A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums

Abstract

Ornithine cyclodeaminase (OCD) is an NAD ⁺-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s C _α–H group to the NAD ⁺ cofactor with concomitant formation of a C _α=NH ₂ ⁺ Schiff base with a barrier of 90.6 kJ mol ⁻¹. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the C _α=NH ₂ ⁺ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the C _α-position. This is then followed by cleavage and loss of the α-NH ₂ group to give the Δ ¹-pyrroline-2-carboxylate that is subsequently reduced to L-proline.