Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

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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
  • Primary Citation of Related Structures:  
    1AXG, 1AXE

  • 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
    • Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution
      Eklund, H., Samama, J.P., Wallen, L., Branden, C.I., Akeson, A., Jones, T.A.
      (1981) J Mol Biol 146: 561
    • 5-Methylnicotinamide-Adenine Dinucleotide. Kinetic Investigation with Major and Minor Isoenzymes of Liver Alcohol Dehydrogenase and Structural Determination of its Binary Complex with Alcohol Dehydrogenase
      Samama, J.P., Wrixon, A.D., Biellmann, J.F.
      (1981) Eur J Biochem 118: 479
    • X-Ray Studies of the Binding of Cibacron Blue F3Ga to Liver Alcohol Dehydrogenase
      Biellmann, J.F., Samama, J.P., Branden, C.I., Eklund, H.
      (1979) Eur J Biochem 102: 107
    • Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
      Eklund, H., Branden, C.I.
      (1979) J Biol Chem 254: 3458
    • Subunit Conformation of Yeast Alcohol Dehydrogenase
      Jornvall, H., Eklund, H., Branden, C.I.
      (1978) J Biol Chem 253: 8414
    • Crystallization of Liver Alcohol Dehydrogenase Activated by the Modification of Amino Groups
      Plapp, B.V., Zeppezauer, E., Branden, C.I.
      (1978) J Mol Biol 119: 451
    • Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates
      Plapp, B.V., Eklund, H., Branden, C.I.
      (1978) J Mol Biol 122: 23
    • X-Ray Investigation of the Binding of 1,10-Phenanthroline and Imidazole to Horse-Liver Alcohol Dehydrogenase
      Boiwe, T., Branden, C.I.
      (1977) Eur J Biochem 77: 173
    • The Crystal Structure of Complexes between Horse Liver Alcohol Dehydrogenase and the Coenzyme Analogues 3-Iodopyridine-Adenine Dinucleotide and Pyridine-Adenine Dinucleotide
      Samama, J.P., Zeppezauer, E., Biellmann, J.F., Branden, C.I.
      (1977) Eur J Biochem 81: 403
    • Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases
      Eklund, H., Branden, C.I., Jornvall, H.
      (1976) J Mol Biol 102: 61
    • 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
    • The Binding of Nucleotides to Horse Liver Alcohol
      Nordstrom, B., Branden, C.I.
      (1975) Structure And Conformation Of Nucleic Acids And Protein-nucleic Acid Interactions : Proceedings Of The Fourth Annual Harry Steenbock Symposium, June 16-19, 1974, Madison, Wisconsin --: 387

    Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALCOHOL DEHYDROGENASEABCD374Equus caballusMutation(s): 1 
Gene Names: LADH CDNA
Find proteins for P00327 (Equus caballus)
Explore P00327 
Go to UniProtKB:  P00327
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download CCD File 
A, B, C, D
C21 H27 N7 O14 P2
 Ligand Interaction
Query on ETF

Download CCD File 
A, B, C, D
C2 H3 F3 O
 Ligand Interaction
Query on ZN

Download CCD File 
A, B, C, D
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.348α = 102.66
b = 86.734β = 99.24
c = 90.635γ = 101.63
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

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