8OGX

Beta-glucuronidase from Acidobacterium capsulatum in complex with inhibitor R3794


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Molecular Basis for Inhibition of Heparanases and beta-Glucuronidases by Siastatin B.

Chen, Y.van den Nieuwendijk, A.M.C.H.Wu, L.Moran, E.Skoulikopoulou, F.van Riet, V.Overkleeft, H.S.Davies, G.J.Armstrong, Z.

(2024) J Am Chem Soc 146: 125-133

  • DOI: https://doi.org/10.1021/jacs.3c04162
  • Primary Citation of Related Structures:  
    8CQI, 8OGX, 8OHQ, 8OHR, 8OHT, 8OHU, 8OHV, 8OHW, 8OHX

  • PubMed Abstract: 

    Siastatin B is a potent and effective iminosugar inhibitor of three diverse glycosidase classes, namely, sialidases, β- d -glucuronidases, and N -acetyl-glucosaminidases. The mode of inhibition of glucuronidases, in contrast to sialidases, has long been enigmatic as siastatin B appears too bulky and incorrectly substituted to be accommodated within a β- d -glucuronidase active site pocket. Herein, we show through crystallographic analysis of protein-inhibitor complexes that siastatin B generates both a hemiaminal and a 3-geminal diol iminosugar (3-GDI) that are, rather than the parent compound, directly responsible for enzyme inhibition. The hemiaminal product is the first observation of a natural product that belongs to the noeuromycin class of inhibitors. Additionally, the 3-GDI represents a new and potent class of the iminosugar glycosidase inhibitor. To substantiate our findings, we synthesized both the gluco - and galacto -configured 3-GDIs and characterized their binding both structurally and kinetically to exo-β- d -glucuronidases and the anticancer target human heparanase. This revealed submicromolar inhibition of exo-β- d -glucuronidases and an unprecedented binding mode by this new class of inhibitor. Our results reveal the mechanism by which siastatin B acts as a broad-spectrum glycosidase inhibitor, identify a new class of glycosidase inhibitor, and suggest new functionalities that can be incorporated into future generations of glycosidase inhibitors.


  • Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta-glucuronidase from Acidobacterium capsulatum475Acidobacterium capsulatumMutation(s): 0 
Gene Names: ACP_2665
UniProt
Find proteins for C1F2K5 (Acidobacterium capsulatum (strain ATCC 51196 / DSM 11244 / BCRC 80197 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161))
Explore C1F2K5 
Go to UniProtKB:  C1F2K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1F2K5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VGO (Subject of Investigation/LOI)
Query on VGO

Download Ideal Coordinates CCD File 
B [auth A](3~{S},4~{S})-4,5,5-tris(oxidanyl)piperidine-3-carboxylic acid
C6 H11 N O5
VJJFPBNJYGLWRR-IMJSIDKUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.999α = 90
b = 44.658β = 97.46
c = 137.023γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Database references