Mouse class II alcohol dehydrogenase complex with NADH

Experimental Data Snapshot

  • Resolution: 2.12 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

Starting Model: experimental
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Crystal Structure of Mouse Class II Alcohol Dehydrogenase Reveal Determinants of Substrate Specificity and Catalytic Efficiency

Svensson, S.Hoeoeg, J.O.Schneider, G.Sandalova, T.

(2000) J Mol Biol 302: 441

  • DOI: https://doi.org/10.1006/jmbi.2000.4039
  • Primary Citation of Related Structures:  
    1E3E, 1E3I, 1E3L

  • PubMed Abstract: 

    The structure of mouse class II alcohol dehydrogenase (ADH2) has been determined in a binary complex with the coenzyme NADH and in a ternary complex with both NADH and the inhibitor N-cyclohexylformamide to 2.2 A and 2.1 A resolution, respectively. The ADH2 dimer is asymmetric in the crystal with different orientations of the catalytic domains relative to the coenzyme-binding domains in the two subunits, resulting in a slightly different closure of the active-site cleft. Both conformations are about half way between the open apo structure and the closed holo structure of horse ADH1, thus resembling that of ADH3. The semi-open conformation and structural differences around the active-site cleft contribute to a substantially different substrate-binding pocket architecture as compared to other classes of alcohol dehydrogenase, and provide the structural basis for recognition and selectivity of alcohols and quinones. The active-site cleft is more voluminous than that of ADH1 but not as open and funnel-shaped as that of ADH3. The loop with residues 296-301 from the coenzyme-binding domain is short, thus opening up the pocket towards the coenzyme. On the opposite side, the loop with residues 114-121 stretches out over the inter-domain cleft. A cavity is formed below this loop and adds an appendix to the substrate-binding pocket. Asp301 is positioned at the entrance of the pocket and may control the binding of omega-hydroxy fatty acids, which act as inhibitors rather than substrates. Mouse ADH2 is known as an inefficient ADH with a slow hydrogen-transfer step. By replacing Pro47 with His, the alcohol dehydrogenase activity is restored. Here, the structure of this P47H mutant was determined in complex with NADH to 2.5 A resolution. His47 is suitably positioned to act as a catalytic base in the deprotonation of the substrate. Moreover, in the more closed subunit, the coenzyme is allowed a position closer to the catalytic zinc. This is consistent with hydrogen transfer from an alcoholate intermediate where the Pro/His replacement focuses on the function of the enzyme.

  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
376Mus musculusMutation(s): 0 
Gene Names: ADH-2
Find proteins for Q9QYY9 (Mus musculus)
Explore Q9QYY9 
Go to UniProtKB:  Q9QYY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QYY9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.12 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.275α = 90
b = 82.9β = 90
c = 105.528γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-12
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2018-01-17
    Changes: Advisory, Data collection
  • Version 1.3: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description