7PSJ

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VL166


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism-based heparanase inhibitors reduce cancer metastasis in vivo.

de Boer, C.Armstrong, Z.Lit, V.A.J.Barash, U.Ruijgrok, G.Boyango, I.Weitzenberg, M.M.Schroder, S.P.Sarris, A.J.C.Meeuwenoord, N.J.Bule, P.Kayal, Y.Ilan, N.Codee, J.D.C.Vlodavsky, I.Overkleeft, H.S.Davies, G.J.Wu, L.

(2022) Proc Natl Acad Sci U S A 119: e2203167119-e2203167119

  • DOI: https://doi.org/10.1073/pnas.2203167119
  • Primary Citation of Related Structures:  
    7PR6, 7PR7, 7PR8, 7PR9, 7PRB, 7PRT, 7PSH, 7PSI, 7PSJ, 7PSK

  • PubMed Abstract: 

    Heparan sulfate proteoglycans (HSPGs) mediate essential interactions throughout the extracellular matrix (ECM), providing signals that regulate cellular growth and development. Altered HSPG composition during tumorigenesis strongly aids cancer progression. Heparanase (HPSE) is the principal enzyme responsible for extracellular heparan sulfate catabolism and is markedly up-regulated in aggressive cancers. HPSE overactivity degrades HSPGs within the ECM, facilitating metastatic dissemination and releasing mitogens that drive cellular proliferation. Reducing extracellular HPSE activity reduces cancer growth, but few effective inhibitors are known, and none are clinically approved. Inspired by the natural glycosidase inhibitor cyclophellitol, we developed nanomolar mechanism-based, irreversible HPSE inhibitors that are effective within physiological environments. Application of cyclophellitol-derived HPSE inhibitors reduces cancer aggression in cellulo and significantly ameliorates murine metastasis. Mechanism-based irreversible HPSE inhibition is an unexplored anticancer strategy. We demonstrate the feasibility of such compounds to control pathological HPSE-driven malignancies.


  • Organizational Affiliation

    Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucuronidase475Acidobacterium capsulatum ATCC 51196Mutation(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
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid
B
2N/AN/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.393α = 90
b = 44.117β = 97.579
c = 136.708γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United KingdomERC-2011-AdG-290836
European Research Council (ERC)United KingdomERC-2012-AdG-322942
Netherlands Organisation for Scientific Research (NWO)United Kingdom--
Israel Science FoundationUnited Kingdom1021/19
European Molecular Biology Organization (EMBO)United KingdomSTF8184
Royal SocietyUnited Kingdom--
Wellcome TrustUnited Kingdom218579/Z/19/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description