6O91

Horse liver L57F alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.118 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer.

Kim, K.Plapp, B.V.

(2020) Biochemistry 59: 862-879

  • DOI: 10.1021/acs.biochem.9b01074
  • Primary Citation of Related Structures:  
    6O91, 6OWP, 6OWM, 6OA7

  • PubMed Abstract: 
  • Previous studies showed that the L57F and F93W alcohol dehydrogenases catalyze the oxidation of benzyl alcohol with some quantum mechanical hydrogen tunneling, whereas the V203A enzyme has diminished tunneling. Here, steady-state kinetics for the L57 ...

    Previous studies showed that the L57F and F93W alcohol dehydrogenases catalyze the oxidation of benzyl alcohol with some quantum mechanical hydrogen tunneling, whereas the V203A enzyme has diminished tunneling. Here, steady-state kinetics for the L57F and F93W enzymes were studied, and microscopic rate constants for the ordered bi-bi mechanism were estimated from simulations of transient kinetics for the S48T, F93A, S48T/F93A, F93W, and L57F enzymes. Catalytic efficiencies for benzyl alcohol oxidation ( V 1 / E t K b ) vary over a range of ∼100-fold for the less active enzymes up to the L57F enzyme and are mostly associated with the binding of alcohol rather than the rate constants for hydride transfer. In contrast, catalytic efficiencies for benzaldehyde reduction ( V 2 / E t K p ) are ∼500-fold higher for the L57F enzyme than for the less active enzymes and are mostly associated with the rate constants for hydride transfer. Atomic-resolution structures (1.1 Å) for the F93W and L57F enzymes complexed with NAD + and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol are almost identical to previous structures for the wild-type, S48T, and V203A enzymes. Least-squares refinement with SHELXL shows that the nicotinamide ring is slightly strained in all complexes and that the apparent donor-acceptor distances from C4N of NAD to C7 of pentafluorobenzyl alcohol range from 3.28 to 3.49 Å (±0.02 Å) and are not correlated with the rate constants for hydride transfer or hydrogen tunneling. How the substitutions affect the dynamics of reorganization during hydrogen transfer and the extent of tunneling remain to be determined.


    Related Citations: 
    • Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis.
      Bahnson, B.J., Park, D.H., Kim, K., Plapp, B.V., Klinman, J.P.
      (1993) Biochemistry 32: 5503
    • Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes.
      Plapp, B.V., Ramaswamy, S.
      (2012) Biochemistry 51: 4035
    • Catalysis by Alcohol Dehydrogenases
      Plapp, B.V.
      (2006) Isotope Effects In Chemistry And Biology --: 811
    • Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93.
      Kim, K., Plapp, B.V.
      (2017) Chem Biol Interact 276: 77

    Organizational Affiliation

    Department of Biochemistry , The University of Iowa , Iowa City , Iowa 52242 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alcohol dehydrogenase E chainAB374Equus caballusMutation(s): 1 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.118 
  • Space Group: P 1
  • Diffraction Data DOI: 10.15785/SBGRID/650 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.5α = 91.8
b = 51.52β = 103.07
c = 92.54γ = 110.42
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata scaling
PDB_EXTRACTdata extraction
d*TREKdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-12 
  • Released Date: 2019-04-10 
  • Deposition Author(s): Plapp, B.V.

Funding OrganizationLocationGrant Number
Department of Health & Human Services (HHS)United StatesAA00279
Department of Health & Human Services (HHS)United StatesGM078446

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-02-12
    Changes: Database references
  • Version 1.3: 2020-03-11
    Changes: Database references