+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30220 | |||||||||
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Title | AdhE spirosome in extended conformation | |||||||||
Map data | AdhE spirosome | |||||||||
Sample |
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Keywords | Spirosome / Aldehyde dehydrogenase / Alcohol dehydrogenase / NADH / HYDROLASE / 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 (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.45 Å | |||||||||
Authors | Kim GJ / Song JJ | |||||||||
Funding support | Korea, Republic Of, 2 items
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Citation | Journal: 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 |
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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_30220.map.gz | 10.1 MB | EMDB map data format | |
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Header (meta data) | emd-30220-v30.xml emd-30220.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_30220.png | 75.4 KB | ||
Filedesc metadata | emd-30220.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30220 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30220 | HTTPS FTP |
-Validation report
Summary document | emd_30220_validation.pdf.gz | 387.7 KB | Display | EMDB validaton report |
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Full document | emd_30220_full_validation.pdf.gz | 387.2 KB | Display | |
Data in XML | emd_30220_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_30220_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30220 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30220 | HTTPS FTP |
-Related structure data
Related structure data | 7bvpMC M: atomic model generated by this map C: citing same article (ref.) |
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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_30220.map.gz / Format: CCP4 / Size: 109.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | AdhE spirosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.144 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : AdhE Spirosome in extended conformation
Entire | Name: AdhE Spirosome in extended conformation |
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Components |
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-Supramolecule #1: AdhE Spirosome in extended conformation
Supramolecule | Name: AdhE Spirosome in extended conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 96.3 kDa/nm |
-Macromolecule #1: Aldehyde-alcohol dehydrogenase
Macromolecule | Name: Aldehyde-alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: alcohol dehydrogenase |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 96.388258 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.76 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7bvp: |