1CRU

SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS IN COMPLEX WITH PQQ AND METHYLHYDRAZINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Active-site structure of the soluble quinoprotein glucose dehydrogenase complexed with methylhydrazine: a covalent cofactor-inhibitor complex.

Oubrie, A.Rozeboom, H.J.Dijkstra, B.W.

(1999) Proc Natl Acad Sci U S A 96: 11787-11791

  • DOI: 10.1073/pnas.96.21.11787
  • Primary Citation of Related Structures:  
    1CRU

  • PubMed Abstract: 
  • Soluble glucose dehydrogenase (s-GDH) from the bacterium Acinetobacter calcoaceticus is a classical quinoprotein. It requires the cofactor pyrroloquinoline quinone (PQQ) to catalyze the oxidation of glucose to gluconolactone. The precise catalytic ro ...

    Soluble glucose dehydrogenase (s-GDH) from the bacterium Acinetobacter calcoaceticus is a classical quinoprotein. It requires the cofactor pyrroloquinoline quinone (PQQ) to catalyze the oxidation of glucose to gluconolactone. The precise catalytic role of PQQ in s-GDH and several other PQQ-dependent enzymes has remained controversial because of the absence of comprehensive structural data. We have determined the crystal structure of a ternary complex of s-GDH with PQQ and methylhydrazine, a competitive inhibitor of the enzyme. This complex, refined at 1.5-A resolution to an R factor of 16.7%, affords a detailed view of a cofactor-binding site of s-GDH. Moreover, it presents the first direct observation of covalent PQQ adduct in the active-site of a PQQ-dependent enzyme, thereby confirming previous evidence that the C5 carbonyl group of the cofactor is the most reactive moiety of PQQ.


    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
    • Structure and Mechanism of Soluble Quinoprotein Glucose Dehydrogenase
      Oubrie, A., Rozeboom, H.J., Kalk, K.H., Olsthoorn, A.J.J., Duine, J.A., Dijsktra, B.W.
      () To be published --: --

    Organizational Affiliation

    Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE)AB454Acinetobacter calcoaceticusMutation(s): 0 
Gene Names: gdhB
EC: 1.1.5.2
Find proteins for P13650 (Acinetobacter calcoaceticus)
Explore P13650 
Go to UniProtKB:  P13650
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 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
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HDN
Query on HDN

Download CCD File 
A, B
METHYLHYDRAZINE
C H4 N2
JYXPWUYLZPYOAH-IHWYPQMZSA-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: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.579α = 90
b = 92.658β = 105.37
c = 85.727γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-01
    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: 2013-08-14
    Changes: Derived calculations, Non-polymer description
  • Version 1.4: 2017-10-04
    Changes: Refinement description