Crystal structure of apo human proheparanase

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): Yes 

  • Deposited: 2016-06-13 Released: 2017-05-31 
  • Deposition Author(s): Wu, L., Jin, Y., Davies, G.J.
  • Funding Organization(s): European Research Council, Netherlands Organization for Scientific Research, China Scholarship Organization

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 

This is version 2.1 of the entry. See complete history


Activity-based probes for functional interrogation of retaining beta-glucuronidases.

Wu, L.Jiang, J.Jin, Y.Kallemeijn, W.W.Kuo, C.L.Artola, M.Dai, W.van Elk, C.van Eijk, M.van der Marel, G.A.Codee, J.D.C.Florea, B.I.Aerts, J.M.F.G.Overkleeft, H.S.Davies, G.J.

(2017) Nat Chem Biol 13: 867-873

  • DOI: https://doi.org/10.1038/nchembio.2395
  • Primary Citation of Related Structures:  
    5G0Q, 5L77, 5L9Y, 5L9Z, 5LA4, 5LA7

  • PubMed Abstract: 

    Humans express at least two distinct β-glucuronidase enzymes that are involved in disease: exo-acting β-glucuronidase (GUSB), whose deficiency gives rise to mucopolysaccharidosis type VII, and endo-acting heparanase (HPSE), whose overexpression is implicated in inflammation and cancers. The medical importance of these enzymes necessitates reliable methods to assay their activities in tissues. Herein, we present a set of β-glucuronidase-specific activity-based probes (ABPs) that allow rapid and quantitative visualization of GUSB and HPSE in biological samples, providing a powerful tool for dissecting their activities in normal and disease states. Unexpectedly, we find that the supposedly inactive HPSE proenzyme proHPSE is also labeled by our ABPs, leading to surprising insights regarding structural relationships between proHPSE, mature HPSE, and their bacterial homologs. Our results demonstrate the application of β-glucuronidase ABPs in tracking pathologically relevant enzymes and provide a case study of how ABP-driven approaches can lead to discovery of unanticipated structural and biochemical functionality.

  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heparanase509Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y251 (Homo sapiens)
Explore Q9Y251 
Go to UniProtKB:  Q9Y251
GTEx:  ENSG00000173083 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y251
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.501α = 90
b = 88.061β = 90
c = 120.497γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomErC-2012-AdG-322942
European Research CouncilNetherlandsErC-2011-AdG-290836
Netherlands Organization for Scientific ResearchNetherlands--
China Scholarship OrganizationChina--

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary