5E9C

Crystal structure of human heparanase in complex with heparin tetrasaccharide dp4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of human heparanase reveals insights into substrate recognition.

Wu, L.Viola, C.M.Brzozowski, A.M.Davies, G.J.

(2015) Nat.Struct.Mol.Biol. 22: 1016-1022

  • DOI: 10.1038/nsmb.3136
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heparan sulfate (HS) is a glycosaminoglycan that forms a key component of the extracellular matrix (ECM). Breakdown of HS is carried out by heparanase (HPSE), an endo-β-glucuronidase of the glycoside hydrolase 79 (GH79) family. Overexpression of HPSE ...

    Heparan sulfate (HS) is a glycosaminoglycan that forms a key component of the extracellular matrix (ECM). Breakdown of HS is carried out by heparanase (HPSE), an endo-β-glucuronidase of the glycoside hydrolase 79 (GH79) family. Overexpression of HPSE results in breakdown of extracellular HS and release of stored growth factors and hence is strongly linked to cancer metastasis. Here we present crystal structures of human HPSE at 1.6-Å to 1.9-Å resolution that reveal how an endo-acting binding cleft is exposed by proteolytic activation of latent proHPSE. We used oligosaccharide complexes to map the substrate-binding and sulfate-recognition motifs. These data shed light on the structure and interactions of a key enzyme involved in ECM maintenance and provide a starting point for the design of HPSE inhibitors for use as biochemical tools and anticancer therapeutics.


    Organizational Affiliation

    Department of Chemistry, University of York, York, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heparanase
A
389Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heparanase
B
77Homo 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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5KV
Query on 5KV

Download SDF File 
Download CCD File 
A
2-deoxy-6-O-sulfo-2-(sulfoamino)-beta-D-glucopyranose
C6 H13 N O11 S2
DQTRACMFIGDHSN-QZABAPFNSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IDR
Query on IDR

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Download CCD File 
A
L-IDURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-VCSGLWQLSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
SGN
Query on SGN

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A
N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
 Ligand Interaction
UAP
Query on UAP

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Download CCD File 
A
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid
C6 H8 O9 S
VJIMUKBSNUBECH-YKKSOZKNSA-N
 Ligand Interaction
NAG
Query on NAG

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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: 1.73 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.220α = 90.00
b = 71.120β = 95.23
c = 78.600γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-10-15 
  • Released Date: 2015-11-18 
  • Deposition Author(s): Wu, L., Davies, G.J.

Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-02
    Type: Database references
  • Version 1.2: 2015-12-16
    Type: Database references