Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Electron flow in hydrogenotrophic methanogens under nickel limitation.
Journal, issue, pages	Nature, Year 2025
Publish date	Jul 2, 2025
Authors	Shunsuke Nomura / Pablo San Segundo-Acosta / Evgenii Protasov / Masanori Kaneko / Jörg Kahnt / Bonnie J Murphy / Seigo Shima /
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 ...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.
External links	Nature / PubMed:40604290
Methods	EM (single particle)
Resolution	1.85 - 2.47 Å
Structure data	EMDB-19530: State 2 Hdr-focused map Elp-Hdr Method: EM (single particle) / Resolution: 2.2 Å EMDB-19531: State 2 mobile-arm-focused map Elp-Hdr Method: EM (single particle) / Resolution: 2.2 Å EMDB-19532: State 2 Elp-Hdr consensus map Method: EM (single particle) / Resolution: 2.3 Å 19533 8rvu EMDB-19533, PDB-8rvu: CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2 (composite structure) Method: EM (single particle) / Resolution: 2.22 Å 19534 8rvv EMDB-19534, PDB-8rvv: CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2, dimer (composite structure) Method: EM (single particle) / Resolution: 2.2 Å EMDB-19535: State 1 Hdr-focused map Elp-Hdr Method: EM (single particle) / Resolution: 2.2 Å EMDB-19536: State 1 Mobile-arm-focused map Elp-Hdr Method: EM (single particle) / Resolution: 2.4 Å EMDB-19537: State 1 Elp-Hdr consensus map Method: EM (single particle) / Resolution: 2.47 Å 19538 8rvy EMDB-19538, PDB-8rvy: CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 1 (composite structure) Method: EM (single particle) / Resolution: 2.36 Å 19564 8rwn EMDB-19564, PDB-8rwn: CryoEM structure of the Hdr(ABC)2 subunits of the Elp-Hdr complex of Methanothermobacter marburgensis Method: EM (single particle) / Resolution: 1.85 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER ChemComp-FAD: FLAVIN-ADENINE DINUCLEOTIDE / FADYM ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-9S8: Non-cubane [4Fe-4S]-cluster ChemComp-HOH*: WATER
Source	methanothermobacter marburgensis (archaea)
Keywords	OXIDOREDUCTASE / Redox / Flavin-based electron bifurcation / methanogenesis / heterodisulfide reductase / F420-H2 oxidase