V203A horse liver alcohol dehydrogenase E complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.120 

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This is version 1.4 of the entry. See complete history


Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis.

Yahashiri, A.Rubach, J.K.Plapp, B.V.

(2014) Biochemistry 53: 881-894

  • DOI: https://doi.org/10.1021/bi401583f
  • Primary Citation of Related Structures:  
    4NFH, 4NFS, 4NG5

  • PubMed Abstract: 

    A role for protein dynamics in enzymatic catalysis of hydrogen transfer has received substantial scientific support, but the connections between protein structure and catalysis remain to be established. Valine residues 203 and 207 are at the binding site for the nicotinamide ring of the coenzyme in liver alcohol dehydrogenase and have been suggested to facilitate catalysis with "protein-promoting vibrations" (PPV). We find that the V207A substitution has small effects on steady-state kinetic constants and the rate of hydrogen transfer; the introduced cavity is empty and is tolerated with minimal effects on structure (determined at 1.2 Å for the complex with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol). Thus, no evidence is found to support a role for Val-207 in the dynamics of catalysis. The protein structures and ligand geometries (including donor-acceptor distances) in the V203A enzyme complexed with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol (determined at 1.1 Å) are very similar to those for the wild-type enzyme, except that the introduced cavity accommodates a new water molecule that contacts the nicotinamide ring. The structures of the V203A enzyme complexes suggest, in contrast to previous studies, that the diminished tunneling and decreased rate of hydride transfer (16-fold, relative to that of the wild-type enzyme) are not due to differences in ground-state ligand geometries. The V203A substitution may alter the PPV and the reorganization energy for hydrogen transfer, but the protein scaffold and equilibrium thermal motions within the Michaelis complex may be more significant for enzyme catalysis.

  • Organizational Affiliation

    Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242-1109, 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
Query on NAJ

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]
C21 H27 N7 O14 P2
Query on PFB

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B]
C7 H3 F5 O
Query on MRD

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
N [auth B]
C6 H14 O2
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth B],
K [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
PFB Binding MOAD:  4NG5 Ki: 1900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.52α = 91.8
b = 51.56β = 103.05
c = 92.55γ = 110.3
Software Package:
Software NamePurpose
Blu-Icedata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2013-11-13 
  • Deposition Author(s): Plapp, B.V.

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2020-02-12
    Changes: Database references
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description