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- PDB-8a5e: Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase H... -
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Basic information
Entry | Database: PDB / ID: 8a5e | |||||||||||||||||||||
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Title | Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state | |||||||||||||||||||||
![]() | (Iron hydrogenase ...) x 3 | |||||||||||||||||||||
![]() | ELECTRON TRANSPORT / flavin-based electron bifurcating hydrogenase / Fe-Fe hydrogenase / NAD / FMN | |||||||||||||||||||||
Function / homology | ![]() ferredoxin hydrogenase / ferredoxin hydrogenase activity / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||||||||
![]() | Kumar, A. / Saura, P. / Gamiz-Hernandez, A.P. / Kaila, V.R.I. / Mueller, V. / Schuller, J.M. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC. Authors: Alexander 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 / ![]() ![]() 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 ...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. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 311.8 KB | Display | ![]() |
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PDB format | ![]() | 252.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 15166MC ![]() 7q4vC ![]() 7q4wC ![]() 8a6tC ![]() 8bewC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Iron hydrogenase ... , 3 types, 4 molecules ADBC
#1: Protein | Mass: 63692.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | | Mass: 64525.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | | Mass: 16999.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 6 types, 19 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HC1.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HC1.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
#4: Chemical | ChemComp-SF4 / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ZN / | #8: Chemical | ChemComp-FMN / | #9: Chemical | ChemComp-NAI / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL |
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Molecular weight | Value: 0.348 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 200 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172189 / Symmetry type: POINT |