1QV7

HORSE LIVER ALCOHOL DEHYDROGENASE HIS51GLN/LYS228ARG MUTANT COMPLEXED WITH NAD+ AND 2,3-DIFLUOROBENZYL ALCOHOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase.

LeBrun, L.A.Park, D.-H.Ramaswamy, S.Plapp, B.V.

(2004) Biochemistry 43: 3014-3026

  • DOI: 10.1021/bi036103m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Histidine-51 in horse liver alcohol dehydrogenase (ADH) is part of a hydrogen-bonded system that appears to facilitate deprotonation of the hydroxyl group of water or alcohol ligated to the catalytic zinc. The contribution of His-51 to catalysis was ...

    Histidine-51 in horse liver alcohol dehydrogenase (ADH) is part of a hydrogen-bonded system that appears to facilitate deprotonation of the hydroxyl group of water or alcohol ligated to the catalytic zinc. The contribution of His-51 to catalysis was studied by characterizing ADH with His-51 substituted with Gln (H51Q). The steady-state kinetic constants for ethanol oxidation and acetaldehyde reduction at pH 8 are similar for wild-type and H51Q enzymes. In contrast, the H51Q substitution significantly shifts the pH dependencies for steady-state and transient reactions and decreases by 11-fold the rate constant for the transient oxidation of ethanol at pH 8. Modest substrate deuterium isotope effects indicate that hydride transfer only partially limits the transient oxidation and turnover. Transient data show that the H51Q substitution significantly decreases the rate of isomerization of the enzyme-NAD(+) complex and becomes a limiting step for ethanol oxidation. Isomerization of the enzyme-NAD(+) complex is rate limiting for acetaldehyde reduction catalyzed by the wild-type enzyme, but release of alcohol is limiting for the H51Q enzyme. X-ray crystallography of doubly substituted His51Gln:Lys228Arg ADH complexed with NAD(+) and 2,3- or 2,4-difluorobenzyl alcohol shows that Gln-51 isosterically replaces histidine in interactions with the nicotinamide ribose of the coenzyme and that Arg-228 interacts with the adenosine monophosphate of the coenzyme without affecting the protein conformation. The difluorobenzyl alcohols bind in one conformation. His-51 participates in, but is not essential for, proton transfers in the mechanism.


    Related Citations: 
    • Control of Coenzyme Binding to Horse Liver Alcohol Dehydrogenase.
      LeBrun, L.A.,Plapp, B.V.
      (1999) Biochemistry 38: 12387
    • Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenase as Determined by NMR and X-Ray Crystallographic Studies.
      Rubach, J.K.,Plapp, B.V.
      (2002) Biochemistry 41: 15770
    • Structures of Liver Alcohol Dehydrogenase Complexed with Nad+ and Substituted Benzyl Alcohols.
      Ramaswamy, S.,Eklund, H.,Plapp, B.V.
      (1994) Biochemistry 33: 5230
    • 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
    • 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
    • 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


    Organizational Affiliation

    Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242-1109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol dehydrogenase E chain
A, B
374Equus caballusMutation(s): 2 
EC: 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
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
DFB
Query on DFB

Download SDF File 
Download CCD File 
A, B
2,3-DIFLUOROBENZYL ALCOHOL
C7 H6 F2 O
JSFGDUIJQWWBGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.050α = 91.61
b = 50.962β = 103.03
c = 92.466γ = 109.86
Software Package:
Software NamePurpose
XDSdata reduction
AMoREphasing
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Data collection, Refinement description