5LA4

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

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: 10.1038/nchembio.2395
  • Primary Citation of Related Structures:  
    5G0Q, 5L77, 5L9Z, 5L9Y, 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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heparanase A509Homo sapiensMutation(s): 1 
Gene Names: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
EC: 3.2.1.166
Find proteins for Q9Y251 (Homo sapiens)
Explore Q9Y251 
Go to UniProtKB:  Q9Y251
NIH Common Fund Data Resources
PHAROS:  Q9Y251
GTEx:  ENSG00000173083
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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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