1N8K

Horse Liver Alcohol Dehydrogenase Val292Thr Mutant Complexed to NAD+ and Pyrazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Amino Acid Residues in the Nicotinamide Binding Site Contribute to Catalysis by Horse Liver Alcohol Dehydrogenase

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

(2003) Biochemistry 42: 2907-2915

  • DOI: 10.1021/bi0272656
  • Primary Citation of Related Structures:  1N92
  • Also Cited By: 4DWV, 4DXH

  • PubMed Abstract: 
  • Amino acid residues Thr-178, Val-203, and Val-292, which interact with the nicotinamide ring of the coenzyme bound to alcohol dehydrogenase (ADH), may facilitate hydride transfer and hydrogen tunneling by orientation and dynamic effects. The T178S, T ...

    Amino acid residues Thr-178, Val-203, and Val-292, which interact with the nicotinamide ring of the coenzyme bound to alcohol dehydrogenase (ADH), may facilitate hydride transfer and hydrogen tunneling by orientation and dynamic effects. The T178S, T178V, V203A, V292A, V292S, and V292T substitutions significantly alter the steady state and transient kinetics of the enzyme. The V292A, V292S, and V292T enzymes have decreased affinity for coenzyme (NAD+ by 30-50-fold and NADH by 35-75-fold) as compared to the wild-type enzyme. The substitutions in the nicotinamide binding site decrease the rate constant of hydride transfer for benzyl alcohol oxidation by 3-fold (for V292T ADH) to 16-fold (for V203A ADH). The modest effects suggest that catalysis does not depend critically on individual residues and that several residues in the nicotinamide binding site contribute to catalysis. The structures of the V292T ADH-NAD+-pyrazole and wild-type ADH-NAD+-4-iodopyrazole ternary complexes are very similar. Only subtle changes in the V292T enzyme cause the large changes in coenzyme binding and the small change in hydride transfer. In these complexes, one pyrazole nitrogen binds to the catalytic zinc, and the other nitrogen forms a partial covalent bond with C4 of the nicotinamide ring, which adopts a boat conformation that is postulated to be relevant for hydride transfer. The results provide an experimental basis for evaluating the contributions of dynamics to hydride transfer.


    Related Citations: 
    • 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
    • Structures of Three Human Beta Alcohol Dehydrogenase Variants. Correlations with their Functional Differences.
      Hurley, T.D.,Bosron, W.F.,Stone, C.L.,Amzel, L.M.
      (1994) J.Mol.Biol. 239: 415
    • X-Ray Structure of Human beta3beta3 Alcohol Dehydrogenase. The contribution of ionic interactions to coenzyme binding.
      Davis, G.J.,Bosron, W.F.,Stone, C.L.,Owusu-Dekyi, K.,Hurley, T.D.
      (1996) J.Biol.Chem. 271: 17057
    • Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
      Eklund, H.,Samama, J.P.,Wallen, L.
      (1982) Biochemistry 21: 4858
    • 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, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol Dehydrogenase E chain
A, B
374Equus caballusEC: 1.1.1.1
Find proteins for P00327 (Equus caballus)
Go to UniProtKB:  P00327
Small Molecules
Ligands 4 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
PZO
Query on PZO

Download SDF File 
Download CCD File 
A, B
PYRAZOLE
C3 H4 N2
WTKZEGDFNFYCGP-UHFFFAOYSA-N
 Ligand Interaction
NAJ
Query on NAJ

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.144 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.310α = 91.94
b = 51.380β = 102.97
c = 92.670γ = 109.93
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance