+Open data
-Basic information
Entry | Database: PDB / ID: 7dag | ||||||||||||
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Title | Vibrio cholera aldehyde-alcohol dehrogenase | ||||||||||||
Components | Aldehyde-alcohol dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE / Enzyme / Fermentation / Alcohol / Aldehyde | ||||||||||||
Function / homology | Function and homology information : / 3-chloroallyl aldehyde dehydrogenase activity / acetaldehyde dehydrogenase (acetylating) activity / fermentation / alcohol metabolic process / carbon utilization / alcohol dehydrogenase (NAD+) activity / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Vibrio cholerae (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.37 Å | ||||||||||||
Authors | Cho, S. / Cho, C. / Song, J. / Kim, G. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Biochem Biophys Res Commun / Year: 2021 Title: Cryo-EM structure of Vibrio cholerae aldehyde-alcohol dehydrogenase spirosomes. Authors: Saehyun Cho / Gijeong Kim / Ji-Joon Song / Carol Cho / Abstract: Aldehyde-alcohol dehydrogenase (AdhE) is a metabolic enzyme and virulence factor in bacteria. E. coli AdhE (eAdhE) multimerizes into spirosomes that are essential for enzymatic activity. However, it ...Aldehyde-alcohol dehydrogenase (AdhE) is a metabolic enzyme and virulence factor in bacteria. E. coli AdhE (eAdhE) multimerizes into spirosomes that are essential for enzymatic activity. However, it is unknown whether AdhE structure is conserved in divergent bacteria. Here, we present the cryo-EM structure of AdhE (vAdhE) from Vibrio cholerae to 4.31 Å resolution. Overall, vAdhE spirosomes are similar to eAdhE with conserved subunit arrangement. However, divergences in key oligomerization residues cause vAdhE to form labile spirosomes with lower enzymatic activity. Mutating the vAdhE oligomerization interface to mimic eAdhE increases spirosome stability and enzymatic activity to levels comparable to eAdhE. These results support the generality of AdhE spirosome structures, and provide a structural basis to target vAdhE to attenuate bacterial virulence. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7dag.cif.gz | 1006.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dag.ent.gz | 835.2 KB | Display | PDB format |
PDBx/mmJSON format | 7dag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dag_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7dag_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7dag_validation.xml.gz | 193.5 KB | Display | |
Data in CIF | 7dag_validation.cif.gz | 283.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7dag ftp://data.pdbj.org/pub/pdb/validation_reports/da/7dag | HTTPS FTP |
-Related structure data
Related structure data | 30625MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 96346.242 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: adhE_1, adhC, adhE, adhE_2, BC353_06450, C9J66_00760, D6U80_02570, ERS013138_00532, ERS013165_00179, ERS013186_01240, ERS013198_03108, ERS013199_01145, ERS013201_00485, ERS013202_01518, ...Gene: adhE_1, adhC, adhE, adhE_2, BC353_06450, C9J66_00760, D6U80_02570, ERS013138_00532, ERS013165_00179, ERS013186_01240, ERS013198_03108, ERS013199_01145, ERS013201_00485, ERS013202_01518, ERS013206_03377, FLM02_10510, FXF03_12520 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E4GKF5, UniProt: Q9KQG5*PLUS |
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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: Aldehyde-alcohol dehydrogenase spirosome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 5 mg/ml / 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 |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62417 / Symmetry type: POINT |