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- PDB-9ldk: The complex structure of Escherichia coli AdhE (compact conformation) -

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Basic information

Entry
Database: PDB / ID: 9ldk
TitleThe complex structure of Escherichia coli AdhE (compact conformation)
ComponentsBifunctional aldehyde-alcohol dehydrogenase AdhE
KeywordsBIOSYNTHETIC PROTEIN / Complex / Enzyme
Function / homology
Function and homology information


ethanol biosynthetic process / mixed acid fermentation / acetaldehyde dehydrogenase (acetylating) / ethanol dehydrogenase (NAD+) activity / 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) / ethanol dehydrogenase (NAD+) activity / 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. / : / 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 ...Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / 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
Bifunctional aldehyde-alcohol dehydrogenase AdhE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsKonno, N. / Miyake, K. / Nishino, S. / Omae, K. / Yanagisawa, H. / Tsuru, S. / Kikkawa, M. / Furusawa, C. / Iwasaki, W.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J20318 Japan
Japan Society for the Promotion of Science (JSPS)24H00870 Japan
Japan Society for the Promotion of Science (JSPS)21H05247 Japan
Japan Society for the Promotion of Science (JSPS)21H05248 Japan
Japan Science and TechnologyJPMJER1902 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121002 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Repeatability of protein structural evolution following convergent gene fusions.
Authors: Naoki Konno / Keita Miyake / Satoshi Nishino / Kimiho Omae / Haruaki Yanagisawa / Saburo Tsuru / Yuki Nishimura / Masahide Kikkawa / Chikara Furusawa / Wataru Iwasaki /
Abstract: Convergent evolution of proteins provides insights into repeatability of genetic adaptation. While local convergence of proteins at residue or domain level has been characterized, global structural ...Convergent evolution of proteins provides insights into repeatability of genetic adaptation. While local convergence of proteins at residue or domain level has been characterized, global structural convergence by inter-domain/molecular interactions remains largely unknown. Here we present structural convergent evolution on fusion enzymes of aldehyde dehydrogenases (ALDHs) and alcohol dehydrogenases (ADHs). We discover BdhE (bifunctional dehydrogenase E), an enzyme clade that emerged independently from the previously known AdhE family through distinct gene fusion events. AdhE and BdhE show shared enzymatic activities and non-overlapping phylogenetic distribution, suggesting common functions in different species. Cryo-electron microscopy reveals BdhEs form donut-like homotetramers, contrasting AdhE's helical homopolymers. Intriguingly, despite distinct quaternary structures and < 30% amino acid sequence identity, both enzymes forms resemble dimeric structure units by ALDH-ADH interactions via convergently elongated loop structures. These findings suggest convergent gene fusions recurrently led to substrate channeling evolution to enhance two-step reaction efficiency. Our study unveils structural convergence at inter-domain/molecular level, expanding our knowledges on patterns behind molecular evolution exploring protein structural universe.
History
DepositionJan 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional aldehyde-alcohol dehydrogenase AdhE
B: Bifunctional aldehyde-alcohol dehydrogenase AdhE
C: Bifunctional aldehyde-alcohol dehydrogenase AdhE
F: Bifunctional aldehyde-alcohol dehydrogenase AdhE


Theoretical massNumber of molelcules
Total (without water)384,9764
Polymers384,9764
Non-polymers00
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
Bifunctional aldehyde-alcohol dehydrogenase AdhE / Alcohol dehydrogenase E


Mass: 96244.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: adhE, ana, b1241, JW1228 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A9Q7, acetaldehyde dehydrogenase (acetylating), alcohol dehydrogenase
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: A structural unit of compact-form helical polymers formed by AdhE
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.38642 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCl (pH 8.0)1
2100 mMSodium chlorideNaCl1
SpecimenConc.: 2.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1750 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 804190 / Symmetry type: POINT
RefinementHighest resolution: 2.79 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00320034
ELECTRON MICROSCOPYf_angle_d0.71327160
ELECTRON MICROSCOPYf_dihedral_angle_d4.6082748
ELECTRON MICROSCOPYf_chiral_restr0.0453106
ELECTRON MICROSCOPYf_plane_restr0.0063512

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