1HF3

ATOMIC X-RAY STRUCTURE OF LIVER ALCOHOL DEHYDROGENASE CONTAINING Cadmium and a hydroxide adduct to NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

On the Enzymatic Activation of Nadh

Meijers, R.Morris, R.J.Adolph, H.W.Merli, A.Lamzin, V.S.Cedergen-Zeppezauer, E.S.

(2001) J.Biol.Chem. 276: 9316

  • DOI: 10.1074/jbc.M010870200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Atomic (1 A) resolution x-ray structures of horse liver alcohol dehydrogenase in complex with NADH revealed the formation of an adduct in the active site between a metal-bound water and NADH. Furthermore, a pronounced distortion of the pyridine ring ...

    Atomic (1 A) resolution x-ray structures of horse liver alcohol dehydrogenase in complex with NADH revealed the formation of an adduct in the active site between a metal-bound water and NADH. Furthermore, a pronounced distortion of the pyridine ring of NADH was observed. A series of quantum chemical calculations on the water-nicotinamide adduct showed that the puckering of the pyridine ring in the crystal structures can only be reproduced when the water is considered a hydroxide ion. These observations provide fundamental insight into the enzymatic activation of NADH for hydride transfer.


    Related Citations: 
    • Substitutions in a Flexible Loop of Horse Liver Alcohol Dehydrogenase Hinder the Conformational Change and Unmask Hydrogen Transfer
      Ramaswamy, S.,Park, D.H.,Plapp, B.V.
      (1999) Biochemistry 38: 13951
    • Refined Crystal Structure of Liver Deresolutionhydrogenase-Nadh Complex at 1.8 Angstrom Alcohol
      Al-Karadaghi, S.,Cedergren-Zeppezauer, E.S.,Petratos, K.,Hovmoeller, S.,Terry, H.,Dauter, Z.,Wilson, K.S.
      (1994) Acta Crystallogr.,Sect.D 50: 793
    • Electrostatic Effects in the Kinetics of Coenzyme Binding to Isozymes of Alcohol Dehydrogenase from Horse Liver
      Adolph, H.W.,Kiefer, M.,Cedergren-Zeppezauer, E.S.
      (1997) Biochemistry 36: 8743
    • Crystal Structures of the Active Site Inspecifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives
      Schneider, G.,Eklund, H.,Cedergren-Zeppezauer, E.,Zeppezauer, M.
      (1983) Proc.Natl.Acad.Sci.USA 80: 5289
    • Crystal-Structure Determination of Reducnicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazoleed
      Cedergren-Zeppezauer, E.
      (1983) Biochemistry 22: 5761


    Organizational Affiliation

    European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALCOHOL DEHYDROGENASE E CHAIN
A, B
374Equus caballusMutation(s): 0 
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
MRD
Query on MRD

Download SDF File 
Download CCD File 
A, B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-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
CD
Query on CD

Download SDF File 
Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.900α = 90.00
b = 179.000β = 107.50
c = 50.500γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance