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PDBsum entry 1gal

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protein ligands links
Oxidoreductase(flavoprotein) PDB id
1gal
Jmol
Contents
Protein chain
581 a.a. *
Ligands
NAG-NAG-BMA-MAN-
MAN
NAG ×4
FAD
Waters ×152
* Residue conservation analysis
PDB id:
1gal
Name: Oxidoreductase(flavoprotein)
Title: Crystal structure of glucose oxidase from aspergillus niger: at 2.3 angstroms resolution
Structure: Glucose oxidase. Chain: a. Engineered: yes
Source: Aspergillus niger. Organism_taxid: 5061
Resolution:
2.30Å     R-factor:   0.181    
Authors: H.J.Hecht,K.Kalisz,J.Hendle,R.D.Schmid,D.Schomburg
Key ref: H.J.Hecht et al. (1993). Crystal structure of glucose oxidase from Aspergillus niger refined at 2.3 A resolution. J Mol Biol, 229, 153-172. PubMed id: 8421298
Date:
27-Aug-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P13006  (GOX_ASPNG) -  Glucose oxidase
Seq:
Struc:
 
Seq:
Struc:
605 a.a.
581 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.3.4  - Glucose oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Beta-D-glucose + O2 = D-glucono-1,5-lactone + H2O2
Beta-D-glucose
Bound ligand (Het Group name = BMA)
matches with 91.67% similarity
+ O(2)
= D-glucono-1,5-lactone
+ H(2)O(2)
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
J Mol Biol 229:153-172 (1993)
PubMed id: 8421298  
 
 
Crystal structure of glucose oxidase from Aspergillus niger refined at 2.3 A resolution.
H.J.Hecht, H.M.Kalisz, J.Hendle, R.D.Schmid, D.Schomburg.
 
  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 2.3 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20951568 B.C.Kim, X.Zhao, H.K.Ahn, J.H.Kim, H.J.Lee, K.W.Kim, S.Nair, E.Hsiao, H.Jia, M.K.Oh, B.I.Sang, B.S.Kim, S.H.Kim, Y.Kwon, S.Ha, M.B.Gu, P.Wang, and J.Kim (2011).
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PDB code: 3fim
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PDB codes: 2jbr 2jbs 2jbt
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PDB codes: 2igk 2igm 2ign 2igo
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Mechanism of the reductive half-reaction in cellobiose dehydrogenase.
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PDB code: 1naa
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Spectroscopic and kinetic properties of recombinant choline oxidase from Arthrobacter globiformis.
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Purification, molecular cloning, and characterization of pyridoxine 4-oxidase from Microbacterium luteolum.
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Monovalent cation-induced conformational change in glucose oxidase leading to stabilization of the enzyme.
  Biochemistry, 40, 1945-1955.  
11320506 B.Shenoy, Y.Wang, W.Shan, and A.L.Margolin (2001).
Stability of crystalline proteins.
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11592997 D.Zhong, and A.H.Zewail (2001).
Femtosecond dynamics of flavoproteins: charge separation and recombination in riboflavine (vitamin B2)-binding protein and in glucose oxidase enzyme.
  Proc Natl Acad Sci U S A, 98, 11867-11872.  
11761335 Y.Yano (2001).
Artificial flavin receptors: effects of hydrogen bonding on redox properties of a flavin mimic.
  Antioxid Redox Signal, 3, 899-909.  
10962107 E.Varela, M.Jesús Martínez, and A.T.Martínez (2000).
Aryl-alcohol oxidase protein sequence: a comparison with glucose oxidase and other FAD oxidoreductases.
  Biochim Biophys Acta, 1481, 202-208.
PDB code: 1qjn
10861408 F.van de Velde, N.D.Lourenço, M.Bakker, F.van Rantwijk, and R.A.Sheldon (2000).
Improved operational stability of peroxidases by coimmobilization with glucose oxidase.
  Biotechnol Bioeng, 69, 286-291.  
10651042 O.Vallon (2000).
New sequence motifs in flavoproteins: evidence for common ancestry and tools to predict structure.
  Proteins, 38, 95.  
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The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site.
  EMBO J, 19, 4204-4215.
PDB codes: 1f8r 1f8s
10712739 Z.Fan, G.B.Oguntimein, and P.J.Reilly (2000).
Characterization of kinetics and thermostability of Acremonium strictum glucooligosaccharide oxidase.
  Biotechnol Bioeng, 68, 231-237.  
10381408 A.Kohen, and J.P.Klinman (1999).
Hydrogen tunneling in biology.
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Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family.
  Structure, 7, 745-756.
PDB code: 1chu
10368296 C.Binda, A.Coda, R.Angelini, R.Federico, P.Ascenzi, and A.Mattevi (1999).
A 30-angstrom-long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase.
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PDB codes: 1b37 1b5q
10077557 D.Gidalevitz, Z.Huang, and S.A.Rice (1999).
Protein folding at the air-water interface studied with x-ray reflectivity.
  Proc Natl Acad Sci U S A, 96, 2608-2611.  
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Modeling the surface phenomena in carbon paste electrodes by low frequency impedance and double-layer capacitance measurements.
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10588687 F.R.Fan, and A.J.Bard (1999).
Imaging of biological macromolecules on mica in humid air by scanning electrochemical microscopy.
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1.8 and 1.9 A resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes.
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PDB codes: 1cf3 1gpe
10587448 J.Contzen, and C.Jung (1999).
Changes in secondary structure and salt links of cytochrome P-450cam induced by photoreduction: a Fourier transform infrared spectroscopic study.
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Second harmonic generation of glucose oxidase at the air/water interface.
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Contribution of the carbohydrate moiety to conformational stability of the carboxypeptidase Y high pressure study.
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Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.
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PDB codes: 1b3m 1l9f 2gb0
10194345 Q.K.Yue, I.J.Kass, N.S.Sampson, and A.Vrielink (1999).
Crystal structure determination of cholesterol oxidase from Streptomyces and structural characterization of key active site mutants.
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PDB codes: 1b4v 1b8s 1cbo 1cc2
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Nature of oxygen activation in glucose oxidase from Aspergillus niger: the importance of electrostatic stabilization in superoxide formation.
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Conformational transitions accompanying oligomerization of yeast alcohol oxidase, a peroxisomal flavoenzyme.
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The PHBH fold: not only flavoenzymes.
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The crystal structure of phenol hydroxylase in complex with FAD and phenol provides evidence for a concerted conformational change in the enzyme and its cofactor during catalysis.
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PDB code: 1foh
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The soluble alpha-glycerophosphate oxidase from Enterococcus casseliflavus. Sequence homology with the membrane-associated dehydrogenase and kinetic analysis of the recombinant enzyme.
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Excited-state dynamics of fully reduced flavins and flavoenzymes studied at subpicosecond time resolution.
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Circularly permuted beta-lactamase from Staphylococcus aureus PC1.
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PDB code: 1alq
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PDB code: 1kif
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Crystal structure of NADH oxidase from Thermus thermophilus.
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PDB code: 1nox
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Effect of protein chemical hydrophobization on antiglucose oxidase immunoglobulin production in mouse.
  Pharmacol Toxicol, 76, 278-285.  
7764643 A.P.Turner (1994).
Biosensors.
  Curr Opin Biotechnol, 5, 49-53.  
8026504 M.Medina, A.Vrielink, and R.Cammack (1994).
ESR and electron nuclear double resonance characterization of the cholesterol oxidase from Brevibacterium sterolicum in its semiquinone state.
  Eur J Biochem, 222, 941-947.  
18618774 P.Saudan, S.M.Zakeeruddin, M.A.Malavallon, M.Grätzel, and D.M.Fraser (1994).
Novel redox surfactants and their interactions with glucose oxidase of Aspergillus niger.
  Biotechnol Bioeng, 44, 407-418.  
  7756982 W.J.van Berkel, M.H.Eppink, and H.A.Schreuder (1994).
Crystal structure of p-hydroxybenzoate hydroxylase reconstituted with the modified FAD present in alcohol oxidase from methylotrophic yeasts: evidence for an arabinoflavin.
  Protein Sci, 3, 2245-2253.
PDB code: 1pdh
8357574 H.J.Hecht, D.Schomburg, H.Kalisz, and R.D.Schmid (1993).
The 3D structure of glucose oxidase from Aspergillus niger. Implications for the use of GOD as a biosensor enzyme.
  Biosens Bioelectron, 8, 197-203.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.