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- EMDB-22807: Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NAD+ ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22807 | |||||||||
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Title | Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NAD+ and Trifluoroethanol | |||||||||
![]() | Cryo-EM Structure of Alcohol Dehyrogenase from Yeast in complex with NAD+ and Pyrazole | |||||||||
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Function / homology | : ![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.77 Å | |||||||||
![]() | Subramanian R / Chang L / Li Z / Plapp BV | |||||||||
![]() | ![]() Title: Yeast alcohol dehydrogenase structure and catalysis. Authors: Savarimuthu Baskar Raj / S Ramaswamy / Bryce V Plapp / ![]() Abstract: Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits ...Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits with 347 amino acid residues. A structure for ADH1 was determined by X-ray crystallography at 2.4 Å resolution. The asymmetric unit contains four different subunits, arranged as similar dimers named AB and CD. The unit cell contains two different tetramers made up of "back-to-back" dimers, AB:AB and CD:CD. The A and C subunits in each dimer are structurally similar, with a closed conformation, bound coenzyme, and the oxygen of 2,2,2-trifluoroethanol ligated to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. In contrast, the B and D subunits have an open conformation with no bound coenzyme, and the catalytic zinc has an alternative, inverted coordination with Cys-43, Cys-153, His-66, and the carboxylate of Glu-67. The asymmetry in the dimeric subunits of the tetramer provides two structures that appear to be relevant for the catalytic mechanism. The alternative coordination of the zinc may represent an intermediate in the mechanism of displacement of the zinc-bound water with alcohol or aldehyde substrates. Substitution of Glu-67 with Gln-67 decreases the catalytic efficiency by 100-fold. Previous studies of structural modeling, evolutionary relationships, substrate specificity, chemical modification, and site-directed mutagenesis are interpreted more fully with the three-dimensional structure. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
Images | ![]() | 235 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kcbMC ![]() 7kc2C ![]() 7kcqC ![]() 7kjyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Cryo-EM Structure of Alcohol Dehyrogenase from Yeast in complex with NAD+ and Pyrazole | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Alcohol Dehydrogenase NAD+ Pyrazole complex
Entire | Name: Alcohol Dehydrogenase NAD+ Pyrazole complex |
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Components |
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-Supramolecule #1: Alcohol Dehydrogenase NAD+ Pyrazole complex
Supramolecule | Name: Alcohol Dehydrogenase NAD+ Pyrazole complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 370 KDa |
-Macromolecule #1: ADH1 isoform 1
Macromolecule | Name: ADH1 isoform 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.759906 KDa |
Sequence | String: SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPVKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQQYA TADAVQAAHI PQGTDLAQVA PILCAGITVY K ALKSANLM ...String: SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPVKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQQYA TADAVQAAHI PQGTDLAQVA PILCAGITVY K ALKSANLM AGHWVAISGA AGGLGSLAVQ YAKAMGYRVL GIDGGEGKEE LFRSIGGEVF IDFTKEKDIV GAVLKATDGG AH GVINVSV SEAAIEASTR YVRANGTTVL VGMPAGAKCC SDVFNQVVKS ISIVGSYVGN RADTREALDF FARGLVKSPI KVV GLSTLP EIYEKMEKGQ IVGRYVVDTS K |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ![]() ChemComp-NAD: |
-Macromolecule #4: TRIFLUOROETHANOL
Macromolecule | Name: TRIFLUOROETHANOL / type: ligand / ID: 4 / Number of copies: 4 / Formula: ETF |
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Molecular weight | Theoretical: 100.04 Da |
Chemical component information | ![]() ChemComp-ETF: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 8.2 / Component - Concentration: 50.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris Details: Tris HCl buffer 5mM with 200mM KCl adjusted to pH 8.2. |
Grid | Model: Quantifoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II |
Details | Purified by Size Exclusion chromatography |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Software - Name: Gctf (ver. 1.06) |
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Final reconstruction | Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 1284904 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |