+Open data
-Basic information
Entry | Database: PDB / ID: 7qv7 | ||||||||||||||||||
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Title | Cryo-EM structure of Hydrogen-dependent CO2 reductase. | ||||||||||||||||||
Components | (Hydrogen dependent carbon dioxide reductase subunit ...) x 4 | ||||||||||||||||||
Keywords | ELECTRON TRANSPORT / Hydrogen-dependent CO2 reduction / Carbon fixation / Protein nanowire filament / enzyme catalysis | ||||||||||||||||||
Function / homology | Function and homology information formate dehydrogenase / formate metabolic process / ferredoxin hydrogenase / formate dehydrogenase (NAD+) activity / ferredoxin hydrogenase activity / Oxidoreductases / molybdopterin cofactor binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...formate dehydrogenase / formate metabolic process / ferredoxin hydrogenase / formate dehydrogenase (NAD+) activity / ferredoxin hydrogenase activity / Oxidoreductases / molybdopterin cofactor binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Thermoanaerobacter kivui (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||
Authors | Dietrich, H.M. / Righetto, R.D. / Kumar, A. / Wietrzynski, W. / Schuller, S.K. / Trischler, R. / Wagner, J. / Schwarz, F.M. / Engel, B.D. / Mueller, V. / Schuller, J.M. | ||||||||||||||||||
Funding support | Germany, European Union, 5items
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Citation | Journal: Nature / Year: 2022 Title: Membrane-anchored HDCR nanowires drive hydrogen-powered CO fixation. Authors: Helge M Dietrich / Ricardo D Righetto / Anuj Kumar / Wojciech Wietrzynski / Raphael Trischler / Sandra K Schuller / Jonathan Wagner / Fabian M Schwarz / Benjamin D Engel / Volker Müller / Jan M Schuller / Abstract: Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO ...Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO fixation-hydrogen-dependent CO reductase (HDCR)-which directly converts H and CO into formic acid. HDCR reduces CO with a higher activity than any other known biological or chemical catalyst, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qv7.cif.gz | 914.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qv7.ent.gz | 760.3 KB | Display | PDB format |
PDBx/mmJSON format | 7qv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/7qv7 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/7qv7 | HTTPS FTP |
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-Related structure data
Related structure data | 14169MC 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
-Hydrogen dependent carbon dioxide reductase subunit ... , 4 types, 16 molecules AGBCJNPXDKQRVZSY
#1: Protein | Mass: 20520.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) / References: UniProt: A0A097ATJ9, Oxidoreductases #2: Protein | Mass: 23052.180 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) / References: UniProt: A0A097ATK6, Oxidoreductases #3: Protein | Mass: 51430.270 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) / References: UniProt: A0A097ATH7, ferredoxin hydrogenase #4: Protein | Mass: 82505.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermoanaerobacter kivui (bacteria) / References: UniProt: A0A097ATK5, formate dehydrogenase |
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-Non-polymers , 2 types, 58 molecules
#5: Chemical | ChemComp-SF4 / #6: Chemical | ChemComp-402 / |
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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: Hydrogen-dependent CO2 reductase (HDCR) complex with iron-sulphur clusters and the H-cluster. Type: COMPLEX Details: A single functional unit of HDCR complex consists of 4 subunits - FdhF, HydA2, HycB3, and HycB4(1) Entity ID: #1-#4 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Thermoanaerobacter kivui LKT-1 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 719937 / Symmetry type: POINT |