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Yorodumi- PDB-8bew: Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase H... -
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-Basic information
Entry | Database: PDB / ID: 8bew | ||||||
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Title | Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state | ||||||
Components | (Electron bifurcating hydrogenase subunit ...) x 3 | ||||||
Keywords | ELECTRON TRANSPORT / Bioenergetics / Acetogenesis / Flavin-based electron bifurcation / [FeFe]-hydrogenase / molecular simulations | ||||||
Function / homology | Function and homology information hydrogen dehydrogenase (NADP+) / hydrogen dehydrogenase (NADP+) activity / cellular anatomical entity / ferredoxin hydrogenase activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding ...hydrogen dehydrogenase (NADP+) / hydrogen dehydrogenase (NADP+) activity / cellular anatomical entity / ferredoxin hydrogenase activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Thermoanaerobacter kivui (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å | ||||||
Authors | Kumar, A. / Schuller, J.M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J Am Chem Soc / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bew.cif.gz | 464.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bew.ent.gz | 382.2 KB | Display | PDB format |
PDBx/mmJSON format | 8bew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bew_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8bew_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8bew_validation.xml.gz | 77.5 KB | Display | |
Data in CIF | 8bew_validation.cif.gz | 116.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/8bew ftp://data.pdbj.org/pub/pdb/validation_reports/be/8bew | HTTPS FTP |
-Related structure data
Related structure data | 16011MC 7q4vC 7q4wC 8a5eC 8a6tC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Electron bifurcating hydrogenase subunit ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 63890.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) References: UniProt: A0A097ATG3, hydrogen dehydrogenase (NADP+) #2: Protein | Mass: 68279.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) References: UniProt: A0A097ATG4, hydrogen dehydrogenase (NADP+) #3: Protein | Mass: 18624.678 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) References: UniProt: A0A097ATI0, hydrogen dehydrogenase (NADP+) |
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-Non-polymers , 4 types, 24 molecules
#4: Chemical | ChemComp-SF4 / #5: Chemical | ChemComp-FES / #6: Chemical | #7: Chemical | |
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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 |
-Sample preparation
Component | Name: Dimer of the trimeric HydABC complex / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL |
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Source (natural) | Organism: Thermoanaerobacter kivui (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 200 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
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 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130283 / Symmetry type: POINT | ||||||||||||||||||||||||
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