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- PDB-8uhw: The structure of the Clostridium thermocellum AdhE spirosome -

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Basic information

Entry
Database: PDB / ID: 8uhw
TitleThe structure of the Clostridium thermocellum AdhE spirosome
ComponentsAldehyde-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde-alcohol dehydrogenase / Complex / Spirosome
Function / homology
Function and homology information


butanol dehydrogenase (NAD+) activity / acetaldehyde dehydrogenase (acetylating) activity / methylglyoxal reductase (NADPH) (acetol producing) activity / alcohol dehydrogenase (NADP+) activity / alcohol metabolic process / carbon utilization / aldehyde dehydrogenase (NAD+) activity / metal ion binding / cytosol
Similarity search - Function
Butanol dehydrogenase-like / Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase ...Butanol dehydrogenase-like / Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / 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
: / Aldehyde-alcohol dehydrogenase
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsZiegler, S.J. / Gruber, J.N.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Elife / Year: 2025
Title: Structural characterization and dynamics of AdhE ultrastructures from show a containment strategy for toxic intermediates.
Authors: Samantha J Ziegler / Brandon C Knott / Josephine N Gruber / Neal N Hengge / Qi Xu / Daniel G Olson / Eduardo E Romero / Lydia-Marie Joubert / Yannick J Bomble /
Abstract: , a cellulolytic thermophilic anaerobe, is considered by many to be a prime candidate for the realization of consolidated bioprocessing (CBP) and is known as an industry standard for biofuel ..., a cellulolytic thermophilic anaerobe, is considered by many to be a prime candidate for the realization of consolidated bioprocessing (CBP) and is known as an industry standard for biofuel production. is among the best biomass degraders identified to date in nature and produces ethanol as one of its main products. Many studies have helped increase ethanol titers in this microbe; however, ethanol production using is still not economically viable. Therefore, a better understanding of its ethanol synthesis pathway is required. The main pathway for ethanol production in involves the bifunctional aldehyde-alcohol dehydrogenase (AdhE). To better understand the function of the AdhE, we used cryo-electron microscopy (cryo-EM) to obtain a 3.28 Å structure of the AdhE complex. This high-resolution structure, in combination with molecular dynamics simulations, provides insight into the substrate channeling of the toxic intermediate acetaldehyde, indicates the potential role of AdhE to regulate activity and cofactor pools, and establishes a basis for future engineering studies. The containment strategy found in this enzyme offers a template that could be replicated in other systems where toxic intermediates need to be sequestered to increase the production of valuable biochemicals.
History
DepositionOct 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)587,91111
Polymers587,6326
Non-polymers2795
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Aldehyde-alcohol dehydrogenase


Mass: 97938.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: adhE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3W5U9
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Homo-oligomer complex of AdhE / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Acetivibrio thermocellus DSM 1313 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(HOCH2)3CNH21
2150 mMSodium ChlorideNaCl1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen 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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.1 / Category: particle selection
CTF correctionType: NONE
Particle selectionNum. of particles selected: 504494
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90912 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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