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TitleCryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase.
Journal, issue, pagesBiochemistry, Vol. 60, Issue 9, Page 663-677, Year 2021
Publish dateMar 9, 2021
AuthorsSai Rohit Guntupalli / Zhuang Li / Leifu Chang / Bryce V Plapp / Ramaswamy Subramanian /
PubMed AbstractStructures 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.
External linksBiochemistry / PubMed:33620215
MethodsEM (single particle)
Resolution2.67 - 3.2 Å
Structure data

22805

7kc2

EMDB-22805: The Cryo-EM Structure of Alcohol Dehyrogenase from Yeast in complex with NADH (open form).
PDB-7kc2: Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NADH
Method: EM (single particle) / Resolution: 2.67 Å

22807

7kcb

EMDB-22807: The Cryo-EM Structure of Alcohol Dehyrogenase from Yeast in complex with NAD+ and Trifluoro Ethanol (TFE)
PDB-7kcb: Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NAD+ and Trifluoroethanol
Method: EM (single particle) / Resolution: 2.77 Å

22817

7kcq

EMDB-22817: The Cryo-EM Structure of Alcohol Dehyrogenase from Yeast in Apo Form
PDB-7kcq: Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme
Method: EM (single particle) / Resolution: 3.2 Å

22902

7kjy

EMDB-22902: The Cryo-EM Structure of Alcohol Dehyrogenase from Yeast in complex with NADH - Open Form
PDB-7kjy: Symmetry in Yeast Alcohol Dehydrogenase 1 - Open Form with NADH
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-HOH:
WATER

ChemComp-ETF:
TRIFLUOROETHANOL

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / NADH complex / holo-enzyme complex / holo-enzymem complex / NADH

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