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Yorodumi- PDB-8c0z: CryoEM structure of a tungsten-containing aldehyde oxidoreductase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c0z | ||||||||||||
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Title | CryoEM structure of a tungsten-containing aldehyde oxidoreductase from Aromatoleum aromaticum | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / Tungsten-containing enzyme / nanowires. | ||||||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the aldehyde or oxo group of donors; With an iron-sulfur protein as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Aromatoleum aromaticum (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å | ||||||||||||
Authors | Winiarska, A. / Ramirez-Amador, F. / Hege, D. / Gemmecker, Y. / Prinz, S. / Hochberg, G. / Heider, J. / Szaleniec, M. / Schuller, J.M. | ||||||||||||
Funding support | European Union, Poland, Germany, 3items
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Citation | Journal: Sci Adv / Year: 2023 Title: A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire. Authors: Agnieszka Winiarska / Fidel Ramírez-Amador / Dominik Hege / Yvonne Gemmecker / Simone Prinz / Georg Hochberg / Johann Heider / Maciej Szaleniec / Jan Michael Schuller / Abstract: Aldehyde oxidoreductases (AORs) are tungsten enzymes catalyzing the oxidation of many different aldehydes to the corresponding carboxylic acids. In contrast to other known AORs, the enzyme from the ...Aldehyde oxidoreductases (AORs) are tungsten enzymes catalyzing the oxidation of many different aldehydes to the corresponding carboxylic acids. In contrast to other known AORs, the enzyme from the denitrifying betaproteobacterium (AOR) consists of three different subunits (AorABC) and uses nicotinamide adenine dinucleotide (NAD) as an electron acceptor. Here, we reveal that the enzyme forms filaments of repeating AorAB protomers that are capped by a single NAD-binding AorC subunit, based on solving its structure via cryo-electron microscopy. The polyferredoxin-like subunit AorA oligomerizes to an electron-conducting nanowire that is decorated with enzymatically active and W-cofactor (W-co) containing AorB subunits. Our structure further reveals the binding mode of the native substrate benzoate in the AorB active site. This, together with quantum mechanics:molecular mechanics (QM:MM)-based modeling for the coordination of the W-co, enables formulation of a hypothetical catalytic mechanism that paves the way to further engineering for applications in synthetic biology and biotechnology. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c0z.cif.gz | 345.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c0z.ent.gz | 277.4 KB | Display | PDB format |
PDBx/mmJSON format | 8c0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/8c0z ftp://data.pdbj.org/pub/pdb/validation_reports/c0/8c0z | HTTPS FTP |
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-Related structure data
Related structure data | 16376MC 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
-Protein , 3 types, 5 molecules ABCFE
#1: Protein | Mass: 65954.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aromatoleum aromaticum (bacteria) / Gene: ebA5005 / Production host: Aromatoleum evansii (bacteria) References: UniProt: Q5P143, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With an iron-sulfur protein as acceptor #2: Protein | Mass: 20524.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: AorA (chain C,F in the model) is fused to a N-terminal Twin-Strep-tag (two Strep-tags linked by a glycin/serin peptide) for purification purposes. Source: (gene. exp.) Aromatoleum aromaticum (bacteria) / Gene: ebA5004 / Production host: Aromatoleum evansii (bacteria) / References: UniProt: Q5P144 #3: Protein | | Mass: 45798.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aromatoleum aromaticum (bacteria) / Gene: TM0395, ebA5007 / Production host: Aromatoleum evansii (bacteria) / References: UniProt: Q5P142 |
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-Non-polymers , 5 types, 17 molecules
#4: Chemical | ChemComp-SF4 / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-FAD / | |
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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: Tungsten-containing aldehyde oxidoreductase from Aromatoleum aromaticum Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.304 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: Aromatoleum aromaticum (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Aromatoleum evansii (bacteria) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Details: 15 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 896 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | |||||||||||||||||||||||||||||||||||
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Image processing |
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CTF correction |
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Particle selection |
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Symmetry |
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3D reconstruction |
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Refinement | Highest resolution: 3.22 Å | |||||||||||||||||||||||||||||||||||
Refine LS restraints |
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