EMD-16011

Single-particle
3.49 Å
EMD-16011 Deposition: 22/10/2022
Map released: 15/02/2023
Last modified: 29/03/2023
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-16011

Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state

EMD-16011

Single-particle
3.49 Å
EMD-16011 Deposition: 22/10/2022
Map released: 15/02/2023
Last modified: 29/03/2023
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Thermoanaerobacter kivui
Sample: Dimer of the trimeric HydABC complex
Fitted models: 8bew (Avg. Q-score: 0.411)

Deposition Authors: Kumar A, Schuller JM
Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC.
PUBMED: 36811855
DOI: doi:10.1021/jacs.2c11683
ISSN: 1520-5126
ASTM: JACSAT
Abstract:
Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO2, 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 (H2). 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 Acetobacterium woodii and Thermoanaerobacter kivui 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.