The HydE Catalytic Mechanism Is Powered by a Radical Relay with Redox-Active Fe(I)-Containing Intermediates

A new publication by Nanhao Chen, Guodong Rao, Lizhi Tao, R. David Britt and Lee-Ping Wang in the Journal of the American Chemical Society sheds new light on the assembly of the [FeFe]-hydrogenase active site.   This computational paper is the result of a collaboration between the Lee-Ping Wang and R. David Britt research groups.

Hydrogenases are enzymes that can catalyze the electrochemical reduction of protons to H₂, and they have generated significant interest in the renewable energy field. The [FeFe] hydrogenase active site contains a unique Fe₂S₂ bimetallic cluster called the "H-cluster" with coordinating CO, CN and azadithiolate ligands. The biosynthesis of this complex with multiple highly toxic and chemically unusual ligands is an immense puzzle that has been the subject of numerous experimental and computational studies. 

In this study, the detailed mechanism of the enzyme HydE - one of three maturase enzymes that catalyze the stepwise synthesis of the H-cluster - is revealed using theoretical calculations. Previous experimental studies have established that the maturase HydG produces a Fe(II)(CO)₂(CN)(cysteinate) complex that becomes the substrate of HydE. A number of key intermediates of the HydE mechanism have been discovered with EPR spectroscopy and X-ray crystallography and described in the literature, but the full mechanism had remained elusive until this study.

This study uses state-of-the-art quantum mechanical/molecular mechanical (QM/MM) free energy calculations to map a detailed catalytic mechanism of HydE, filling in the knowledge gaps between the experimental intermediates. Central to the study is how HydE is able to cleave a highly stable carbon-sulfur bond that is present in two of the experimentally detected intermediates. The calculations showed that the Fe(I) center of the intermediates can effect homolytic cleavage of the C—S bond, transferring the unpaired electron from the Fe(I) to the C and generating a radical in the inner coordination sphere. A series of radical chemistry steps - called a radical relay - provides the mechanistic stepping stones leading to the next experimentally detected intermediate. The study also showed how two equivalents of a Fe(I)-containing intermediate, previously described in crystallography studies, is capable of dimerization in the interior of HydE forming the Fe₂S₂ diamond core of the H-cluster. These simulation results take us further down the path to a more complete understanding of these enzymes that synthesize one of Nature’s most efficient energy conversion catalysts.

Read the full article (open access) here.