Biochemistry: mechanistic enzymology, metalloenzymes, EPR/ESR

Methyl Coenzyme M Reductase

Methyl-coenzyme M reductase (MCR) is the key enzyme in both the biological formation of methane by methanogenic Archaea and anaerobic oxidation of methane by methanotrophic Archaea. The activity of MCR is critically dependent on the unique nickel-containing tetrapyrrole, coenzyme F₄₃₀. Recently we successfully produced recombinant MCR with low methane-forming activity. This is already a milestone, but to be able to obtain fully active recombinant MCR, we need to characterize the mechanism of protein assembly and optimize its activation. A very large protein complex is required for MCR activation in a process that appears to involve both electron bifurcation and ATP hydrolysis. Our research is aimed at understanding the biochemical mechanism of this activation using recombinant proteins and a simplified MCR activation assay. The long-term goals of our research are to understand the actual mechanism of methane production and the regulation of MCR activity by the cell. A successful outcome will provide important insight into how to slow down livestock methane production and production in rice fields. Both processes contribute to climate change due to the fact that methane is a potent greenhouse gas.

Heterodisulfide Reductase

Heterodisulfide reductase (HDR) plays a role in the conversion of CO₂ into CH₄ and is also part of the activating complex of MCR. In both cases it uses electron bifurcation for the production of low-potential electrons. HDR contains several cofactors, including iron-sulfur clusters, but the key role is played by FAD, which can accept two medium potential electrons together and deliver one electron with a high potential and one electron with a low potential. In addition, there is the need to physically separate the electron flow into a high-potential branch and a low-potential branch via a conformational change in the enzyme complex. Site directed-mutagenesis, in combination with redox titration and rapid-mix/rapid freeze studies, should provide information on the cofactors that interact with the central FAD and how they help in the bifurcation process. Electron bifurcation has now been shown for several protein complexes and is expected to be a wide spread process in nature but the mechanism is not understood. Therefore the results of the research should be of considerable interest to the biochemistry, microbiology and biofuel communities. 

1. Duin, E.C., Wagner, T., Shima, S., Prakash, D., Cronin, B., Yáñez-Ruiz, D.R., Duval, S., Ruembeli, R., Stemmler, R.T., Thauer, R.K., Kindermann, M. (2016) Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol. PNAS 113, 6172–6177.

2. Prakash, D., Wu, Y., Suh, S.-J., Duin, E.C. (2014) Elucidating the Process of Activation of Methyl-Coenzyme M Reductase. J. Bacteriol., 196, 2491-2498.

3. Duin, E.C., Prakash, D., and Brungess, C.* (2011) Methyl-coenzyme M reductase from Methanothermobacter marburgensis. Meth. Enzymol., 494, 159-187.

4. Duin, E.C. (2008) Role of coenzyme F430 in methanogenesis. In: Tetrapyrroles: their birth, life and death, Chapter 23 (Eds. Warren, M.J., Smith, A.), Landes Bioscience, Georgetown, pp 352-374.

5. Harmer, J., Finazzo, C., Piskorski, R., Ebner, S., Duin, E.C., Goenrich, M, Thauer, R.K., Reiher, M., Schweiger, A., Hinderberger, D., Jaun, B. (2008) A Nickel Hydride Complex in the Active Site of Methyl-Coenzyme M Reductase: Implications for the Catalytic Cycle, J. Am. Chem. Soc., 130, 10907-10920.

6. Duin, E.C., McKee, M.L. (2008) A New Mechanism for Methane Production from Methyl-Coenzyme M Reductase As Derived from Density Functional Calculations. J. Phys. Chem. B, 112, 2466-2482.Yang, N., Reiher, M., Wang, M., Harmer, J., Duin, E.C. (2007) Formation of a nickel-methyl species in methyl-coenzyme M reductase, an enzyme catalyzing methane formation. J. Am. Chem. Soc., 129, 11028-11029.