1HET

atomic X-ray structure of liver alcohol dehydrogenase containing a hydroxide adduct to NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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
    • 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
    • Refined Structure of Cu-Substituted Alcohol Dehydrogenase at 2.1 A Resolution
      Al-Karadaghi, S., Cedergren-Zeppezauer, E.S., Dauter, Z., Wilson, K.S.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 805
    • Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstrom Resolution
      Al-Karadaghi, S., Cedergren-Zeppezauer, E.S., Petratos, K., Hovmoeller, S., Terry, H., Dauter, Z., Wilson, K.S.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 793
    • Interdomain Motion in Liver Alcohol Dehydrogenase. {S}Tructural and Energetic Analysis of the Hinge Bending Mode
      Colonna-Cesari, F., Perahia, D., Karplus, M., Eklund, H., Branden, C.I., Tapia, O.
      (1986) J Biol Chem 261: 15273
    • Crystallographic Investigations of Nicotinamide Adenine Dinucleotide
      Eklund, H., Samama, J.-P., Jones, T.A.
      (1984) Biochemistry 23: 5982
    • Crystal Structures of the Active Site in Specifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives
      Schneider, G., Eklund, H., Cedergren-Zeppezauer, E., Zeppezauer, M.
      (1983) Proc Natl Acad Sci U S A 80: 5289
    • Crystal-Structure Determination of Reduced Nicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazole
      Cedergren-Zeppezauer, E.
      (1983) Biochemistry 22: 5761
    • Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase: Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-({N},{N}-Dimethylamino)Cinnamaldehyde to the Enzyme
      Cedergren-Zeppezauer, E., Samama, J.-P., Eklund, H.
      (1982) Biochemistry 21: 4895
    • Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstrom 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
    • Structure of Liver Alcohol Dehydrogenase at 2.9 Angstrom Resolution
      Branden, C.-I., Eklund, H., Nordstrom, B., Boiwe, T., Soderlund, G., Zeppezauer, E., Ohlsson, I., Akeson, A.
      (1973) Proc Natl Acad Sci U S A 70: 2439

    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 CHAINA, B374Equus caballusMutation(s): 0 
EC: 1.1.1.1
Find proteins for P00327 (Equus caballus)
Explore P00327 
Go to UniProtKB:  P00327
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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

Download CCD File 
A, B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.123 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.1α = 104.6
b = 44.4β = 101.5
c = 94γ = 70.5
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection