5E98

Crystal structure of human heparanase in complex with HepMer M04S02a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 

wwPDB Validation   3D Report Full Report


This is version 3.0 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:  
    5E9B, 5E9C, 5E98, 5E97, 5E8M

  • 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 results in breakdown of extracellular HS and release of stored growth factors and hence is strongly linked to cancer metastasis ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heparanase A389Homo 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
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
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid
C
3 N/A Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
NPO
Query on NPO

Download Ideal Coordinates CCD File 
A
P-NITROPHENOL
C6 H5 N O3
BTJIUGUIPKRLHP-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 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: 1.63 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.79α = 90
b = 71.29β = 95.06
c = 77.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-10-14 
  • Released Date: 2015-11-18 
  • Deposition Author(s): Wu, L., Davies, G.J.

Funding OrganizationLocationGrant Number
European Research Council (ERC)United KingdomAdG 322942

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 1.2: 2015-12-16
    Changes: Database references
  • Version 2.0: 2020-07-15
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary