1GCO

CRYSTAL STRUCTURE OF GLUCOSE DEHYDROGENASE COMPLEXED WITH NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 A resolution.

Yamamoto, K.Kurisu, G.Kusunoki, M.Tabata, S.Urabe, I.Osaki, S.

(2001) J.Biochem.(Tokyo) 129: 303-312


  • PubMed Abstract: 
  • The crystal structure of glucose dehydrogenase (GlcDH) from Bacillus megaterium IWG3 has been determined to an R-factor of 17.9% at 1.7 A resolution. The enzyme consists of four identical subunits, which are similar to those of other short-chain redu ...

    The crystal structure of glucose dehydrogenase (GlcDH) from Bacillus megaterium IWG3 has been determined to an R-factor of 17.9% at 1.7 A resolution. The enzyme consists of four identical subunits, which are similar to those of other short-chain reductases/dehydrogenases (SDRs) in their overall folding and subunit architecture, although cofactor binding sites and subunit interactions differ. Whereas a pair of basic residues is well conserved among NADP(+)-preferring SDRs, only Arg39 was found around the adenine ribose moiety of GlcDH. This suggests that one basic amino acid is enough to determine the coenzyme specificity. The four subunits are interrelated by three mutually perpendicular diad axes (P, Q, and R). While subunit interactions through the P-axis for GlcDH are not so different from those of the other SDRs, those through the Q-axis differ significantly. GlcDH was found to have weaker hydrophobic interactions in the Q-interface. Moreover, GlcDH lacks the salt bridge that stabilizes the subunit interaction in the Q-interface in the other SDRs. Hydrogen bonds between Q-axis related subunits are also less common than in the other SDRs. The GlcDH tetramer dissociates into inactive monomers at pH 9.0, which can be attributed mainly to the weakness of the Q-axis interface.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Bacillus megaterium IWG3
      Yamamoto, K.,Kusunoki, M.,Urabe, I.,Tabata, S.,Osaki, S.
      (2000) Acta Crystallogr.,Sect.D 56: 1443


    Organizational Affiliation

    Department of Chemistry, Nara Medical University, Shijo, Kashihara, Nara 634-8521, Japan. kama@naramed-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOSE DEHYDROGENASE
A, B, E, F
261Bacillus megateriumEC: 1.1.1.47
Find proteins for P40288 (Bacillus megaterium)
Go to UniProtKB:  P40288
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, E, F
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 120.675α = 90.00
b = 66.557β = 93.21
c = 119.528γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-28
    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