We are excited to bring to your attention our recent research article published in ACS Catalysis (IF 13.08). In this paper we used molecular dynamics, quantum mechanics and continuum electrostatic methods to solve the catalytic mechanism of the light-dependent protochlorophyllide oxidoreductase, a key enzyme in chlorophyll biosynthesis in cyanobacteria and plants.
An Alternative Proposal for the Reaction Mechanism of Light-Dependent Protochlorophyllide Oxidoreductase
Silva, P.J. and Cheng, Q.
ACS Catalysis (2022) | DOI: 10.1021/acscatal.1c05351
The light-dependent protochlorophyllide oxidoreductase is one of the few known enzymes that require a quantum of light to start their catalytic cycle. Upon excitation, it uses NADPH to reduce the C17-C18 in its substrate (protochlorophyllide) through a complex mechanism which has heretofore eluded precise determination. Isotopic-labelling experiments have shown that the hydride transfer step is very fast, with a small barrier close to 9 kcal∙mol-1, and is followed by a proton-transfer step, which has been postulated to be the protonation of the product by the strictly conserved Tyr189 residue. Since the structure of the enzyme-substrate complex has not been determined experimentally yet, we first used modelling techniques to discover the actual substrate binding mode. Two possible binding modes were found, both yielding stable binding (as ascertained through molecular dynamics simulations) but only one of which placed the critical C17=C18 bond consistently close to the NADPH pro–S hydrogen and to Tyr189. This binding pose was then used as starting point for the testing of the previous mechanistic proposals using time-dependent density functional theory. The quantum-chemical computations clearly showed that such mechanisms have prohibitively high activation energies. Instead, these computations showed the feasibility of an alternative mechanism begun by excited-state electron transfer from the key Tyr189 to the substrate. This mechanism appears to agree with the extant experimental data, and re-interprets the final protonation step as a proton transfer to the active site itself, rather than to the product, aimed at regenerating it for another round of catalysis.