5L9Z

Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted glucuronic acid configured aziridine probe JJB355

  • 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 Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 2.1 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 A389Homo sapiensMutation(s): 2 
Gene Names: HPSEHEPHPAHPA1HPR1HPSE1HSE1
EC: 3.2.1.166
Find proteins for Q9Y251 (Homo sapiens)
Explore Q9Y251 
Go to UniProtKB:  Q9Y251
NIH Common Fund Data Resources
PHAROS:  Q9Y251
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Heparanase B77Homo sapiensMutation(s): 0 
Gene Names: HPSEHEPHPAHPA1HPR1HPSE1HSE1
EC: 3.2.1.166
Find proteins for Q9Y251 (Homo sapiens)
Explore Q9Y251 
Go to UniProtKB:  Q9Y251
NIH Common Fund Data Resources
PHAROS:  Q9Y251
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GUX
Query on GUX

Download Ideal Coordinates CCD File 
A
(1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(azanylidene-{4}-azanylidene)amino]octyl]-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid
C15 H26 N4 O5
APKXYKNLAPKFAH-AAFBOLKUSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.19α = 90
b = 71.05β = 95.2
c = 78.69γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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 CouncilChina--

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: 2019-10-23
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary