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- PDB-9flz: Alcohol dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9flz
TitleAlcohol dehydrogenase
Componentsalcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / tetramer
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
alcohol dehydrogenase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLamers, M.H. / Schada von Borzyskowski, L. / Ren, M.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship CouncilCSC202207720003 China
CitationJournal: Nat Commun / Year: 2025
Title: NAD-dependent dehydrogenases enable efficient growth of Paracoccus denitrificans on the PET monomer ethylene glycol.
Authors: Minrui Ren / Danni Li / Holly Addison / Willem E M Noteborn / Elisabeth H Andeweg / Timo Glatter / Johannes H de Winde / Johannes G Rebelein / Meindert H Lamers / Lennart Schada von Borzyskowski /
Abstract: Ethylene glycol is a monomer of the plastic polyethylene terephthalate (PET) and an environmental pollutant of increasing concern. Although it is generally accepted that bacteria use ethylene glycol ...Ethylene glycol is a monomer of the plastic polyethylene terephthalate (PET) and an environmental pollutant of increasing concern. Although it is generally accepted that bacteria use ethylene glycol as growth substrate, not all involved enzymes are well understood. Here, we show that Paracoccus denitrificans assimilates ethylene glycol solely via NAD-dependent alcohol and aldehyde dehydrogenases. Using comparative proteomics, we identify a gene cluster that is strongly expressed in the presence of ethylene glycol. We report the functional and structural characterization of EtgB and EtgA, key enzymes encoded by this etg gene cluster. We furthermore show that the transcriptional activator EtgR controls expression of the gene cluster. Adaptive laboratory evolution on ethylene glycol results in faster growth, enabled by increased production of EtgB and EtgA. Bioinformatic analysis reveals that the etg gene cluster is widely distributed among bacteria, suggesting a common role of NAD-dependent dehydrogenases in microbial ethylene glycol assimilation.
History
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alcohol dehydrogenase
B: alcohol dehydrogenase
C: alcohol dehydrogenase
D: alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,30812
Polymers154,7854
Non-polymers5238
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
alcohol dehydrogenase


Mass: 38696.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: Pden_2367 / Production host: Escherichia coli (E. coli) / References: UniProt: A1B4L3, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: PDEN_2367 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.3 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 FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 206685 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310102
ELECTRON MICROSCOPYf_angle_d0.53813726
ELECTRON MICROSCOPYf_dihedral_angle_d14.6863618
ELECTRON MICROSCOPYf_chiral_restr0.0461557
ELECTRON MICROSCOPYf_plane_restr0.0041803

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