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Yorodumi- EMDB-9623: Cryo-EM structure of aldehyde-alcohol dehydrogenase reveals a hig... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9623 | |||||||||
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Title | Cryo-EM structure of aldehyde-alcohol dehydrogenase reveals a high-order helical architecture critical for its activity | |||||||||
Map data | mrc map file from cisTEM program | |||||||||
Sample |
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Keywords | acetyl CoA / ethanol / regulation / high-order structure / HYDROLASE | |||||||||
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 K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.45 Å | |||||||||
Authors | Kim G / Song JJ | |||||||||
Funding support | Korea, Republic Of, 2 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity. Authors: Gijeong Kim / Liyana Azmi / Seongmin Jang / Taeyang Jung / Hans Hebert / Andrew J Roe / Olwyn Byron / Ji-Joon Song / Abstract: Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 Å resolution cryo- ...Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 Å resolution cryo-EM structure of full-length AdhE revealing a high-order spirosome architecture. The structure shows that the aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) active sites reside at the outer surface and the inner surface of the spirosome respectively, thus topologically separating these two activities. Furthermore, mutations disrupting the helical structure abrogate enzymatic activity, implying that formation of the spirosome structure is critical for AdhE activity. In addition, we show that this spirosome structure undergoes conformational change in the presence of cofactors. This work presents the atomic resolution structure of AdhE and suggests that the high-order helical structure regulates its enzymatic 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_9623.map.gz | 95.5 MB | EMDB map data format | |
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Header (meta data) | emd-9623-v30.xml emd-9623.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_9623.png | 296.4 KB | ||
Filedesc metadata | emd-9623.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9623 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9623 | HTTPS FTP |
-Validation report
Summary document | emd_9623_validation.pdf.gz | 720.3 KB | Display | EMDB validaton report |
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Full document | emd_9623_full_validation.pdf.gz | 719.9 KB | Display | |
Data in XML | emd_9623_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_9623_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9623 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9623 | HTTPS FTP |
-Related structure data
Related structure data | 6ahcMC 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_9623.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | mrc map file from cisTEM program | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 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 : Helical structure of AdhE
Entire | Name: Helical structure of AdhE |
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Components |
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-Supramolecule #1: Helical structure of AdhE
Supramolecule | Name: Helical structure of AdhE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Aldehyde-alcohol dehydrogenase
Macromolecule | Name: Aldehyde-alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: alcohol dehydrogenase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 |
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 |
-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 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160830 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |