1AXE

CRYSTAL STRUCTURE OF THE ACTIVE-SITE MUTANT PHE93->TRP OF HORSE LIVER ALCOHOL DEHYDROGENASE IN COMPLEX WITH NAD AND INHIBITOR TRIFLUOROETHANOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A link between protein structure and enzyme catalyzed hydrogen tunneling.

Bahnson, B.J.Colby, T.D.Chin, J.K.Goldstein, B.M.Klinman, J.P.

(1997) Proc Natl Acad Sci U S A 94: 12797-12802

  • DOI: 10.1073/pnas.94.24.12797
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We present evidence that the size of an active site side chain may modulate the degree of hydrogen tunneling in an enzyme-catalyzed reaction. Primary and secondary kH/kT and kD/kT kinetic isotope effects have been measured for the oxidation of benzyl ...

    We present evidence that the size of an active site side chain may modulate the degree of hydrogen tunneling in an enzyme-catalyzed reaction. Primary and secondary kH/kT and kD/kT kinetic isotope effects have been measured for the oxidation of benzyl alcohol catalyzed by horse liver alcohol dehydrogenase at 25 degrees C. As reported in earlier studies, the relationship between secondary kH/kT and kD/kT isotope effects provides a sensitive probe for deviations from classical behavior. In the present work, catalytic efficiency and the extent of hydrogen tunneling have been correlated for the alcohol dehydrogenase-catalyzed hydride transfer among a group of site-directed mutants at position 203. Val-203 interacts with the opposite face of the cofactor NAD+ from the alcohol substrate. The reduction in size of this residue is correlated with diminished tunneling and a two orders of magnitude decrease in catalytic efficiency. Comparison of the x-ray crystal structures of a ternary complex of a high-tunneling (Phe-93 --> Trp) and a low-tunneling (Val-203 --> Ala) mutant provides a structural basis for the observed effects, demonstrating an increase in the hydrogen transfer distance for the low-tunneling mutant. The Val-203 --> Ala ternary complex crystal structure also shows a hyperclosed interdomain geometry relative to the wild-type and the Phe-93 --> Trp mutant ternary complex structures. This demonstrates a flexibility in interdomain movement that could potentially narrow the distance between the donor and acceptor carbons in the native enzyme and may enhance the role of tunneling in the hydride transfer reaction.


    Related Citations: 
    • Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 A Resolution
      Al-Karadaghi, S., Cedergren-Zeppezauer, E.S., Hovmoller, S., Petratos, K., Terry, H., Wilson, K.S.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 793
    • Interdomain Motion in Liver Alcohol Dehydrogenase. Structural and Energetic Analysis of the Hinge Bending Mode
      Colonna-Cesari, F., Perahia, D., Karplus, M., Eklund, H., Branden, C.I., Tapia, O.
      (1986) J Biol Chem 261: 15273
    • Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase
      Eklund, H., Samama, J.P., Jones, T.A.
      (1984) Biochemistry 23: 5982
    • Crystal-Structure Determination of Reduced Nicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazole
      Cedergren-Zeppezauer, E.
      (1983) Biochemistry 22: 5761
    • Three-Dimensional Structure of Isonicotinimidylated Liver Alcohol Dehydrogenase
      Plapp, B.V., Eklund, H., Jones, T.A., Branden, C.I.
      (1983) J Biol Chem 258: 5537
    • Crystal Structures of the Active Site in Specifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives
      Schneider, G., Eklund, H., Cedergren-Zeppezauer, E., Zeppezauer, M.
      (1983) Proc Natl Acad Sci U S A 80: 5289
    • Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
      Eklund, H., Samama, J.P., Wallen, L.
      (1982) Biochemistry 21: 4858
    • Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N-Dimethylamino)Cinnamaldehyde to the Enzyme
      Cedergren-Zeppezauer, E., Samama, J.P., Eklund, H.
      (1982) Biochemistry 21: 4895
    • Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase
      Eklund, H., Plapp, B.V., Samama, J.P., Branden, C.I.
      (1982) J Biol Chem 257: 14349
    • Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
      Eklund, H., Branden, C.I.
      (1979) J Biol Chem 254: 3458
    • Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution
      Eklund, H., Nordstrom, B., Zeppezauer, E., Soderlund, G., Ohlsson, I., Boiwe, T., Soderberg, B.O., Tapia, O., Branden, C.I., Akeson, A.
      (1976) J Mol Biol 102: 27

    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley 94720, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALCOHOL DEHYDROGENASEA, B374Equus caballusMutation(s): 1 
Gene Names: LADH CDNA
EC: 1.1.1.1
Find proteins for P00327 (Equus caballus)
Explore P00327 
Go to UniProtKB:  P00327
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
ETF
Query on ETF

Download CCD File 
A, B
TRIFLUOROETHANOL
C2 H3 F3 O
RHQDFWAXVIIEBN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.82α = 103.1
b = 44.58β = 87.59
c = 93.28γ = 70.55
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance