+Open data
-Basic information
Entry | Database: PDB / ID: 7kc2 | ||||||
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Title | Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NADH | ||||||
Components | Alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Alcohol dehydrogenase / NADH complex | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 Å | ||||||
Authors | Subramanian, R. / Chang, L. / Li, Z. / Plapp, B.V. | ||||||
Citation | Journal: Biochemistry / Year: 2021 Title: Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Authors: Sai Rohit Guntupalli / Zhuang Li / Leifu Chang / Bryce V Plapp / Ramaswamy Subramanian / Abstract: Structures of yeast alcohol dehydrogenase determined by X-ray crystallography show that the subunits have two different conformational states in each of the two dimers that form the tetramer. ...Structures of yeast alcohol dehydrogenase determined by X-ray crystallography show that the subunits have two different conformational states in each of the two dimers that form the tetramer. Apoenzyme and holoenzyme complexes relevant to the catalytic mechanism were described, but the asymmetry led to questions about the cooperativity of the subunits in catalysis. This study used cryo-electron microscopy (cryo-EM) to provide structures for the apoenzyme, two different binary complexes with NADH, and a ternary complex with NAD and 2,2,2-trifluoroethanol. All four subunits in each of these complexes are identical, as the tetramers have 2 symmetry, suggesting that there is no preexisting asymmetry and that the subunits can be independently active. The apoenzyme and one enzyme-NADH complex have "open" conformations and the inverted coordination of the catalytic zinc with Cys-43, His-66, Glu-67, and Cys-153, whereas another enzyme-NADH complex and the ternary complex have closed conformations with the classical coordination of the zinc with Cys-43, His-66, Cys-153, and a water or the oxygen of trifluoroethanol. The conformational change involves interactions of Arg-340 with the pyrophosphate group of the coenzyme and Glu-67. The cryo-EM and X-ray crystallography studies provide structures relevant for the catalytic mechanism. #1: Journal: Biochemistry / Year: 2014 Title: Yeast alcohol dehydrogenase structure and catalysis. Authors: Raj, S.B. / Ramaswamy, S. / Plapp, B.V. #2: Journal: Arch Biochem Biophys / Year: 2016 Title: Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol. Authors: Plapp, B.V. / Charlier, H.A. / Ramaswamy, S. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7kc2.cif.gz | 232.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kc2.ent.gz | 186.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kc2_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7kc2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7kc2_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 7kc2_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/7kc2 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/7kc2 | HTTPS FTP |
-Related structure data
Related structure data | 22805MC 7kcbC 7kcqC 7kjyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 36749.824 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: S5RZC2, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Alcohol Dehydrogenase NAD+ Pyrazole complex / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 0.37 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 8.2 Details: Tris HCl buffer 5mM with 200mM KCl adjusted to pH 8.2. |
Buffer component | Conc.: 50 mM / Name: Tris / Formula: C4H11NO3 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified by Size Exclusion chromatography |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 923969 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 41.4 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation Coefficient | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 5ENV Pdb chain-ID: A / Accession code: 5ENV / Pdb chain residue range: 1-347 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.17 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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