5LA7

Crystal structure of human proheparanase, in complex with glucuronic acid configured aziridine probe JJB355

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

  • 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: 1.94 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 im ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heparanase
A
509Homo sapiensMutation(s): 0 
Gene Names: HPSE (HEP, HPA, HPA1, HPR1, HPSE1, HSE1)
EC: 3.2.1.166
Find proteins for Q9Y251 (Homo sapiens)
Go to Gene View: HPSE
Go to UniProtKB:  Q9Y251
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6S6
Query on 6S6

Download SDF File 
Download CCD File 
A
(1~{S},2~{R},3~{S},4~{S},5~{S},6~{R})-2-(8-azidooctylamino)-3,4,5,6-tetrakis(oxidanyl)cyclohexane-1-carboxylic acid
C15 H28 N4 O6
HMWYQBVREFKFKY-KTEZLCCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.410α = 90.00
b = 88.020β = 90.00
c = 118.200γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
MOLREPphasing
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-14
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Database references