Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.22 kDa 
• Atom Count: 4171 
• Modelled Residue Count: 459 
• Deposited Residue Count: 466 
• Unique protein chains: 2

5E97

Glycoside Hydrolase ligand structure 1

• DOI: 10.2210/pdb5E97/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2015-10-14 Released: 2015-11-18 
• Deposition Author(s): Wu, L., Davies, G.J.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.197 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

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

• PubMed: 26575439 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparanase	A	389	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparanase	B	77	Homo sapiens	Mutation(s): 0  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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid	C	4		N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NPO	A	P-NITROPHENOL C6 H5 N O3 BTJIUGUIPKRLHP-UHFFFAOYSA-N
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.197 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.88	α = 90
b = 70.89	β = 94.91
c = 78.23	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	--

Revision History  

• 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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary