3AUU

Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in complex with D-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided mutagenesis for the improvement of substrate specificity of Bacillus megaterium glucose 1-dehydrogenase IV

Nishioka, T.Yasutake, Y.Nishiya, Y.Tamura, T.

(2012) Febs J. 279: 3264-3275

  • DOI: 10.1111/j.1742-4658.2012.08713.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacillus megaterium IAM 1030 (Bacillus sp. JCM 20016) possesses four d-glucose 1-dehydrogenase isozymes (BmGlcDH-I, -II, -III and -IV) that belong to the short-chain dehydrogenase/reductase superfamily. The BmGlcDHs are currently used for a clinical ...

    Bacillus megaterium IAM 1030 (Bacillus sp. JCM 20016) possesses four d-glucose 1-dehydrogenase isozymes (BmGlcDH-I, -II, -III and -IV) that belong to the short-chain dehydrogenase/reductase superfamily. The BmGlcDHs are currently used for a clinical assay to examine blood glucose levels. Of these four isozymes, BmGlcDH-IV has relatively high thermostability and catalytic activity, but the disadvantage of its broad substrate specificity remains to be overcome. Here, we describe the crystal structures of BmGlcDH-IV in ligand-free, NADH-bound and β-D-glucose-bound forms to a resolution of 2.0 Å. No major conformational differences were found among these structures. The structure of BmGlcDH-IV in complex with β-D-glucose revealed that the carboxyl group at the C-terminus, derived from a neighboring subunit, is inserted into the active-site pocket and directly interacts with β-D-glucose. A site-directed mutagenic study showed that destabilization of the BmGlcDH-IV C-terminal region by substitution with more bulky and hydrophobic amino acid residues greatly affects the activity of the enzyme, as well as its thermostability and substrate specificity. Of the six mutants created, the G259A variant exhibited the narrowest substrate specificity, whilst retaining comparable catalytic activity and thermostability to the wild-type enzyme.


    Organizational Affiliation

    Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucose 1-dehydrogenase 4
A, B
269Bacillus megateriumMutation(s): 0 
Gene Names: gdhIV
EC: 1.1.1.47
Find proteins for P39485 (Bacillus megaterium)
Go to UniProtKB:  P39485
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.032α = 90.00
b = 127.525β = 109.95
c = 64.519γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-09-19
    Type: Database references