Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 101.67 kDa 
• Atom Count: 8003 
• Modelled Residue Count: 900 
• Deposited Residue Count: 908 
• Unique protein chains: 1

1CRU

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

• PDB DOI: 10.2210/pdb1CRU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter calcoaceticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-08-16 Released: 2000-03-01 
• Deposition Author(s): Oubrie, A., Rozeboom, H.J., Dijkstra, B.W.

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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 

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

• PubMed: 10518528 
• 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 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.

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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 --: --

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE)	A, B	454	Acinetobacter calcoaceticus	Mutation(s): 0  Gene Names: gdhB EC: 1.1.5.2
UniProt
Find proteins for P13650 (Acinetobacter calcoaceticus) Explore P13650  Go to UniProtKB:  P13650

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PQQ	F [auth A], M [auth B]	PYRROLOQUINOLINE QUINONE C14 H6 N2 O8 MMXZSJMASHPLLR-UHFFFAOYSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
HDN	G [auth A], I [auth B]	METHYLHYDRAZINE C H4 N2 JYXPWUYLZPYOAH-IHWYPQMZSA-N
CA	C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 60.579	α = 90
b = 92.658	β = 105.37
c = 85.727	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-08-16 
• Released Date: 2000-03-01 
Deposition Author(s): Oubrie, A., Rozeboom, H.J., Dijkstra, B.W.

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