1GCO

CRYSTAL STRUCTURE OF GLUCOSE DEHYDROGENASE COMPLEXED WITH NAD+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

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This is version 1.4 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 129: 303-312

  • DOI: 10.1093/oxfordjournals.jbchem.a002858
  • Primary Citation of Related Structures:  
    1GCO

  • 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 reductases/dehydrogenases (SDRs) in their overall folding and subunit architecture, although cofactor binding sites and subunit interactions differ ...

    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 D Biol Crystallogr 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSE DEHYDROGENASEA,
B,
C [auth E],
D [auth F]		261Priestia megateriumMutation(s): 0 
EC: 1.1.1.47
UniProt
Find proteins for P40288 (Priestia megaterium)
Explore P40288 
Go to UniProtKB:  P40288
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40288
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth E],
H [auth F]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.675α = 90
b = 66.557β = 93.21
c = 119.528γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-06-13
    Changes: Data collection, Derived calculations
  • Version 1.4: 2019-10-16
    Changes: Data collection, Database references