The crystal structure of O-glycoside cleaving beta-eliminase from A. tumefaciens AtOGE

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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Enzymatic beta-elimination in natural product O- and C-glycoside deglycosylation.

Bitter, J.Pfeiffer, M.Borg, A.J.E.Kuhlmann, K.Pavkov-Keller, T.Sanchez-Murcia, P.A.Nidetzky, B.

(2023) Nat Commun 14: 7123-7123

  • DOI: https://doi.org/10.1038/s41467-023-42750-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Biological degradation of natural product glycosides involves, alongside hydrolysis, β-elimination for glycosidic bond cleavage. Here, we discover an O-glycoside β-eliminase (OGE) from Agrobacterium tumefaciens that converts the C3-oxidized O-β-D-glucoside of phloretin (a plant-derived flavonoid) into the aglycone and the 2-hydroxy-3-keto-glycal elimination product. While unrelated in sequence, OGE is structurally homologous to, and shows effectively the same Mn 2+ active site as, the C-glycoside deglycosylating enzyme (CGE) from a human intestinal bacterium implicated in β-elimination of 3-keto C-β-D-glucosides. We show that CGE catalyzes β-elimination of 3-keto O- and C-β-D-glucosides while OGE is specific for the O-glycoside substrate. Substrate comparisons and mutagenesis for CGE uncover positioning of aglycone for protonic assistance by the enzyme as critically important for C-glycoside cleavage. Collectively, our study suggests convergent evolution of active site for β-elimination of 3-keto O-β-D-glucosides. C-Glycoside cleavage is a specialized feature of this active site which is elicited by substrate through finely tuned enzyme-aglycone interactions.

  • Organizational Affiliation

    Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase
A, B
259Agrobacterium tumefaciensMutation(s): 0 
Gene Names: BV900_26275
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.58α = 90
b = 93.67β = 90
c = 123.68γ = 90
Software Package:
Software NamePurpose
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Austrian Science FundAustriaDOC130

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references