4W6Z

YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Yeast alcohol dehydrogenase structure and catalysis.

Raj, S.B.Ramaswamy, S.Plapp, B.V.

(2014) Biochemistry 53: 5791-5803

  • DOI: 10.1021/bi5006442
  • Also Cited By: 5ENV

  • PubMed 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 with 347 amino acid residues. A structure for ADH1 ...

    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.


    Related Citations: 
    • Crystallization and preliminary crystallographic studies of Saccharomyces cerevisiae alcohol dehydrogenase I.
      Ramaswamy, S.,Kratzer, D.A.,Hershey, A.D.,Rogers, P.H.,Arnone, A.,Eklund, H.,Plapp, B.V.
      (1994) J. Mol. Biol. 235: 777
    • Kinetic characterization of yeast alcohol dehydrogenases. Amino acid residue 294 and substrate specificity.
      Ganzhorn, A.J.,Green, D.W.,Hershey, A.D.,Gould, R.M.,Plapp, B.V.
      (1987) J. Biol. Chem. 262: 3754


    Organizational Affiliation

    Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol dehydrogenase 1
A, B, C, D
347Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ADH1 (ADC1)
EC: 1.1.1.1
Find proteins for P00330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00330
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ETF
Query on ETF

Download SDF File 
Download CCD File 
A, B, C, D
TRIFLUOROETHANOL
C2 H3 F3 O
RHQDFWAXVIIEBN-UHFFFAOYSA-N
 Ligand Interaction
8ID
Query on 8ID

Download SDF File 
Download CCD File 
A, C
NICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE
3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(6-AMINO-8-IODO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]PYRIDINIUM
C21 H27 I N7 O14 P2
UVGUXLRSEVQZMG-NAJQWHGHSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ETFKi: 2800000 nM BINDINGMOAD
8IDKd: 920000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.338α = 90.00
b = 144.338β = 90.00
c = 128.204γ = 120.00
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesMCB 918657
National Institutes of Health/National Institute on Alcohol Abuse and AlcoholismUnited StatesAA00279

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy