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

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Basic information

Entry
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 / alcohol dehydrogenase (NAD+) activity / carbon utilization / alcohol dehydrogenase / membrane / identical protein binding / metal ion binding / cytosol
Aldehyde dehydrogenase domain / Iron-type alcohol dehydrogenase-like / Alcohol dehydrogenase, iron-type, conserved site / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Aldehyde dehydrogenase family / Iron-containing alcohol dehydrogenase ...Aldehyde dehydrogenase domain / Iron-type alcohol dehydrogenase-like / Alcohol dehydrogenase, iron-type, conserved site / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Aldehyde dehydrogenase family / Iron-containing alcohol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain
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 ...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
History
DepositionAug 17, 2018-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateAug 21, 2019-
Current statusAug 21, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 5
Minimum - Maximum-20.700056 - 33.644750000000002
Average (Standard dev.)-0.02017183 (±1.6110227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
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
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-20.70033.645-0.020

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Supplemental data

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Sample components

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Entire Helical structure of AdhE

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

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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)

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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)

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Experimental details

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Sample preparation

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

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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)

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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

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Atomic model buiding

Output model

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