Closing the gap between CO2 fixation and methane generation

September 14, 2017
Methane is a potent greenhouse gas and at the same time an important renewable energy source. The study of methane formation is, therefore, of great relevance for basic and applied science. Microbes called methanogens produce half of the methane on our planet. Most methanogens use hydrogen and CO2 in a process called hydrogenotrophic methanogenesis to generate methane. Scientists at the Max Planck Institute for Terrestrial Microbiology in Marburg together with collaborators at the Max Planck Institute of Biophysics in Frankfurt have now shown how methane generation and CO2 fixation are connected. The work can potentially improve future attempts to reduce atmospheric methane levels as well as to generate methane as a renewable energy source. This work was recently published in the international journal Science.

The research group of Dr. Seigo Shima at the Max Planck Institute in Marburg together with scientists at the Max Planck Institute of Biophysics in Frankfurt have a longstanding interest in deciphering how methanogens generate methane. To this end, they have determined the 3D structure of several of the enzymes involved in this process. The final step in the methanogenesis pathway generates two products: methane and a heterodisulfide compound made of coenzyme M and coenzyme B (CoM-S-S-CoB). The reduced coenzymes M and B have to be regenerated from CoM-S-S-CoB to generate methane again. This reduction reaction is performed by a large protein complex that consists of the heterodisulfide-reductase HdrABC in complex with the hydrogenase MvhAGD (HdrABC-MvhAGD).

In this reaction, the electrons extracted from H2 are transferred to HdrA by a relay of iron-sulfur clusters (Fig. 1). HdrA is an enzyme that uses a novel energy-coupling mechanism called “Flavin-based electron bifurcation”. This mechanism was recently discovered by Prof. Wolfgang Buckel at the Philipps-Universität Marburg and Prof. Rolf Thauer at the Max Planck Institute for Terrestrial Microbiology. In this reaction, electrons of the same energy are distributed into electrons with higher energy and electrons with lower energy. In the case of HdrA, flavin splits the electrons into two different directions: the first electron goes to the heterodisulfide reductase center to reduce the CoM-S-S-CoB molecule (low-energy required) while the second electron reduces an electron-carrier protein, ferredoxin (high-energy required). After these reactions, the released coenzymes M and B can be reused for generation of methane and the reduced ferredoxin can participate in a novel round of CO2 fixation.

To explore the tricks of the enzymatic reactions of HdrABC-MvhAGD, Dr. Seigo Shima together with Dr. Tristan Wagner, a postdoctoral fellow, determined and solved the 3D structure of the HdrABC-MvhAGD enzyme from the methanogen Methanothermococcus thermolithotrophicus. Jürgen Koch, a technical assistant, synthesized the complicated CoM-S-S-CoB molecule, which was the key to unravel the secrets of the heterodisulfide reductase reaction. The crystal structure of the HdrABC-MvhAGD complex has now allowed the scientists to sketch out in details how the complete reaction from the hydrogenase to the heterodisulfide reductase occurs. However, the most striking discovery was waiting in the HdrB subunit. Here, a new type of iron-sulfur cluster was identified (Fig. 2). “The identification of a new catalytically active metallocofactor and its mode of action in a protein environment is a rare and exciting event” says Seigo Shima. These so-called non-cubane iron-sulfur clusters perform the reduction of the CoM-S-S-CoB molecule. The binding sequence motif that serves as a marker for this type of iron-sulfur cluster is present in more than 2000 proteins, suggesting that these iron-sulfur clusters are widespread among anaerobic microorganisms. “This finding will contribute to elucidate the function of a wide range of proteins that contain this binding motif” explains Tristan Wagner. HdrA homologues are also found in many other microorganisms, for instance anaerobic methanotrophic archaea, sulfate-reducing-bacteria and -archaea, sulfur-oxidizing bacteria, acetogenic bacteria, knallgas bacteria and metal-reducing bacteria, and might be used as universal electron-bifurcating module. Most of the HdrA homologs are, however, not biochemically studied. The HdrABC-MvhAGD structure serves as the prototype for these widespread protein classes and contributes to their functional and mechanistic characterization.


Wagner, T., Koch, J., Ermler, U. & Shima, S. (2017) Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science 357, 699–703.

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