8A5E

Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state

Summary for 8A5E

• Entry DOI: 10.2210/pdb8a5e/pdb
• EMDB information: 15166
• Descriptor: Iron hydrogenase HydA1, Iron hydrogenase HydB, Iron hydrogenase HydC, ... (9 entities in total)
• Functional Keywords: flavin-based electron bifurcating hydrogenase, fe-fe hydrogenase, nad, fmn, electron transport
• Biological source: Acetobacterium woodii DSM 1030; More
• Total number of polymer chains: 4
• Total formula weight: 215205.99

Authors

Kumar, A.,Saura, P.,Gamiz-Hernandez, A.P.,Kaila, V.R.I.,Mueller, V.,Schuller, J.M. (deposition date: 2022-06-14, release date: 2023-02-22, Last modification date: 2023-03-29)

Primary citation

Katsyv, A.,Kumar, A.,Saura, P.,Poverlein, M.C.,Freibert, S.A.,T Stripp, S.,Jain, S.,Gamiz-Hernandez, A.P.,Kaila, V.R.I.,Muller, V.,Schuller, J.M.
Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC.
J.Am.Chem.Soc., 145:5696-5709, 2023

PubMed Abstract: Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO, but the molecular mechanisms have remained enigmatic. The key enzyme responsible for powering these thermodynamically challenging reactions is the electron-bifurcating [FeFe]-hydrogenase HydABC that reduces low-potential ferredoxins (Fd) by oxidizing hydrogen gas (H). By combining single-particle cryo-electron microscopy (cryoEM) under catalytic turnover conditions with site-directed mutagenesis experiments, functional studies, infrared spectroscopy, and molecular simulations, we show that HydABC from the acetogenic bacteria and employ a single flavin mononucleotide (FMN) cofactor to establish electron transfer pathways to the NAD(P) and Fd reduction sites by a mechanism that is fundamentally different from classical flavin-based electron bifurcation enzymes. By modulation of the NAD(P) binding affinity via reduction of a nearby iron-sulfur cluster, HydABC switches between the exergonic NAD(P) reduction and endergonic Fd reduction modes. Our combined findings suggest that the conformational dynamics establish a redox-driven kinetic gate that prevents the backflow of the electrons from the Fd reduction branch toward the FMN site, providing a basis for understanding general mechanistic principles of electron-bifurcating hydrogenases.

PubMed: 36811855
DOI: 10.1021/jacs.2c11683

Experimental method

ELECTRON MICROSCOPY (3.4 Å)