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- EMDB-10555: Escherichia coli AdhE structure in its compact conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-10555
TitleEscherichia coli AdhE structure in its compact conformation
Map data
Sample
  • Complex: AdhE dimer in complex with NADH and Fe2+
    • Protein or peptide: Aldehyde-alcohol dehydrogenase
  • Ligand: FE (III) ION
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Keywordsbacterial metabolism / OXIDOREDUCTASE
Function / homology
Function and homology information


ethanol biosynthetic process / mixed acid fermentation / alcohol dehydrogenase (NAD+) activity, iron-dependent / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization ...ethanol biosynthetic process / mixed acid fermentation / alcohol dehydrogenase (NAD+) activity, iron-dependent / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization / response to oxidative stress / membrane / identical protein binding / 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. / 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 ...Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Bifunctional aldehyde-alcohol dehydrogenase AdhE
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsFronzes R / Pony P
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)TransfoPneumoEuropean Union
CitationJournal: Nat Commun / Year: 2020
Title: Filamentation of the bacterial bi-functional alcohol/aldehyde dehydrogenase AdhE is essential for substrate channeling and enzymatic regulation.
Authors: Pauline Pony / Chiara Rapisarda / Laurent Terradot / Esther Marza / Rémi Fronzes /
Abstract: Acetaldehyde-alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanol via an acetaldehyde intermediate during ...Acetaldehyde-alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanol via an acetaldehyde intermediate during ethanol fermentation in an anaerobic environment. This two-step reaction is associated to NAD regeneration, essential for glycolysis. The bifunctional AdhE enzyme is conserved in all bacterial kingdoms but also in more phylogenetically distant microorganisms such as green microalgae. It is found as an oligomeric form called spirosomes, for which the function remains elusive. Here, we use cryo-electron microscopy to obtain structures of Escherichia coli spirosomes in different conformational states. We show that spirosomes contain active AdhE monomers, and that AdhE filamentation is essential for its activity in vitro and function in vivo. The detailed analysis of these structures provides insight showing that AdhE filamentation is essential for substrate channeling within the filament and for the regulation of enzyme activity.
History
DepositionDec 16, 2019-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10555.png

Downloads & links

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Map

FileDownload / File: emd_10555.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.13 Å
Density
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.022365017 - 0.04739375
Average (Standard dev.)-0.00037658215 (±0.0019488649)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 293.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z293.800293.800293.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0220.047-0.000

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Supplemental data

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Additional map: #1

Fileemd_10555_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10555_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10555_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AdhE dimer in complex with NADH and Fe2+

EntireName: AdhE dimer in complex with NADH and Fe2+
Components
  • Complex: AdhE dimer in complex with NADH and Fe2+
    • Protein or peptide: Aldehyde-alcohol dehydrogenase
  • Ligand: FE (III) ION
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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Supramolecule #1: AdhE dimer in complex with NADH and Fe2+

SupramoleculeName: AdhE dimer in complex with NADH and Fe2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: Aldehyde-alcohol dehydrogenase

MacromoleculeName: Aldehyde-alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: alcohol dehydrogenase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 96.244117 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAVTNVAELN ALVERVKKAQ REYASFTQEQ VDKIFRAAAL AAADARIPLA KMAVAESGMG IVEDKVIKNH FASEYIYNAY KDEKTCGVL SEDDTFGTIT IAEPIGIICG IVPTTNPTST AIFKSLISLK TRNAIIFSPH PRAKDATNKA ADIVLQAAIA A GAPKDLIG ...String:
MAVTNVAELN ALVERVKKAQ REYASFTQEQ VDKIFRAAAL AAADARIPLA KMAVAESGMG IVEDKVIKNH FASEYIYNAY KDEKTCGVL SEDDTFGTIT IAEPIGIICG IVPTTNPTST AIFKSLISLK TRNAIIFSPH PRAKDATNKA ADIVLQAAIA A GAPKDLIG WIDQPSVELS NALMHHPDIN LILATGGPGM VKAAYSSGKP AIGVGAGNTP VVIDETADIK RAVASVLMSK TF DNGVICA SEQSVVVVDS VYDAVRERFA THGGYLLQGK ELKAVQDVIL KNGALNAAIV GQPAYKIAEL AGFSVPENTK ILI GEVTVV DESEPFAHEK LSPTLAMYRA KDFEDAVEKA EKLVAMGGIG HTSCLYTDQD NQPARVSYFG QKMKTARILI NTPA SQGGI GDLYNFKLAP SLTLGCGSWG GNSISENVGP KHLINKKTVA KRAENMLWHK LPKSIYFRRG SLPIALDEVI TDGHK RALI VTDRFLFNNG YADQITSVLK AAGVETEVFF EVEADPTLSI VRKGAELANS FKPDVIIALG GGSPMDAAKI MWVMYE HPE THFEELALRF MDIRKRIYKF PKMGVKAKMI AVTTTSGTGS EVTPFAVVTD DATGQKYPLA DYALTPDMAI VDANLVM DM PKSLCAFGGL DAVTHAMEAY VSVLASEFSD GQALQALKLL KEYLPASYHE GSKNPVARER VHSAATIAGI AFANAFLG V CHSMAHKLGS QFHIPHGLAN ALLICNVIRY NANDNPTKQT AFSQYDRPQA RRRYAEIADH LGLSAPGDRT AAKIEKLLA WLETLKAELG IPKSIREAGV QEADFLANVD KLSEDAFDDQ CTGANPRYPL ISELKQILLD TYYGRDYVEG ETAAKKEAAP AKAEKKAKK SA

UniProtKB: Bifunctional aldehyde-alcohol dehydrogenase AdhE

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 25.0 µm / Calibrated defocus min: 5.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 599988
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 226646
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6tqh


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6tqm:
Escherichia coli AdhE structure in its compact conformation

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