Properties and Reaction Mechanism of

Methyl-coenzyme M Reductase

Methyl-coenzyme M reductase (MCR) is the enzyme present in methanogenic Archaea that is responsible for the actual formation of methane in a process called methanogenesis. MCR catalyzes the reduction of methyl-coenzyme M (CH₃-S-CoM) with coenzyme B (HS-CoB) to CH₄ and the mixed disulfide of coenzyme M and coenzyme B (CoM-S-S-CoB):

It has been proposed that the same enzyme is also involved in anaerobic methane oxidation [1]. It is not clear, however, if the catalyzed reaction would be an exact reversal of the forward reaction.

It is expected that the nickel-containing tetrapyrrole factor 430 (F₄₃₀) plays a central role in the reaction mechanism:

Several hypothetical catalytic mechanisms of MCR are presently discussed [2-5]. The main difference between these mechanisms is the initial interaction between the substrate methyl-coenzyme M and the nickel atom in F₄₃₀, being either a metalloorganic Ni-methyl complex or a Ni-thiolate complex.

Recently, this lab and other groups we were able to show the presence of a Ni(III)-CH₃ complex in MCR giving plausibility for hypothetical mechanisms with such an intermediate [6,7]. In addition it was shown that incubation of the Ni(III)-CH₃ species with the substrate analog coenzyme M resulted in the formation of methyl-coenzyme M. Although it is no proof, it adds plausibility to the working hypothesis that archaea which perform anaerobic methane oxidation contain an MCR-like protein that works in reverse.

The proposed hypothetical reaction mechanism in the literature are not reversible. Recently, together with the group of Dr Michael McKee, we used DFT calculations to explore new mechanisms that do take the possible reversibility of the reaction in consideration [8]:

The cycle begins with the protonation of F₄₃₀, either on Ni or on the C-ring nitrogen of the tetrapyrrole ring, both of which are nearly equally favorable. The C-ring protonated form is predicted to oxidatively add CH₃SCoM‾ to give a 4-coordinate Ni center where the Ni moves out of the plane of the four ring-nitrogens. The movement of Ni (and the attached CH₃ and SCH₂CH₂SO₃²‾ ligands) toward the SCoB‾ cofactor allows a 2c-3e interaction to form between the two sulfur atoms. The release of the heterodisulfide yields a Ni(III) center with a methyl group attached. The reaction finishes with the concerted elimination of methane where the methyl group coordinated to Ni abstracts the proton from the C-ring nitrogen.

To gain a better understanding of the reaction mechanism, our current research concentrates on the characterization of different enzyme forms that can be generated in the presence of substrates, analogs and inhibitors. Isotopic labeling of key atoms allows the determination of the distances of these atoms to the paramagnetic nickel center using the technique of ENDOR spectroscopy.

This research is done in collaboration with the group of Dr. Bernhard Jaun at the ETH Zürich and Dr. Jeffrey Harmer at Oxford University.

Students working on this project: 

Mi Wang

1. Shima, S. and Thauer, R. K. (2005) Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea. Current Opinion in Microbiology 8:643-648.

2. Grabarse, W., Mahlert, F., Duin, E. C., Goubeaud, M., Shima, S., Thauer, R. K., Lamzin, V., and Ermler, U. (2001) On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding. J. Mol. Biol. 309:315-330.

3. Horng, Y.-C., Becker, D. F., and Ragsdale, S. W. (2001) Mechanistic studies of methane biogenesis by methyl-coenzyme M reductase: evidence that coenzyme B participates in cleaving the C-S bond of methyl-coenzyme M. Biochemistry 40:12875-12885.

4. Pelmenschikov, V., Blomberg, M. R. A., Siegbahn, P. E. M., and Crabtree, R. H. (2002) A mechanism from quantum chemical studies for methane formation in methanogenesis. J. Am. Chem. Soc. 124:4039-4049.

5. Pelmenschikov, V. and Siegbahn, P. E. M. (2003) Catalysis by methyl-coenzyme M reductase: A theoretical study for heterodisulfide product formation. J. Biol. Inorg. Chem. 8:653-662.

6. 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.

7. Dey, M., Telser, J., Kunz, R. C., Lees, N. S., Ragsdale, S. W., and Hoffman, B. M. (2007) Biochemical and Spectroscopic Studies of the Electronic Structure and Reactivity of a Methyl-Ni Species Formed on Methyl-Coenzyme M Reductase. J. Am. Chem. Soc., 129, 11030 - 11032.

8. 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.