis. The computational results show that the rate‐determining step of the catalytic process is not the nucleophilic attack leading to the cycle formation (a very easy and fast process with a negligible barrier of 0.8 kcal mol−1), but a proton transfer, which is assisted by the Glu201 residue acting as a proton shuttle (general base and general acid). A complex network of hydrogen bonds (involving Asp248 and other residues) contribute to lower the activation barrier for the proton shift which affords the formation of an ammonia molecule bonded to the substrate. The ammonia molecule is a good leaving group which is easily expelled from the substrate in the last step of the catalytic cycle, but remains anchored to the enzyme as a ligand of the zinc cation. The metal plays a key‐role in assisting the nucleophilic attack (electrostatic catalysis) since it polarizes the substrate γ‐amide carbonyl group (its electrophilic character increases). Also, the strength of the nucleophilic nitrogen (substrate α‐amino group) is enhanced by hydrogen bonds involving the Glu201 residue. The computations outline the important role of Trp329 in helping the substrate binding process and stabilizing the cyclization transition state. Proteins, 2008. © 2008 Wiley‐Liss, Inc.