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Structure paper

TitleMolecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC.
Journal, issue, pagesJ Am Chem Soc, Vol. 145, Issue 10, Page 5696-5709, Year 2023
Publish dateMar 15, 2023
AuthorsAlexander Katsyv / Anuj Kumar / Patricia Saura / Maximilian C Pöverlein / Sven A Freibert / Sven T Stripp / Surbhi Jain / Ana P Gamiz-Hernandez / Ville R I Kaila / Volker Müller / Jan M Schuller /
PubMed AbstractElectron 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 ...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.
External linksJ Am Chem Soc / PubMed:36811855 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 4.7 Å
Structure data

13818

7q4v

EMDB-13818, PDB-7q4v:
Electron bifurcating hydrogenase - HydABC from A. woodii
Method: EM (single particle) / Resolution: 4.7 Å

13819

7q4w

EMDB-13819, PDB-7q4w:
CryoEM structure of electron bifurcating Fe-Fe hydrogenase HydABC complex A. woodii in the oxidised state
Method: EM (single particle) / Resolution: 3.78 Å

15166

8a5e

EMDB-15166, PDB-8a5e:
Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state
Method: EM (single particle) / Resolution: 3.4 Å

15212

8a6t

EMDB-15212, PDB-8a6t:
Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the reduced state
Method: EM (single particle) / Resolution: 3.1 Å

16011

8bew

EMDB-16011, PDB-8bew:
Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state
Method: EM (single particle) / Resolution: 3.49 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

ChemComp-ZN:
Unknown entry

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

ChemComp-HC1:
2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

Source
  • acetobacterium woodii dsm 1030 (bacteria)
  • thermoanaerobacter kivui (bacteria)
KeywordsELECTRON TRANSPORT / flavin-based electron bifurcating hydrogenase / FeFe hydrogenase / nicotine amide adenine dinucleotide / ferredoxin / Fe-Fe hydrogenase / NAD / FMN / NAD(p) / Bioenergetics / Acetogenesis / Flavin-based electron bifurcation / [FeFe]-hydrogenase / molecular simulations

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