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Yorodumi- EMDB-15166: Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase H... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15166 | |||||||||||||||||||||
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Title | Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state | |||||||||||||||||||||
Map data | Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state | |||||||||||||||||||||
Sample |
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Function / homology | Function and homology information ferredoxin hydrogenase / ferredoxin hydrogenase activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | Thermoanaerobacter kivui (bacteria) / Acetobacterium woodii DSM 1030 (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||||||||
Authors | Kumar A / Saura P / Gamiz-Hernandez AP / Kaila VRI / Mueller V / Schuller JM | |||||||||||||||||||||
Funding support | Germany, European Union, Sweden, 6 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15166.map.gz | 4.6 MB | EMDB map data format | |
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Header (meta data) | emd-15166-v30.xml emd-15166.xml | 20 KB 20 KB | Display Display | EMDB header |
Images | emd_15166.png | 73.6 KB | ||
Others | emd_15166_half_map_1.map.gz emd_15166_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15166 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15166 | HTTPS FTP |
-Validation report
Summary document | emd_15166_validation.pdf.gz | 669.4 KB | Display | EMDB validaton report |
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Full document | emd_15166_full_validation.pdf.gz | 669 KB | Display | |
Data in XML | emd_15166_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_15166_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15166 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15166 | HTTPS FTP |
-Related structure data
Related structure data | 8a5eMC 7q4vC 7q4wC 8a6tC 8bewC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15166.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_15166_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_15166_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermo...
+Supramolecule #1: Electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermo...
+Macromolecule #1: Iron hydrogenase HydA1
+Macromolecule #2: Iron hydrogenase HydB
+Macromolecule #3: Iron hydrogenase HydC
+Macromolecule #4: IRON/SULFUR CLUSTER
+Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #6: 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER
+Macromolecule #7: ZINC ION
+Macromolecule #8: FLAVIN MONONUCLEOTIDE
+Macromolecule #9: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | JEOL CRYO ARM 200 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172189 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |