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- EMDB-9623: Cryo-EM structure of aldehyde-alcohol dehydrogenase reveals a hig... -

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Basic information

Database: EMDB / ID: EMD-9623
TitleCryo-EM structure of aldehyde-alcohol dehydrogenase reveals a high-order helical architecture critical for its activity
Map data
SampleHelical structure of AdhE:
Aldehyde-alcohol dehydrogenase
Function / homology
Function and homology information

ethanol biosynthetic process / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / membrane / identical protein binding / metal ion binding / cytosol
Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Aldehyde dehydrogenase, N-terminal / Iron-type alcohol dehydrogenase-like / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Alcohol dehydrogenase, iron-type, conserved site / Aldehyde dehydrogenase, C-terminal / Bifunctional aldehyde-alcohol dehydrogenase / Aldehyde dehydrogenase domain / Aldehyde/histidinol dehydrogenase
Aldehyde-alcohol dehydrogenase
Biological speciesEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsKim G / Song JJ
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016K1A1A2912057 Korea, Republic Of
National Research Foundation (Korea)NRF-2016R1A2B3006293 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2019
Title: Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity.
Authors: Gijeong Kim / Liyana Azmi / Seongmin Jang / Taeyang Jung / Hans Hebert / Andrew J Roe / Olwyn Byron / Ji-Joon Song /
Abstract: Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 Å resolution cryo- ...Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 Å resolution cryo-EM structure of full-length AdhE revealing a high-order spirosome architecture. The structure shows that the aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) active sites reside at the outer surface and the inner surface of the spirosome respectively, thus topologically separating these two activities. Furthermore, mutations disrupting the helical structure abrogate enzymatic activity, implying that formation of the spirosome structure is critical for AdhE activity. In addition, we show that this spirosome structure undergoes conformational change in the presence of cofactors. This work presents the atomic resolution structure of AdhE and suggests that the high-order helical structure regulates its enzymatic activity.
Validation ReportPDB-ID: 6ahc

SummaryFull reportAbout validation report
DepositionAug 17, 2018-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBj / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ahc
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_9623.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 300 pix.
= 336. Å
1.12 Å/pix.
x 300 pix.
= 336. Å
1.12 Å/pix.
x 300 pix.
= 336. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Contour LevelBy AUTHOR: 3 / Movie #1: 5
Minimum - Maximum-20.700056 - 33.64475
Average (Standard dev.)-0.02017183 (±1.6110227)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-20.70033.645-0.020

Supplemental data

Sample components

Entire Helical structure of AdhE

EntireName: Helical structure of AdhE / Number of components: 2

Component #1: protein, Helical structure of AdhE

ProteinName: Helical structure of AdhE / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

Component #2: protein, Aldehyde-alcohol dehydrogenase

ProteinName: Aldehyde-alcohol dehydrogenase / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 96.388258 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (engineered)Expression System: Escherichia coli (E. coli)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 44.6 e/Å2 / Illumination mode: OTHER
LensCs: 0 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 160830
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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