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- PDB-7dag: Vibrio cholera aldehyde-alcohol dehrogenase -

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Basic information

Entry
Database: PDB / ID: 7dag
TitleVibrio cholera aldehyde-alcohol dehrogenase
ComponentsAldehyde-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Enzyme / Fermentation / Alcohol / Aldehyde
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity, iron-dependent / 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
Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde-alcohol dehydrogenase / Aldehyde-alcohol dehydrogenase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.37 Å
AuthorsCho, S. / Cho, C. / Song, J. / Kim, G.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2016K1A1A2912057 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A2B5B03001517 Korea, Republic Of
National Research Foundation (NRF, Korea)2019R1A6A1A10073887 Korea, Republic Of
CitationJournal: 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
DepositionOct 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Aldehyde-alcohol dehydrogenase
B: Aldehyde-alcohol dehydrogenase
C: Aldehyde-alcohol dehydrogenase
D: Aldehyde-alcohol dehydrogenase
E: Aldehyde-alcohol dehydrogenase
F: Aldehyde-alcohol dehydrogenase
G: Aldehyde-alcohol dehydrogenase
H: Aldehyde-alcohol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)770,7708
Polymers770,7708
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area30240 Å2
ΔGint-152 kcal/mol
Surface area245310 Å2

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Components

#1: Protein
Aldehyde-alcohol dehydrogenase


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Aldehyde-alcohol dehydrogenase spirosome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Vibrio cholerae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62417 / Symmetry type: POINT

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