9FL2

Crystal structure of Oscillatoria princeps pyranose oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 
    0.250 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: in silico
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Literature

Identification of a robust bacterial pyranose oxidase that displays an unusual pH dependence.

Santema, L.L.Rozeboom, H.J.Borger, V.P.Kaya, S.G.Fraaije, M.W.

(2024) J Biol Chem 300: 107885-107885

  • DOI: https://doi.org/10.1016/j.jbc.2024.107885
  • Primary Citation of Related Structures:  
    9FL2

  • PubMed Abstract: 

    Pyranose oxidases are valuable biocatalysts, yet only a handful of bacterial pyranose oxidases are known. These bacterial enzymes exhibit noteworthy distinctions from their extensively characterized fungal counterparts, encompassing variations in substrate specificity and structural attributes. Herein a bacterial pyranose oxidase from Oscillatoria princeps (OPOx) was biochemically characterized in detail. In contrast to the fungal pyranose oxidases, OPOx could be well expressed in Escherichia coli as soluble, fully flavinylated and active oxidase. It was found to be highly thermostable (melting temperature >90 ⁰C) and showed activity on glucose, exhibiting an exceptionally low K M value (48 μM). Elucidation of its crystal structure revealed similarities with fungal pyranose oxidases, such as being a tetramer with a large central void leading to a narrow substrate access tunnel. In the active site, the FAD cofactor is covalently bound to a histidine. OPOx displays a relatively narrow pH optimum for activity with a sharp decline at relatively basic pH values which is accompanied with a drastic change in its flavin absorbance spectrum. The pH-dependent switch in flavin absorbance features and oxidase activity was shown to be fully reversible. It is hypothesized that a glutamic acid helps to stabilize the protonated form of the histidine that is tethered to the FAD. OPOx presents itself as a valuable biocatalyst as it is highly robust, well-expressed in E. coli, shows low K M values for monosaccharides and has a peculiar pH dependent "on-off switch".


  • Organizational Affiliation

    Molecular Enzymology, University of Groningen, Nijenborgh 3, 9747AG Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
pyranose oxidase
A, B, C, D
539Oscillatoria princeps RMCB-10Mutation(s): 0 
EC: 1.1.3.10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free:  0.250 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.971α = 90
b = 137.406β = 90
c = 143.619γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionH2020-NMBP-BIO-2017

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Database references