Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with multivalent inhibitors.

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Structural basis of the inhibition of GH1 beta-glucosidases by multivalent pyrrolidine iminosugars.

Martinez-Bailen, M.Jimenez-Ortega, E.Carmona, A.T.Robina, I.Sanz-Aparicio, J.Talens-Perales, D.Polaina, J.Matassini, C.Cardona, F.Moreno-Vargas, A.J.

(2019) Bioorg Chem 89: 103026-103026

  • DOI: https://doi.org/10.1016/j.bioorg.2019.103026
  • Primary Citation of Related Structures:  
    6QWI, 6R4K

  • PubMed Abstract: 

    The synthesis of multivalent pyrrolidine iminosugars via CuAAC click reaction between different pyrrolidine-azide derivatives and tri- or hexavalent alkynyl scaffolds is reported. The new multimeric compounds, together with the monomeric reference, were evaluated as inhibitors against two homologous GH1 β-glucosidases (BglA and BglB from Paenibacillus polymyxa). The multivalent inhibitors containing an aromatic moiety in the linker between the pyrrolidine and the scaffold inhibited the octameric BglA (µM range) but did not show affinity against the monomeric BglB, despite the similarity between the active site of both enzymes. A modest multivalent effect (rp/n = 12) was detected for the hexavalent inhibitor 12. Structural analysis of the complexes between the monomeric and the trimeric iminosugar inhibitors (4 and 10) and BglA showed the insertion of the inhibitors at the active site of BglA, confirming a competitive mode of inhibition as indicated by enzyme kinetics. Additionally, structural comparison of the BglA/4 complex with the reported BglB/2F-glucose complex illustrates the key determinants responsible for the inhibitory effect and explains the reasons of the inhibition of BglA and the no inhibition of BglB. Potential inhibition of other β-glucosidases with therapeutic relevance is discussed under the light of these observations.

  • Organizational Affiliation

    Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/Prof. García González, 1, 41012 Seville, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucosidase A
A, B
448Paenibacillus polymyxaMutation(s): 0 
Gene Names: bglA
Find proteins for P22073 (Paenibacillus polymyxa)
Explore P22073 
Go to UniProtKB:  P22073
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22073
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JJW

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C17 H24 N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.096α = 90
b = 146.096β = 90
c = 140.345γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description