4W6Z

YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    4W6Z

  • 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 was determined by X-ray crystallography at 2 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alcohol dehydrogenase 1A, B, C, D347Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ADH1ADC1YOL086CO0947
EC: 1.1.1.1
UniProt
Find proteins for P00330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00330 
Go to UniProtKB:  P00330
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8ID
Query on 8ID

Download Ideal Coordinates CCD File 
G [auth A], N [auth C]NICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE
C21 H27 I N7 O14 P2
UVGUXLRSEVQZMG-NAJQWHGHSA-O
 Ligand Interaction
ETF
Query on ETF

Download Ideal Coordinates CCD File 
H [auth A], K [auth B], O [auth C], R [auth D]TRIFLUOROETHANOL
C2 H3 F3 O
RHQDFWAXVIIEBN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], I [auth B], J [auth B], L [auth C], M [auth C], P [auth D], Q [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8IDKd:  920000   nM  Binding MOAD
ETFKi:  2800000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.338α = 90
b = 144.338β = 90
c = 128.204γ = 120
Software Package:
Software NamePurpose
d*TREKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB 918657
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)United StatesAA00279

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence, Data collection