8RVY

CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 1 (composite structure)

Summary for 8RVY

• Entry DOI: 10.2210/pdb8rvy/pdb
• EMDB information: 19538
• Descriptor: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A, Non-cubane [4Fe-4S]-cluster, Formate dehydrogenase, beta subunit, ... (11 entities in total)
• Functional Keywords: redox, flavin-based electron bifurcation, methanogenesis, heterodisulfide reductase, f420-h2 oxidase, oxidoreductase
• Biological source: Methanothermobacter marburgensis; More
• Total number of polymer chains: 9
• Total formula weight: 359509.36

Authors

San Segundo-Acosta, P.,Murphy, B.J. (deposition date: 2024-02-02, release date: 2025-05-14, Last modification date: 2025-07-16)

Primary citation

Nomura, S.,San Segundo-Acosta, P.,Protasov, E.,Kaneko, M.,Kahnt, J.,Murphy, B.J.,Shima, S.
Electron flow in hydrogenotrophic methanogens under nickel limitation.
Nature, 2025

PubMed Abstract: Methanogenic archaea are the main producers of the potent greenhouse gas methane. In the methanogenic pathway from CO and H studied under laboratory conditions, low-potential electrons for CO reduction are generated by a flavin-based electron-bifurcation reaction catalysed by heterodisulfide reductase (Hdr) complexed with the associated [NiFe]-hydrogenase (Mvh). F-reducing [NiFe]-hydrogenase (Frh) provides electrons to the methanogenic pathway through the electron carrier F (ref. ). Here we report that under strictly nickel-limited conditions, in which the nickel concentration is similar to those often observed in natural habitats, the production of both [NiFe]-hydrogenases in Methanothermobacter marburgensis is strongly downregulated. The Frh reaction is substituted by a coupled reaction with [Fe]-hydrogenase (Hmd), and the role of Mvh is taken over by F-dependent electron-donating proteins (Elp). Thus, Hmd provides all electrons for the reducing metabolism under these nickel-limited conditions. Biochemical and structural characterization of Elp-Hdr complexes confirms the electronic interaction between Elp and Hdr. The conservation of the genes encoding Elp and Hmd in CO-reducing hydrogenotrophic methanogens suggests that the Hmd system is an alternative pathway for electron flow in CO-reducing hydrogenotrophic methanogens under nickel-limited conditions.

PubMed: 40604290
DOI: 10.1038/s41586-025-09229-y

Experimental method

ELECTRON MICROSCOPY (2.36 Å)