1HTB

CRYSTALLIZATION OF HUMAN BETA3 ALCOHOL DEHYDROGENASE (10 MG/ML) IN 100 MM SODIUM PHOSPHATE (PH 7.5), 7.5 MM NAD+ AND 1 MM 4-IODOPYRAZOLE AT 25 C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 17057-17061

  • Primary Citation of Related Structures:  1DEH

  • PubMed Abstract: 
  • The three-dimensional structure of the human beta3beta3 dimeric alcohol dehydrogenase (beta3) was determined to 2.4-A resolution. beta3 was crystallized as a ternary complex with the coenzyme NAD+ and the competitive inhibitor 4-iodopyrazole. beta3 i ...

    The three-dimensional structure of the human beta3beta3 dimeric alcohol dehydrogenase (beta3) was determined to 2.4-A resolution. beta3 was crystallized as a ternary complex with the coenzyme NAD+ and the competitive inhibitor 4-iodopyrazole. beta3 is a polymorphic variant at ADH2 that differs from beta1 by a single amino acid substitution of Arg-369 --> Cys. The available x-ray structures of mammalian alcohol dehydrogenases show that the side chain of Arg-369 forms an ion pair with the NAD(H) pyrophosphate to stabilize the E.NAD(H) complex. The Cys-369 side chain of beta3 cannot form this interaction. The three-dimensional structures of beta3 and beta1 are virtually identical, with the exception that Cys-369 and two water molecules in beta3 occupy the position of Arg-369 in beta1. The two waters occupy the same positions as two guanidino nitrogens of Arg-369. Hence, the number of hydrogen bonding interactions between the enzyme and NAD(H) are the same for both isoenzymes. However, beta3 differs from beta1 by the loss of the electrostatic interaction between the NAD(H) pyrophosphate and the Arg-369 side chain. The equilibrium dissociation constants of beta3 for NAD+ and NADH are 350-fold and 4000-fold higher, respectively, than those for beta1. These changes correspond to binding free energy differences of 3.5 kcal/mol for NAD+ and 4.9 kcal/mol for NADH. Thus, the Arg-369 --> Cys substitution of beta3 isoenzyme destabilizes the interaction between coenzyme and beta3 alcohol dehydrogenase.


    Related Citations: 
    • Structure of Three Human Beta Alcohol Dehydrogenase Variants
      Hurley, T.D.,Bosron, W.F.,Stone, C.L.,Amzel, L.M.
      (1994) J.Mol.Biol. 239: 415


    Organizational Affiliation

    Department of Biochemistry, Indiana University School of Medicine, Indianapolis, Indiana 46202-5122, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA3 ALCOHOL DEHYDROGENASE
A, B
374Homo sapiensGene Names: ADH1B (ADH2)
EC: 1.1.1.1
Find proteins for P00325 (Homo sapiens)
Go to Gene View: ADH1B
Go to UniProtKB:  P00325
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
PYZ
Query on PYZ

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Download CCD File 
A, B
4-IODOPYRAZOLE
C3 H3 I N2
LLNQWPTUJJYTTE-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NADKd: 670000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.175 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 54.030α = 92.71
b = 44.430β = 103.17
c = 92.740γ = 69.15
Software Package:
Software NamePurpose
RAXISdata collection
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
R-AXISdata reduction
RIGAKUdata collection
JAPANdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance