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- EMDB-22805: Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NADH -

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Basic information

Entry
Database: EMDB / ID: EMD-22805
TitleSymmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NADH
Map dataYADH with NADH and PZO. PZO not found in map
Sample
  • Complex: Alcohol Dehydrogenase NAD+ Pyrazole complex
    • Protein or peptide: Alcohol dehydrogenase
  • Ligand: ZINC ION
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: water
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
alcohol dehydrogenase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsSubramanian R / Chang L / Li Z / Plapp BV
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 SB / Ramaswamy S / Plapp BV
#2: Journal: Arch Biochem Biophys / Year: 2016
Title: Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol.
Authors: Plapp BV / Charlier HA / Ramaswamy S
History
DepositionOct 4, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kc2
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22805.png

Downloads & links

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Map

FileDownload / File: emd_22805.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYADH with NADH and PZO. PZO not found in map
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.16577628 - 0.25676563
Average (Standard dev.)0.0004960239 (±0.008440718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 188.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z189.000189.000189.000
α/β/γ90.00090.00090.000
start NX/NY/NZ15150
NX/NY/NZ9999114
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1660.2570.000

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Supplemental data

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Sample components

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Entire : Alcohol Dehydrogenase NAD+ Pyrazole complex

EntireName: Alcohol Dehydrogenase NAD+ Pyrazole complex
Components
  • Complex: Alcohol Dehydrogenase NAD+ Pyrazole complex
    • Protein or peptide: Alcohol dehydrogenase
  • Ligand: ZINC ION
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: water

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Supramolecule #1: Alcohol Dehydrogenase NAD+ Pyrazole complex

SupramoleculeName: Alcohol Dehydrogenase NAD+ Pyrazole complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 370 KDa

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Macromolecule #1: Alcohol dehydrogenase

MacromoleculeName: Alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: alcohol dehydrogenase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 36.749824 KDa
SequenceString: SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPTKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQEYA TADAVQAAHI PQGTDLAEVA PVLCAGITVY K ALKSANLM ...String:
SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPTKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQEYA TADAVQAAHI PQGTDLAEVA PVLCAGITVY K ALKSANLM AGHWVAISGA AGGLGSLAVQ YAKAMGYRVL GIDGGEGKEE LFRSIGGEVF IDFTKEKDIV GAVLKATDGG AH GVINVSV SEAAIEASTR YVRANGTTVL VGMPAGAKCC SDVFNQVVKS ISIVGSYVGN RADTREALDF FARGLVKSPI KVV GLSTLP EIYEKMEKGQ IVGRYVVDTS K

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 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.
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II
DetailsPurified by Size Exclusion chromatography

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 923969

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Atomic model buiding 1

Initial modelPDB ID:

5env


Chain - Chain ID: A / Chain - Residue range: 1-347
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 41.4 / Target criteria: Correlation Coefficient
Output model

PDB-7kc2:
Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NADH

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