6R4K | pdb_00006r4k

Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with a monovalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.241 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 104 kDa 
  • Atom Count: 7,808 
  • Modeled Residue Count: 896 
  • Deposited Residue Count: 896 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-glucosidase A
A, B
448Paenibacillus polymyxaMutation(s): 0 
Gene Names: bglA
EC: 3.2.1.21
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JSK

Query on JSK



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
(2~{S},3~{S},4~{R})-2-[[4-[4-[2-[2-(2-azanylidenehydrazinyl)ethoxy]ethoxy]phenyl]-1,2,3-triazol-1-yl]methyl]pyrrolidine-3,4-diol
C17 H25 N7 O4
WVTAXSQMBJVQAL-BBWFWOEESA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.241 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.725α = 90
b = 146.725β = 90
c = 140.055γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

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