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 

wwPDB Validation 3D Report Full Report


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
  • Structures With Same Primary Citation

  • 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 controversia ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE
A, B
454Acinetobacter calcoaceticusMutation(s): 0 
Gene Names: gdhB
EC: 1.1.5.2
Find proteins for P13650 (Acinetobacter calcoaceticus)
Go to UniProtKB:  P13650
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PQQ
Query on PQQ

Download CCD File 
A, B
PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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