1C9U

CRYSTAL STRUCTURE OF THE SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE IN COMPLEX WITH PQQ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

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This is version 1.7 of the entry. See complete history


Literature

Structure and mechanism of soluble quinoprotein glucose dehydrogenase.

Oubrie, A.Rozeboom, H.J.Kalk, K.H.Olsthoorn, A.J.Duine, J.A.Dijkstra, B.W.

(1999) EMBO J 18: 5187-5194

  • DOI: 10.1093/emboj/18.19.5187
  • Primary Citation of Related Structures:  
    1C9U, 1CQ1

  • PubMed Abstract: 
  • Soluble glucose dehydrogenase (s-GDH; EC 1.1.99.17) is a classical quinoprotein which requires the cofactor pyrroloquinoline quinone (PQQ) to oxidize glucose to gluconolactone. The reaction mechanism of PQQ-dependent enzymes has remained controversial due to the absence of comprehensive structural data ...

    Soluble glucose dehydrogenase (s-GDH; EC 1.1.99.17) is a classical quinoprotein which requires the cofactor pyrroloquinoline quinone (PQQ) to oxidize glucose to gluconolactone. The reaction mechanism of PQQ-dependent enzymes has remained controversial due to the absence of comprehensive structural data. We have determined the X-ray structure of s-GDH with the cofactor at 2.2 A resolution, and of a complex with reduced PQQ and glucose at 1.9 A resolution. These structures reveal the active site of s-GDH, and show for the first time how a functionally bound substrate interacts with the cofactor in a PQQ-dependent enzyme. Twenty years after the discovery of PQQ, our results finally provide conclusive evidence for a reaction mechanism comprising general base-catalyzed hydride transfer, rather than the generally accepted covalent addition-elimination mechanism. Thus, PQQ-dependent enzymes use a mechanism similar to that of nicotinamide- and flavin-dependent oxidoreductases.


    Related Citations: 
    • The 1.7 Angstrom crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal sequence repeat
      Oubrie, A., Rozeboom, H.J., Kalk, K.H., Duine, J.A., Dijkstra, B.W.
      (1999) J Mol Biol 289: 319

    Organizational Affiliation

    Laboratory of Biophysical Chemistry and BIOSON Research Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASEA, B454Acinetobacter calcoaceticusMutation(s): 0 
Gene Names: gdhB
EC: 1.1.5.2
UniProt
Find proteins for P13650 (Acinetobacter calcoaceticus)
Explore P13650 
Go to UniProtKB:  P13650
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.59α = 90
b = 158.72β = 90
c = 221.39γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
REFMACrefinement
BIOMOLdata reduction
BIOMOLdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2018-04-11
    Changes: Data collection
  • Version 1.6: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.7: 2019-08-14
    Changes: Data collection