1JQA

Bacillus stearothermophilus glycerol dehydrogenase complex with glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase.

Ruzheinikov, S.N.Burke, J.Sedelnikova, S.Baker, P.J.Taylor, R.Bullough, P.A.Muir, N.M.Gore, M.G.Rice, D.W.

(2001) Structure 9: 789-802

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacillus stearothermophilus glycerol dehydrogenase (GlyDH) (glycerol:NAD(+) 2-oxidoreductase, EC 1.1.1.6) catalyzes the oxidation of glycerol to dihydroxyacetone (1,3-dihydroxypropanone) with concomitant reduction of NAD(+) to NADH. Analysis of the s ...

    Bacillus stearothermophilus glycerol dehydrogenase (GlyDH) (glycerol:NAD(+) 2-oxidoreductase, EC 1.1.1.6) catalyzes the oxidation of glycerol to dihydroxyacetone (1,3-dihydroxypropanone) with concomitant reduction of NAD(+) to NADH. Analysis of the sequence of this enzyme indicates that it is a member of the so-called iron-containing alcohol dehydrogenase family. Despite this sequence similarity, GlyDH shows a strict dependence on zinc for activity. On the basis of this, we propose to rename this group the family III metal-dependent polyol dehydrogenases. To date, no structural data have been reported for any enzyme in this group.


    Related Citations: 
    • Purification, crystallization and quaternary structure analysis of a glycerol dehydrogenase S305C mutant from Bacillus stearothemophilus.
      Burke, J.,Ruzheinikov, S.N.,Sedelnikova, S.,Baker, P.J.,Holmes, D.,Muir, N.M.,Gore, M.G.,Rice, D.W.
      (2001) Acta Crystallogr.,Sect.D 57: 165


    Organizational Affiliation

    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol Dehydrogenase
A
370Geobacillus stearothermophilusMutation(s): 1 
Gene Names: gldA (gld)
EC: 1.1.1.6
Find proteins for P32816 (Geobacillus stearothermophilus)
Go to UniProtKB:  P32816
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.158 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 105.910α = 90.00
b = 105.910β = 90.00
c = 149.500γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model