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Yorodumi- PDB-7xy9: Cryo-EM structure of secondary alcohol dehydrogenases TbSADH afte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xy9 | |||||||||
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Title | Cryo-EM structure of secondary alcohol dehydrogenases TbSADH after carrier-free immobilization based on weak intermolecular interactions | |||||||||
Components | NADP-dependent isopropanol dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Coordination complex / Activity / Stability / Enzyme Immobilization | |||||||||
Function / homology | Function and homology information isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding Similarity search - Function | |||||||||
Biological species | Thermoanaerobacter brockii (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.12 Å | |||||||||
Authors | Chen, Q. / Li, X. / Yang, F. / Qu, G. / Sun, Z.T. / Wang, Y.J. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Active and stable alcohol dehydrogenase-assembled hydrogels via synergistic bridging of triazoles and metal ions. Authors: Qiang Chen / Ge Qu / Xu Li / Mingjian Feng / Fan Yang / Yanjie Li / Jincheng Li / Feifei Tong / Shiyi Song / Yujun Wang / Zhoutong Sun / Guangsheng Luo / Abstract: Biocatalysis is increasingly replacing traditional methods of manufacturing fine chemicals due to its green, mild, and highly selective nature, but biocatalysts, such as enzymes, are generally ...Biocatalysis is increasingly replacing traditional methods of manufacturing fine chemicals due to its green, mild, and highly selective nature, but biocatalysts, such as enzymes, are generally costly, fragile, and difficult to recycle. Immobilization provides protection for the enzyme and enables its convenient reuse, which makes immobilized enzymes promising heterogeneous biocatalysts; however, their industrial applications are limited by the low specific activity and poor stability. Herein, we report a feasible strategy utilizing the synergistic bridging of triazoles and metal ions to induce the formation of porous enzyme-assembled hydrogels with increased activity. The catalytic efficiency of the prepared enzyme-assembled hydrogels toward acetophenone reduction is 6.3 times higher than that of the free enzyme, and the reusability is confirmed by the high residual catalytic activity after 12 cycles of use. A near-atomic resolution (2.1 Å) structure of the hydrogel enzyme is successfully analyzed via cryogenic electron microscopy, which indicates a structure-property relationship for the enhanced performance. In addition, the possible mechanism of gel formation is elucidated, revealing the indispensability of triazoles and metal ions, which guides the use of two other enzymes to prepare enzyme-assembled hydrogels capable of good reusability. The described strategy can pave the way for the development of practical catalytic biomaterials and immobilized biocatalysts. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xy9.cif.gz | 272.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xy9.ent.gz | 217.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xy9_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7xy9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7xy9_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 7xy9_validation.cif.gz | 75.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/7xy9 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/7xy9 | HTTPS FTP |
-Related structure data
Related structure data | 33514MC 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
#1: Protein | Mass: 38524.695 Da / Num. of mol.: 4 / Mutation: I86N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter brockii (bacteria) / Gene: adh / Production host: Escherichia coli (E. coli) References: UniProt: P14941, isopropanol dehydrogenase (NADP+) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: enzyme assembled gel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Thermoanaerobacter brockii (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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 FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: D2 (2x2 fold dihedral) |
3D reconstruction | Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1254312 / Symmetry type: POINT |