1CDO

ALCOHOL DEHYDROGENASE (E.C.1.1.1.1) (EE ISOZYME) COMPLEXED WITH NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD), AND ZINC

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of cod liver class I alcohol dehydrogenase: substrate pocket and structurally variable segments.

Ramaswamy, S., el Ahmad, M., Danielsson, O., Jornvall, H., Eklund, H.

(1996) Protein Sci 5: 663-671

  • DOI: 10.1002/pro.5560050410
  • Primary Citation of Related Structures:  
    1CDO

  • PubMed Abstract: 

    • The structural framework of cod liver alcohol dehydrogenase is similar to that of horse and human alcohol dehydrogenases. In contrast, the substrate pocket differs significantly, and main differences are located in three loops. Nevertheless, the substrate pocket is hydrophobic like that of the mammalian class I enzymes and has a similar topography in spite of many main-chain and side-chain differences ...

    The structural framework of cod liver alcohol dehydrogenase is similar to that of horse and human alcohol dehydrogenases. In contrast, the substrate pocket differs significantly, and main differences are located in three loops. Nevertheless, the substrate pocket is hydrophobic like that of the mammalian class I enzymes and has a similar topography in spite of many main-chain and side-chain differences. The structural framework of alcohol dehydrogenase is also present in a number of related enzymes like glucose dehydrogenase and quinone oxidoreductase. These enzymes have completely different substrate specificity, but also for these enzymes, the corresponding loops of the substrate pocket have significantly different structures. The domains of the two subunits in the crystals of the cod enzyme further differ by a rotation of the catalytic domains by about 6 degrees. In one subunit, they close around the coenzyme similarly as in coenzyme complexes of the horse enzyme, but form a more open cleft in the other subunit, similar to the situation in coenzyme-free structures of the horse enzyme. The proton relay system differs from the mammalian class I alcohol dehydrogenases. His 51, which has been implicated in mammalian enzymes to be important for proton transfer from the buried active site to the surface is not present in the cod enzyme. A tyrosine in the corresponding position is turned into the substrate pocket and a water molecule occupies the same position in space as the His side chain, forming a shorter proton relay system.

    Related Citations: 
    • Structures of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Substituted Benzyl Alcohols
      Ramaswamy, S., Eklund, H., Plapp, B.V.
      (1994) Biochemistry 33: 5230
    Organizational Affiliation: 

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALCOHOL DEHYDROGENASEA, B374Gadus morhua callariasMutation(s): 0 
EC: 1.1.1.1
UniProt
Find proteins for P26325 (Gadus morhua subsp. callarias)
Explore P26325 
Go to UniProtKB:  P26325
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26325
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.95α = 90
b = 47.6β = 104.66
c = 80.43γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1995-09-29 
  • Released Date: 1996-03-08 
    • Deposition Author(s): Eklund, H.

Revision History  (Full details and data files)

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance