1TEH

STRUCTURE OF HUMAN LIVER CHICHI ALCOHOL DEHYDROGENASE (A GLUTATHIONE-DEPENDENT FORMALDEHYDE DEHYDROGENASE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of human chi chi alcohol dehydrogenase: a glutathione-dependent formaldehyde dehydrogenase.

Yang, Z.N.Bosron, W.F.Hurley, T.D.

(1997) J.Mol.Biol. 265: 330-343

  • DOI: 10.1006/jmbi.1996.0731

  • PubMed Abstract: 
  • The crystal structure of the human class III chi chi alcohol dehydrogenase (ADH) in a binary complex with NAD+(gamma) was solved to 2.7 A resolution by molecular replacement with human class I beta1 beta1 ADH. chi chi ADH catalyzes the oxidation of l ...

    The crystal structure of the human class III chi chi alcohol dehydrogenase (ADH) in a binary complex with NAD+(gamma) was solved to 2.7 A resolution by molecular replacement with human class I beta1 beta1 ADH. chi chi ADH catalyzes the oxidation of long-chain alcohols such as omega-hydroxy fatty acids as well as S-hydroxymethyl-glutathione, a spontaneous adduct between formaldehyde and glutathione. There are two subunits per asymmetric unit in the chi chi ADH structure. Both subunits display a semi-open conformation of the catalytic domain. This conformation is half-way between the open and closed conformations described for the horse EE ADH enzyme. The semi-open conformation and key changes in elements of secondary structure provide a structural basis for the ability of chi chi ADH to bind S-hydroxymethyl-glutathione and 10-hydroxydecanoate. Direct coordination of the catalytic zinc ion by Glu68 creates a novel environment for the catalytic zinc ion in chi chi ADH. This new configuration of the catalytic zinc is similar to an intermediate for horse EE ADH proposed through theoretical computations and is consistent with the spectroscopic data of the Co(II)-substituted chi chi enzyme. The position for residue His47 in the chi chi ADH structure suggests His47 may function both as a catalytic base for proton transfer and in the binding of the adenosine phosphate of NAD(H). Modeling of substrate binding to this enzyme structure is consistent with prior mutagenesis data which showed that both Asp57 and Arg115 contribute to glutathione binding and that Arg115 contributes to the binding of omega-hydroxy fatty acids and identifies additional residues which may contribute to substrate binding.


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN CHICHI ALCOHOL DEHYDROGENASE
A, B
373Homo sapiensGene Names: ADH5 (ADHX, FDH)
EC: 1.1.1.1
Find proteins for P11766 (Homo sapiens)
Go to Gene View: ADH5
Go to UniProtKB:  P11766
Small Molecules
Ligands 2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 141.250α = 90.00
b = 201.550β = 90.00
c = 69.610γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
SCALEdata scaling
PROCESSdata reduction
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance