PDBsum entry 1gpe

Oxidoreductase(flavoprotein)

PDB id: 1gpe

Contents

Protein chains

587 a.a. *

Ligands

NAG-NAG-BMA-MAN-MAN ×2

NAG-NAG ×2

NAG ×4

FAD ×2

Waters ×709

* Residue conservation analysis

PDB id:

1gpe

Name:

Oxidoreductase(flavoprotein)

Title:

Glucose oxidase from penicillium amagasakiense

Structure:

Protein (glucose oxidase). Chain: a, b. Ec: 1.1.3.4

Source:

Penicillium amagasakiense. Organism_taxid: 63559

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

1.80Å R-factor: 0.164 R-free: 0.198

Authors:

J.Hendle,H.M.Kalisz,H.J.Hecht

Key ref:

G.Wohlfahrt et al. (1999). 1.8 and 1.9 A resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes. Acta Crystallogr D Biol Crystallogr, 55, 969-977. PubMed id: 10216293 DOI: 10.1107/S0907444999003431

Date:

24-Mar-99 Release date: 06-May-99

Protein chains

P81156  (GOX_PENAG) -  Glucose oxidase from Penicillium amagasakiense

Seq: 587 a.a.

Struc: 587 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.3.4 - glucose oxidase.
• 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) + O2 = D-glucono-1,5-lactone + H2O2

• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444999003431

Acta Crystallogr D Biol Crystallogr 55:969-977 (1999)

PubMed id: 10216293

1.8 and 1.9 A resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes.

G.Wohlfahrt, S.Witt, J.Hendle, D.Schomburg, H.M.Kalisz, H.J.Hecht.

ABSTRACT

Glucose oxidase is a flavin-dependent enzyme which catalyses the oxidation of beta-D-glucose by molecular oxygen to delta-gluconolactone and hydrogen peroxide. The structure of the enzyme from Aspergillus niger, previously refined at 2.3 A resolution, has been refined at 1.9 A resolution to an R value of 19.0%, and the structure of the enzyme from Penicillium amagasakiense, which has 65% sequence identity, has been determined by molecular replacement and refined at 1.8 A resolution to an R value of 16.4%. The structures of the partially deglycosylated enzymes have an r.m.s. deviation of 0.7 A for main-chain atoms and show four N-glycosylation sites, with an extended carbohydrate moiety at Asn89. Substrate complexes of the enzyme from A. niger were modelled by force-field methods. The resulting model is consistent with results from site-directed mutagenesis experiments and shows the beta-D-glucose molecule in the active site of glucose oxidase, stabilized by 12 hydrogen bonds and by hydrophobic contacts to three neighbouring aromatic residues and to flavin adenine dinucleotide. Other hexoses, such as alpha-D-glucose, mannose and galactose, which are poor substrates for the enzyme, and 2-deoxy-D-glucose, form either fewer bonds or unfavourable contacts with neighbouring amino acids. Simulation of the complex between the reduced enzyme and the product, delta-gluconolactone, has provided an explanation for the lack of product inhibition by the lactone.

Selected figure(s)

Figure 1.
Figure 1 Schematic representation of the glucose oxidase reaction showing the inhibitor D-glucal in the insert. For -D-glucose and the flavin group the atom-numbering scheme used in the text is indicated. Gluconolactone, gluconic acid and the inhibitor D-glucal are numbered accordingly.

Figure 6.
Figure 6 Schematic representation of the hydrogen bonds and hydrophobic interactions of the modelled substrate -D-glucose with active-site residues in glucose oxidase from A. niger (LIGPLOT; Wallace et al., 1995[Wallace, A. C., Laskowski, R. A. & Thornton, J. M. (1995). Protein Eng. 8, 127-134.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 969-977) copyright 1999.

Figures were selected by the author.