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- EMDB-30220: AdhE spirosome in extended conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-30220
TitleAdhE spirosome in extended conformation
Map dataAdhE spirosome
Sample
  • Complex: AdhE Spirosome in extended conformation
    • Protein or peptide: Aldehyde-alcohol dehydrogenase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: ZINC ION
KeywordsSpirosome / Aldehyde dehydrogenase / Alcohol dehydrogenase / NADH / HYDROLASE / 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 (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsKim GJ / Song JJ
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A2B5B03001517 Korea, Republic Of
National Research Foundation (NRF, Korea)2016K1A1A2912057 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2020
Title: Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling.
Authors: Gijeong Kim / Jinsol Yang / Juwon Jang / Jin-Seok Choi / Andrew J Roe / Olwyn Byron / Chaok Seok / Ji-Joon Song /
Abstract: Aldehyde-alcohol dehydrogenase (AdhE) is an enzyme responsible for converting acetyl-CoA to ethanol via acetaldehyde using NADH. AdhE is composed of two catalytic domains of aldehyde dehydrogenase ...Aldehyde-alcohol dehydrogenase (AdhE) is an enzyme responsible for converting acetyl-CoA to ethanol via acetaldehyde using NADH. AdhE is composed of two catalytic domains of aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH), and forms a spirosome architecture critical for AdhE activity. Here, we present the atomic resolution (3.43 Å) cryo-EM structure of AdhE spirosomes in an extended conformation. The cryo-EM structure shows that AdhE spirosomes undergo a structural transition from compact to extended forms, which may result from cofactor binding. This transition leads to access to a substrate channel between ALDH and ADH active sites. Furthermore, prevention of this structural transition by crosslinking hampers the activity of AdhE, suggesting that the structural transition is important for AdhE activity. This work provides a mechanistic understanding of the regulation mechanisms of AdhE activity via structural transition, and a platform to modulate AdhE activity for developing antibiotics and for facilitating biofuel production.
History
DepositionApr 11, 2020-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bvp
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30220.png

Downloads & links

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Map

FileDownload / File: emd_30220.map.gz / Format: CCP4 / Size: 109.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAdhE spirosome
Voxel sizeX=Y=Z: 1.144 Å
Density
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.20277803 - 0.36573505
Average (Standard dev.)0.00048467796 (±0.0088106245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions306306306
Spacing306306306
CellA=B=C: 350.06403 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1441.1441.144
M x/y/z306306306
origin x/y/z0.0000.0000.000
length x/y/z350.064350.064350.064
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS306306306
D min/max/mean-0.2030.3660.000

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Supplemental data

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Sample components

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Entire : AdhE Spirosome in extended conformation

EntireName: AdhE Spirosome in extended conformation
Components
  • Complex: AdhE Spirosome in extended conformation
    • Protein or peptide: Aldehyde-alcohol dehydrogenase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: ZINC ION

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Supramolecule #1: AdhE Spirosome in extended conformation

SupramoleculeName: AdhE Spirosome in extended conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 96.3 kDa/nm

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Macromolecule #1: Aldehyde-alcohol dehydrogenase

MacromoleculeName: Aldehyde-alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: alcohol dehydrogenase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
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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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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 / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.76 e/Å2

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Image processing

Particle selectionNumber selected: 412581
Startup modelType of model: OTHER / Details: Relion Initial Model
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 71599

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7bvp:
AdhE spirosome in extended conformation

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