6OWP

Horse liver F93W alcohol dehydrogenase complexed with NAD and trifluoroethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.122 

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Ligand Structure Quality Assessment 


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, 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 ...

    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
    • Active site modifications in a double mutant of liver alcohol dehydrogenase: structural studies of two enzyme-ligand complexes.
      Colby, T.D., Bahnson, B.J., Chin, J.K., Klinman, J.P., Goldstein, B.M.
      (1998) Biochemistry 37: 9295
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alcohol dehydrogenase E chainA, B374Equus caballusMutation(s): 1 
EC: 1.1.1.1
UniProt
Find proteins for P00327 (Equus caballus)
Explore P00327 
Go to UniProtKB:  P00327
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00327
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAJ (Subject of Investigation/LOI)
Query on NAJ

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MRD
Query on MRD

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth B]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
ETF (Subject of Investigation/LOI)
Query on ETF

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
TRIFLUOROETHANOL
C2 H3 F3 O
RHQDFWAXVIIEBN-UHFFFAOYSA-N
 Ligand Interaction
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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.122 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.28α = 92.12
b = 51.2β = 102.98
c = 92.31γ = 110.04
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



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: 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