1GAL

CRYSTAL STRUCTURE OF GLUCOSE OXIDASE FROM ASPERGILLUS NIGER: REFINED AT 2.3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

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This is version 2.0 of the entry. See complete history


Literature

Crystal structure of glucose oxidase from Aspergillus niger refined at 2.3 A resolution.

Hecht, H.J.Kalisz, H.M.Hendle, J.Schmid, R.D.Schomburg, D.

(1993) J Mol Biol 229: 153-172

  • DOI: 10.1006/jmbi.1993.1015
  • Primary Citation of Related Structures:  
    1GAL

  • PubMed Abstract: 
  • Glucose oxidase (beta-D-glucose: oxygen 1-oxidoreductase, EC 1.1.3.4) is an FAD-dependent enzyme that catalyzes the oxidation of beta-D-glucose by molecular oxygen. The crystal structure of the partially deglycosylated enzyme from Aspergillus niger has been determined by isomorphous replacement and refined to 2 ...

    Glucose oxidase (beta-D-glucose: oxygen 1-oxidoreductase, EC 1.1.3.4) is an FAD-dependent enzyme that catalyzes the oxidation of beta-D-glucose by molecular oxygen. The crystal structure of the partially deglycosylated enzyme from Aspergillus niger has been determined by isomorphous replacement and refined to 2.3 A resolution. The final crystallographic R-value is 18.1% for reflections between 10.0 and 2.3 A resolution. The refined model includes 580 amino acid residues, the FAD cofactor, six N-acetylglucosamine residues, three mannose residues and 152 solvent molecules. The FAD-binding domain is topologically very similar to other FAD-binding proteins. The substrate-binding domain is formed from non-continuous segments of sequence and is characterized by a deep pocket. One side of this pocket is formed by a six-stranded antiparallel beta-sheet with the flavin ring system of FAD located at the bottom of the pocket on the opposite side. Part of the entrance to the active site pocket is at the interface to the second subunit of the dimeric enzyme and is formed by a 20-residue lid, which in addition covers parts of the FAD-binding site. The carbohydrate moiety attached to Asn89 at the tip of this lid forms a link between the subunits of the dimer.


    Related Citations: 
    • Effects of Carbohydrate Depletion on the Structure, Stability and Activity of Glucose Oxidase from Aspergillus Niger
      Kalisz, H.M., Hecht, H.-J., Schomburg, D., Schmid, R.D.
      (1991) Biochim Biophys Acta 1080: 138

    Organizational Affiliation

    GBF (Gesellschaft für Biotechnologische Forschung), Department of Molecular Structure, Braunschweig, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSE OXIDASEA583Aspergillus nigerMutation(s): 0 
Gene Names: gox
EC: 1.1.3.4
UniProt
Find proteins for P13006 (Aspergillus niger)
Explore P13006 
Go to UniProtKB:  P13006
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13006
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42227JK
GlyCosmos:  G42227JK
GlyGen:  G42227JK
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.5α = 90
b = 66.5β = 90
c = 214.5γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary