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- EMDB-30625: Vibrio cholera aldehyde-alcohol dehrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-30625
TitleVibrio cholera aldehyde-alcohol dehrogenase
Map data
Sample
  • Complex: Aldehyde-alcohol dehydrogenase spirosome
    • Protein or peptide: Aldehyde-alcohol dehydrogenase
KeywordsEnzyme / Fermentation / Alcohol / Aldehyde / OXIDOREDUCTASE
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity, iron-dependent / 3-chloroallyl aldehyde dehydrogenase activity / acetaldehyde dehydrogenase (acetylating) activity / fermentation / alcohol metabolic process / carbon utilization / alcohol dehydrogenase (NAD+) activity / metal ion 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
Aldehyde-alcohol dehydrogenase / Aldehyde-alcohol dehydrogenase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.37 Å
AuthorsCho S / Cho C
Funding support Korea, Republic Of, 3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2016K1A1A2912057 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A2B5B03001517 Korea, Republic Of
National Research Foundation (NRF, Korea)2019R1A6A1A10073887 Korea, Republic Of
CitationJournal: Biochem Biophys Res Commun / Year: 2021
Title: Cryo-EM structure of Vibrio cholerae aldehyde-alcohol dehydrogenase spirosomes.
Authors: Saehyun Cho / Gijeong Kim / Ji-Joon Song / Carol Cho /
Abstract: Aldehyde-alcohol dehydrogenase (AdhE) is a metabolic enzyme and virulence factor in bacteria. E. coli AdhE (eAdhE) multimerizes into spirosomes that are essential for enzymatic activity. However, it ...Aldehyde-alcohol dehydrogenase (AdhE) is a metabolic enzyme and virulence factor in bacteria. E. coli AdhE (eAdhE) multimerizes into spirosomes that are essential for enzymatic activity. However, it is unknown whether AdhE structure is conserved in divergent bacteria. Here, we present the cryo-EM structure of AdhE (vAdhE) from Vibrio cholerae to 4.31 Å resolution. Overall, vAdhE spirosomes are similar to eAdhE with conserved subunit arrangement. However, divergences in key oligomerization residues cause vAdhE to form labile spirosomes with lower enzymatic activity. Mutating the vAdhE oligomerization interface to mimic eAdhE increases spirosome stability and enzymatic activity to levels comparable to eAdhE. These results support the generality of AdhE spirosome structures, and provide a structural basis to target vAdhE to attenuate bacterial virulence.
History
DepositionOct 16, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 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: 0.31
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.31
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dag
  • Surface level: 0.31
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30625.png

Downloads & links

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Map

FileDownload / File: emd_30625.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.863 Å
Density
Contour LevelBy AUTHOR: 0.31 / Movie #1: 0.31
Minimum - Maximum-0.33060017 - 0.93223447
Average (Standard dev.)0.0071369894 (±0.065510936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 293.41998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8630.8630.863
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z293.420293.420293.420
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.3310.9320.007

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Supplemental data

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Sample components

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Entire : Aldehyde-alcohol dehydrogenase spirosome

EntireName: Aldehyde-alcohol dehydrogenase spirosome
Components
  • Complex: Aldehyde-alcohol dehydrogenase spirosome
    • Protein or peptide: Aldehyde-alcohol dehydrogenase

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Supramolecule #1: Aldehyde-alcohol dehydrogenase spirosome

SupramoleculeName: Aldehyde-alcohol dehydrogenase spirosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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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
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 96.346242 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPVTNLAELD ALVARVKAAQ AEFATFSQEQ VDKIFRAASL AANQARIPLA QMAVEESGMG IVEDKVIKNH FASEFIYNKY KDEKTCGIL EEDDNLGTMT IAEPVGIICG IVPTTNPTST AIFKSLISLK TRNGIIFSPH PRAKNSTNAA AKLVLDAAIA A GAPKDIIG ...String:
MPVTNLAELD ALVARVKAAQ AEFATFSQEQ VDKIFRAASL AANQARIPLA QMAVEESGMG IVEDKVIKNH FASEFIYNKY KDEKTCGIL EEDDNLGTMT IAEPVGIICG IVPTTNPTST AIFKSLISLK TRNGIIFSPH PRAKNSTNAA AKLVLDAAIA A GAPKDIIG WIDQPSVELS NALMKHDGIA LILATGGPGM VKAAYSSGKP AIGVGAGNVP VVIDETADIK RAVASILMSK TF DNGVVCA SEQAAIVVSE VYDEVKERFA THKAHVLSKA DADKVRKVLL IDGALNAKIV GQPAAAIAEM AGVKVPADTK VLV GEGLGK VSYDDEFAHE KLSPTLGLFR ADNFEDAVAQ AVTMVEIGGI GHTSGLYTNQ DVNADRIRYF GDKLKTARIL VNIP TTHGG IGDLYNFNVA PSLTLGCGSW GGNSISENVG PKHLINKKTV AKRAENMLWH KLPKSIYFRR GSLPIALSDL EGKKR AFLV TDRFLFNNGY ADDVVALLKA QGMEVQTFFE VEADPTLSVV EKGAAAMQSF QPDVILALGG GSPMDAAKIM WVMYEH PDT HFEELAMRFM DIRKRIYKFP KMGKKAELVC ITTTSGTGSE VTPFAVVTDD KTGAKYPLAD YELTPQMAIV DANLVMN MP KSLTAFGGYD AVTHALEAYV SVLANEYSDG QALQALKMLK EYLPSSYANG AKDPIAREKV HNAATIAGIA FANAFLGV C HSMAHKIGAE FHLPHGLANA LLIANVVRYN ANDNPTKQTA FSQYDRPQAR RRYAEVADHL GLSQPGDRTA QKIERLLTW LDELKVNLDI PKSIQAAGVA EADFLAKVDE LAVEAFDDQC TGANPRYPLI AELKEVLLAS YYGKPFVEGQ TFEGTTVIVK KADQEAAKA PKAKK

UniProtKB: Aldehyde-alcohol dehydrogenase

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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

Concentration5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 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: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62417

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