1MG5

Crystal structure of Drosophila melanogaster alcohol dehydrogenase complexed with NADH and acetate at 1.6 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Drosophila alcohol dehydrogenase: acetate-enzyme interactions and novel insights into the effects of electrostatics on catalysis

Benach, J.Winberg, J.O.Svendsen, J.S.Atrian, S.Gonzalez-Duarte, R.Ladenstein, R.

(2005) J Mol Biol 345: 579-598

  • DOI: 10.1016/j.jmb.2004.10.028
  • Primary Citation of Related Structures:  
    1MG5

  • PubMed Abstract: 
  • Drosophila alcohol dehydrogenase (DADH) is an NAD+-dependent enzyme that catalyzes the oxidation of alcohols to aldehydes/ketones and that is also able to further oxidize aldehydes to their corresponding carboxylic acids. The structure of the ternary enzyme-NADH-acetate complex of the slow alleloform of Drosophila melanogaster ADH (DmADH-S) was solved at 1 ...

    Drosophila alcohol dehydrogenase (DADH) is an NAD+-dependent enzyme that catalyzes the oxidation of alcohols to aldehydes/ketones and that is also able to further oxidize aldehydes to their corresponding carboxylic acids. The structure of the ternary enzyme-NADH-acetate complex of the slow alleloform of Drosophila melanogaster ADH (DmADH-S) was solved at 1.6 A resolution by X-ray crystallography. The coenzyme stereochemistry of the aldehyde dismutation reaction showed that the obtained enzyme-NADH-acetate complex reflects a productive ternary complex although no enzymatic reaction occurs. The stereochemistry of the acetate binding in the bifurcated substrate-binding site, along with previous stereochemical studies of aldehyde reduction and alcohol oxidation shows that the methyl group of the aldehyde in the reduction reaction binds to the R1 and in the oxidation reaction to the R2 sub-site. NMR studies along with previous kinetic studies show that the formed acetaldehyde intermediate in the oxidation of ethanol to acetate leaves the substrate site prior to the reduced coenzyme, and then binds to the newly formed enzyme-NAD+ complex. Here, we compare the three-dimensional structure of D.melanogaster ADH-S and a previous theoretically built model, evaluate the differences with the crystal structures of five Drosophila lebanonensis ADHs in numerous complexed forms that explain the substrate specificity as well as subtle kinetic differences between these two enzymes based on their crystal structures. We also re-examine the electrostatic influence of charged residues on the surface of the protein on the catalytic efficiency of the enzyme.


    Related Citations: 
    • The refined crystal structure of Drosophila lebanonensis alcohol dehydrogenase at 1.9 A resolution
      Benach, J., Atrian, S., Gonzalez-Duarte, R., Ladenstein, R.
      (1998) J Mol Biol 282: 383
    • The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: Observation of an enzyme-bound NAD-ketone adduct at 1.4 A resolution by X-ray crystallography
      Benach, J., Atrian, S., Gonzalez-Duarte, R., Ladenstein, R.
      (1999) J Mol Biol 289: 335

    Organizational Affiliation

    Center for Structural Biochemistry, Karolinska Institutet, 141 57 Huddinge, Sweden. jb1343@columbia.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
alcohol dehydrogenaseA, B255Drosophila melanogasterMutation(s): 0 
Gene Names: AdhCG3481
EC: 1.1.1.1
UniProt
Find proteins for P00334 (Drosophila melanogaster)
Explore P00334 
Go to UniProtKB:  P00334
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.481α = 90
b = 69.519β = 89.13
c = 75.923γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-10-30
    Changes: Non-polymer description