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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 datamrc map file from cisTEM program
Sample
  • Complex: Helical structure of AdhE
    • Protein or peptide: Aldehyde-alcohol dehydrogenase
Keywordsacetyl CoA / ethanol / regulation / high-order structure / HYDROLASE
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 (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.
History
DepositionAug 17, 2018-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing 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

emd_9623.png

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)
Annotationmrc map file from cisTEM program
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

Histogram

Histogram (log scale)
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
Components
  • Complex: Helical structure of AdhE
    • Protein or peptide: Aldehyde-alcohol dehydrogenase

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Supramolecule #1: Helical structure of AdhE

SupramoleculeName: Helical structure of AdhE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Aldehyde-alcohol dehydrogenase

MacromoleculeName: Aldehyde-alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: alcohol dehydrogenase
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 96.388258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMAVTNVAE LNALVERVKK AQREYASFTQ EQVDKIFRAA ALAAADARIP LAKMAVAESG MGIVEDKVIK NHFASEYIYN AYKDEKTCG VLSEDDTFGT ITIAEPIGII CGIVPTTNPT STAIFKSLIS LKTRNAIIFS PHPRAKDATN KAADIVLQAA I AAGAPKDL ...String:
GSMAVTNVAE LNALVERVKK AQREYASFTQ EQVDKIFRAA ALAAADARIP LAKMAVAESG MGIVEDKVIK NHFASEYIYN AYKDEKTCG VLSEDDTFGT ITIAEPIGII CGIVPTTNPT STAIFKSLIS LKTRNAIIFS PHPRAKDATN KAADIVLQAA I AAGAPKDL IGWIDQPSVE LSNALMHHPD INLILATGGP GMVKAAYSSG KPAIGVGAGN TPVVIDETAD IKRAVASVLM SK TFDNGVI CASEQSVVVV DSVYDAVRER FATHGGYLLQ GKELKAVQDV ILKNGALNAA IVGQPAYKIA ELAGFSVPEN TKI LIGEVT VVDESEPFAH EKLSPTLAMY RAKDFEDAVE KAEKLVAMGG IGHTSCLYTD QDNQPARVSY FGQKMKTARI LINT PASQG GIGDLYNFKL APSLTLGCGS WGGNSISENV GPKHLINKKT VAKRAENMLW HKLPKSIYFR RGSLPIALDE VITDG HKRA LIVTDRFLFN NGYADQITSV LKAAGVETEV FFEVEADPTL SIVRKGAELA NSFKPDVIIA LGGGSPMDAA KIMWVM YEH PETHFEELAL RFMDIRKRIY KFPKMGVKAK MIAVTTTSGT GSEVTPFAVV TDDATGQKYP LADYALTPDM AIVDANL VM DMPKSLCAFG GLDAVTHAME AYVSVLASEF SDGQALQALK LLKEYLPASY HEGSKNPVAR ERVHSAATIA GIAFANAF L GVCHSMAHKL GSQFHIPHGL ANALLICNVI RYNANDNPTK QTAFSQYDRP QARRRYAEIA DHLGLSAPGD RTAAKIEKL LAWLETLKAE LGIPKSIREA GVQEADFLAN VDKLSEDAFD DQCTGANPRY PLISELKQIL LDTYYGRDYV EGETAAKKEA APAKAEKKA KKSA

UniProtKB: Bifunctional aldehyde-alcohol dehydrogenase AdhE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160830
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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