7QFD

Crystal structure of a bacterial pyranose 2-oxidase complex with D-glucose

Summary for 7QFD

• Entry DOI: 10.2210/pdb7qfd/pdb
• Descriptor: GMC oxidoreductase family protein, FLAVIN-ADENINE DINUCLEOTIDE, alpha-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: p2ox, fad, bacteria, glucose, flavoproteins, oxidoreductase
• Biological source: Pseudarthrobacter siccitolerans
• Total number of polymer chains: 1
• Total formula weight: 56581.60

Authors

Borges, P.T.,Frazao, T.,Taborda, A.,Frazao, C.,Martins, L.O. (deposition date: 2021-12-05, release date: 2023-07-05, Last modification date: 2024-05-01)

Primary citation

Taborda, A.,Frazao, T.,Rodrigues, M.V.,Fernandez-Luengo, X.,Sancho, F.,Lucas, M.F.,Frazao, C.,Melo, E.P.,Ventura, M.R.,Masgrau, L.,Borges, P.T.,Martins, L.O.
Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms.
Nat Commun, 14:7289-7289, 2023

PubMed Abstract: C-glycosides are natural products with important biological activities but are recalcitrant to degradation. Glycoside 3-oxidases (G3Oxs) are recently identified bacterial flavo-oxidases from the glucose-methanol-coline (GMC) superfamily that catalyze the oxidation of C-glycosides with the concomitant reduction of O to HO. This oxidation is followed by C-C acid/base-assisted bond cleavage in two-step C-deglycosylation pathways. Soil and gut microorganisms have different oxidative enzymes, but the details of their catalytic mechanisms are largely unknown. Here, we report that PsG3Ox oxidizes at 50,000-fold higher specificity (k/K) the glucose moiety of mangiferin to 3-keto-mangiferin than free D-glucose to 2-keto-glucose. Analysis of PsG3Ox X-ray crystal structures and PsG3Ox in complex with glucose and mangiferin, combined with mutagenesis and molecular dynamics simulations, reveal distinctive features in the topology surrounding the active site that favor catalytically competent conformational states suitable for recognition, stabilization, and oxidation of the glucose moiety of mangiferin. Furthermore, their distinction to pyranose 2-oxidases (P2Oxs) involved in wood decay and recycling is discussed from an evolutionary, structural, and functional viewpoint.

PubMed: 37963862
DOI: 10.1038/s41467-023-42000-3

Experimental method

X-RAY DIFFRACTION (2.35 Å)