3AUS

Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in ligand-free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

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
  • Structures With Same Primary Citation

  • 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 4A, B269Bacillus megateriumMutation(s): 0 
Gene Names: gdhIV
EC: 1.1.1.47
Find proteins for P39485 (Bacillus megaterium)
Explore P39485 
Go to UniProtKB:  P39485
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.06α = 90
b = 128.531β = 110.7
c = 64.717γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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