Crystal structure of a bacterial pyranose 2-oxidase in complex with mangiferin

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms.

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.

(2023) Nat Commun 14: 7289-7289

  • DOI: https://doi.org/10.1038/s41467-023-42000-3
  • Primary Citation of Related Structures:  
    7QF8, 7QFD, 7QVA

  • 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 2 to H 2 O 2 . 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 cat /K m ) 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.

  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GMC oxidoreductase family protein519Pseudarthrobacter siccitoleransMutation(s): 0 
Gene Names: ARTSIC4J27_4061
Find proteins for A0A024H8G7 (Pseudarthrobacter siccitolerans)
Explore A0A024H8G7 
Go to UniProtKB:  A0A024H8G7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024H8G7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.65α = 90
b = 78.858β = 90
c = 147.348γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean UnionB-LigZymes H2020-MSCA-RISE 2018
Foundation for Science and Technology (FCT)PortugalPTDC/BII-BBF/29564/2017

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Author supporting evidence, Database references