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- PDB-7bvp: AdhE spirosome in extended conformation -

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Basic information

Entry
Database: PDB / ID: 7bvp
TitleAdhE spirosome in extended conformation
ComponentsAldehyde-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Spirosome / Aldehyde dehydrogenase / Alcohol dehydrogenase / NADH / HYDROLASE
Function / homology
Function and homology information


: / ethanol biosynthetic process / mixed acid fermentation / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization ...: / ethanol biosynthetic process / mixed acid fermentation / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization / response to oxidative stress / identical protein binding / membrane / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Bifunctional aldehyde-alcohol dehydrogenase AdhE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsKim, G.J. / Song, J.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A2B5B03001517 Korea, Republic Of
National Research Foundation (NRF, Korea)2016K1A1A2912057 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2020
Title: Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling.
Authors: Gijeong Kim / Jinsol Yang / Juwon Jang / Jin-Seok Choi / Andrew J Roe / Olwyn Byron / Chaok Seok / Ji-Joon Song /
Abstract: Aldehyde-alcohol dehydrogenase (AdhE) is an enzyme responsible for converting acetyl-CoA to ethanol via acetaldehyde using NADH. AdhE is composed of two catalytic domains of aldehyde dehydrogenase ...Aldehyde-alcohol dehydrogenase (AdhE) is an enzyme responsible for converting acetyl-CoA to ethanol via acetaldehyde using NADH. AdhE is composed of two catalytic domains of aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH), and forms a spirosome architecture critical for AdhE activity. Here, we present the atomic resolution (3.43 Å) cryo-EM structure of AdhE spirosomes in an extended conformation. The cryo-EM structure shows that AdhE spirosomes undergo a structural transition from compact to extended forms, which may result from cofactor binding. This transition leads to access to a substrate channel between ALDH and ADH active sites. Furthermore, prevention of this structural transition by crosslinking hampers the activity of AdhE, suggesting that the structural transition is important for AdhE activity. This work provides a mechanistic understanding of the regulation mechanisms of AdhE activity via structural transition, and a platform to modulate AdhE activity for developing antibiotics and for facilitating biofuel production.
History
DepositionApr 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)586,68324
Polymers578,3306
Non-polymers8,35418
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area56530 Å2
ΔGint-506 kcal/mol
Surface area166710 Å2

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Components

#1: Protein
Aldehyde-alcohol dehydrogenase


Mass: 96388.258 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: adhE, ana, b1241, JW1228 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A9Q7, alcohol dehydrogenase, acetaldehyde dehydrogenase (acetylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: AdhE Spirosome in extended conformation / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 96.3 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40.76 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4RELION3CTF correction
7Cootmodel fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 412581
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71599 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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