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Yorodumi- PDB-7z0s: Structure of the Escherichia coli formate hydrogenlyase complex (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z0s | ||||||
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Title | Structure of the Escherichia coli formate hydrogenlyase complex (anaerobic preparation, without formate dehydrogenase H) | ||||||
Components | (Formate hydrogenlyase subunit ...) x 6 | ||||||
Keywords | MEMBRANE PROTEIN / FHL / group-4 membrane bound hydrogenase / [NiFe] hydrogenase | ||||||
Function / homology | Function and homology information formate oxidation / formate dehydrogenase complex / plasma membrane respiratory chain complex I / anaerobic electron transport chain / glucose catabolic process / anaerobic respiration / oxidoreductase activity, acting on NAD(P)H / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / quinone binding ...formate oxidation / formate dehydrogenase complex / plasma membrane respiratory chain complex I / anaerobic electron transport chain / glucose catabolic process / anaerobic respiration / oxidoreductase activity, acting on NAD(P)H / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Steinhilper, R. / Murphy, B.J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli. Authors: Ralf Steinhilper / Gabriele Höff / Johann Heider / Bonnie J Murphy / Abstract: The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase ...The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H during fermentation, its reversibility, allowing H-dependent CO reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z0s.cif.gz | 363.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z0s.ent.gz | 293.9 KB | Display | PDB format |
PDBx/mmJSON format | 7z0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/7z0s ftp://data.pdbj.org/pub/pdb/validation_reports/z0/7z0s | HTTPS FTP |
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-Related structure data
Related structure data | 14429MC 7z0tC 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
-Formate hydrogenlyase subunit ... , 6 types, 6 molecules CEBGFD
#1: Protein | Mass: 64121.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: MG059e1 / Strain: K12 / References: UniProt: P16429 |
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#2: Protein | Mass: 66589.859 Da / Num. of mol.: 1 / Mutation: internal deca-His-Gly-Ser sequence after Gly83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: hycE, hevE, b2721, JW2691 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K12 / Variant (production host): MG059e1 / References: UniProt: P16431 |
#3: Protein | Mass: 21899.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: MG059e1 / Strain: K12 / References: UniProt: P0AAK1 |
#4: Protein | Mass: 28033.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: MG059e1 / Strain: K12 / References: UniProt: P16433 |
#5: Protein | Mass: 20336.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: MG059e1 / Strain: K12 / References: UniProt: P16432 |
#6: Protein | Mass: 33049.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: MG059e1 / Strain: K12 / References: UniProt: P16430 |
-Non-polymers , 9 types, 124 molecules
#7: Chemical | ChemComp-CDL / | ||||||||||||||
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#8: Chemical | #9: Chemical | ChemComp-NI / | #10: Chemical | ChemComp-FCO / | #11: Chemical | ChemComp-DR9 / | #12: Chemical | ChemComp-SF4 / #13: Chemical | ChemComp-FE / | #14: Chemical | ChemComp-LMN / | #15: Water | ChemComp-HOH / | |
-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: Escherichia coli formate hydrogenlyase complex without formate dehydrogenase H Type: COMPLEX / Details: Sample was prepared anaerobically / Entity ID: #1-#6 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: C-flat-1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-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: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 61 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300386 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
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