+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10555 | |||||||||
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Title | Escherichia coli AdhE structure in its compact conformation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | bacterial metabolism / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information ethanol biosynthetic process / mixed acid fermentation / : / 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 / : / acetaldehyde dehydrogenase (acetylating) / 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 | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Fronzes R / Pony P | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10555.map.gz | 51.4 MB | EMDB map data format | |
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Header (meta data) | emd-10555-v30.xml emd-10555.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10555_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_10555.png | 90.9 KB | ||
Filedesc metadata | emd-10555.cif.gz | 6.1 KB | ||
Others | emd_10555_additional.map.gz emd_10555_half_map_1.map.gz emd_10555_half_map_2.map.gz | 62.6 MB 51.9 MB 51.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10555 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10555 | HTTPS FTP |
-Validation report
Summary document | emd_10555_validation.pdf.gz | 885.6 KB | Display | EMDB validaton report |
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Full document | emd_10555_full_validation.pdf.gz | 885.1 KB | Display | |
Data in XML | emd_10555_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_10555_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10555 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10555 | HTTPS FTP |
-Related structure data
Related structure data | 6tqmMC 6tqhC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10555.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_10555_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10555_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10555_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AdhE dimer in complex with NADH and Fe2+
Entire | Name: AdhE dimer in complex with NADH and Fe2+ |
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Components |
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-Supramolecule #1: AdhE dimer in complex with NADH and Fe2+
Supramolecule | Name: AdhE dimer in complex with NADH and Fe2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
-Macromolecule #1: Aldehyde-alcohol dehydrogenase
Macromolecule | Name: Aldehyde-alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: alcohol dehydrogenase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 96.244117 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #3: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Macromolecule | Name: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAI |
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Molecular weight | Theoretical: 665.441 Da |
Chemical component information | ChemComp-NAI: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 25.0 µm / Calibrated defocus min: 5.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |