1AXG

CRYSTAL STRUCTURE OF THE VAL203->ALA MUTANT OF LIVER ALCOHOL DEHYDROGENASE COMPLEXED WITH COFACTOR NAD AND INHIBITOR TRIFLUOROETHANOL SOLVED TO 2.5 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.214 

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.USA 94: 12797-12802

  • Primary Citation of Related Structures:  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: 
    • 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
    • 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
    • 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.,Sect.D 50: 793
    • Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates
      Plapp, B.V.,Eklund, H.,Branden, C.I.
      (1978) J.Mol.Biol. 122: 23
    • 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.USA 80: 5289
    • 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
    • Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Samama, J.P.,Jones, T.A.
      (1984) Biochemistry 23: 5982
    • Subunit Conformation of Yeast Alcohol Dehydrogenase
      Jornvall, H.,Eklund, H.,Branden, C.I.
      (1978) J.Biol.Chem. 253: 8414
    • 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
    • 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
    • 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
    • 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
    • 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
    • Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases
      Eklund, H.,Branden, C.I.,Jornvall, H.
      (1976) J.Mol.Biol. 102: 61
    • 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
    • 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
    • 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
    • Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
      Eklund, H.,Samama, J.P.,Wallen, L.
      (1982) Biochemistry 21: 4858
    • 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
    • Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Branden, C.I.
      (1979) J.Biol.Chem. 254: 3458
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALCOHOL DEHYDROGENASE
A, B, C, D
374Equus caballusEC: 1.1.1.1
Find proteins for P00327 (Equus caballus)
Go to UniProtKB:  P00327
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ETF
Query on ETF

Download SDF File 
Download CCD File 
A, B, C, D
TRIFLUOROETHANOL
C2 H3 F3 O
RHQDFWAXVIIEBN-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 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
SCALEPACKdata scaling
X-PLORmodel building
DENZOdata reduction
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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