1NXQ

Crystal Structure of R-alcohol dehydrogenase (RADH) (apoenyzme) from Lactobacillus brevis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of R-specific alcohol dehydrogenase from Lactobacillus brevis suggests the structural basis of its metal dependency

Niefind, K.Muller, J.Riebel, B.Hummel, W.Schomburg, D.

(2003) J.Mol.Biol. 327: 317-328

  • Also Cited By: 1ZK4, 1ZK3, 1ZK2, 1ZK1, 1ZK0, 1ZJZ, 1ZJY

  • PubMed Abstract: 
  • The crystal structure of the apo-form of an R-specific alcohol dehydrogenase from Lactobacillus brevis (LB-RADH) was solved and refined to 1.8A resolution. LB-RADH is a member of the short-chain dehydrogenase/reductase (SDR) enyzme superfamily. It is ...

    The crystal structure of the apo-form of an R-specific alcohol dehydrogenase from Lactobacillus brevis (LB-RADH) was solved and refined to 1.8A resolution. LB-RADH is a member of the short-chain dehydrogenase/reductase (SDR) enyzme superfamily. It is a homotetramer with 251 amino acid residues per subunit and uses NADP(H) as co-enzyme. NADPH and the substrate acetophenone were modelled into the active site. The enantiospecificity of the enzyme can be explained on the basis of the resulting hypothetical ternary complex. In contrast to most other SDR enzymes, the catalytic activity of LB-RADH depends strongly on the binding of Mg(2+). Mg(2+) removal by EDTA inactivates the enzyme completely. In the crystal structure, the Mg(2+)-binding site is well defined. The ion has a perfect octahedral coordination sphere and occupies a special position concerning crystallographic and molecular point symmetry, meaning that each RADH tetramer contains two magnesium ions. The magnesium ion is no direct catalytic cofactor. However, it is structurally coupled to the putative C-terminal hinge of the substrate-binding loop and, via an extended hydrogen bonding network, to some side-chains forming the substrate binding region. Therefore, the presented structure of apo-RADH provides plausible explanations for the metal dependence of the enzyme.


    Related Citations: 
    • Crystallization and preliminary characterization of crystals of R-alcohol dehydrogenase from Lactobacillus brevis
      Niefind, K.,Riebel, B.,Muller, J.,Hummel, W.,Schomburg, D.
      (2000) ACTA CRYSTALLOGR.,SECT.D 56: 1696


    Organizational Affiliation

    Universität zu Köln, Institut für Biochemie, Zülpicher Strasse 47, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
R-alcohol dehydrogenase
A
251Lactobacillus brevisMutation(s): 0 
Gene Names: radh
Find proteins for Q84EX5 (Lactobacillus brevis)
Go to UniProtKB:  Q84EX5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.150 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.444α = 90.00
b = 85.065β = 90.00
c = 115.336γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
X-PLORphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance