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

Area of Science:

• Biochemistry and Molecular Biology
• Bioinorganic Chemistry
• Computational Chemistry

Background:

• [FeFe]-hydrogenases are critical enzymes for H2 production, utilizing a unique H-cluster active site.
• The biosynthesis of the [2Fe] subcluster, essential for the H-cluster, involves enzymes HydG, HydE, and HydF.
• HydE processes an organometallic iron complex, converting it to an Fe(I) species, with its mechanism and product remaining challenging to characterize experimentally.

Purpose of the Study:

• To elucidate the catalytic mechanism of the enzyme HydE in the biosynthesis of the [2Fe] subcluster.
• To investigate the proposed Fe(I)Fe(I) dimer formation within HydE.
• To provide a deeper mechanistic understanding of [FeFe]-hydrogenase maturation.

Main Methods:

• Hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations were employed.
• Analysis focused on the catalytic steps, including substrate processing and potential dimerization.
• Computational results were compared with existing experimental data from EPR spectroscopy and X-ray crystallography.

Main Results:

• A radical relay mechanism was identified as the energetically favored pathway for cysteine S-Cβ bond cleavage by HydE.
• A plausible pathway for the dimerization of two Fe(I) complexes within HydE's hydrophobic cavity was proposed.
• The proposed dimerization pathway is consistent with experimental findings on HydF-mediated maturation using synthetic dimer complexes.

Conclusions:

• The study provides significant insights into the complex catalytic mechanism of HydE.
• The findings support a radical-based mechanism for key transformations in [FeFe]-hydrogenase biosynthesis.
• This work advances the understanding of the intricate enzymatic machinery responsible for producing efficient biological catalysts for energy conversion.