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 

wwPDB Validation 3D Report Full Report


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

  • 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 subs ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALCOHOL DEHYDROGENASE
A, B
374Gadus morhua subsp. callariasMutation(s): 0 
EC: 1.1.1.1
Find proteins for P26325 (Gadus morhua subsp. callarias)
Go to UniProtKB:  P26325
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD
Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 102.950α = 90.00
b = 47.600β = 104.66
c = 80.430γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
X-PLORmodel building
CCP4data reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History 

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