Horse liver F93W alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 

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This is version 1.5 of the entry. See complete history


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

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alcohol dehydrogenase E chain
A, B
374Equus caballusMutation(s): 1 
Find proteins for P00327 (Equus caballus)
Explore P00327 
Go to UniProtKB:  P00327
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00327
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAJ (Subject of Investigation/LOI)
Query on NAJ

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
C21 H27 N7 O14 P2
PFB (Subject of Investigation/LOI)
Query on PFB

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
C7 H3 F5 O
MRD (Subject of Investigation/LOI)
Query on MRD

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G [auth A],
H [auth A],
M [auth B]
C6 H14 O2
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.47α = 92.09
b = 51.44β = 102.95
c = 92.56γ = 110.25
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
Omodel building
d*TREKdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-05-22 
  • 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  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2020-02-12
    Changes: Database references
  • Version 1.4: 2020-03-11
    Changes: Database references
  • Version 1.5: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description