5BWI | pdb_00005bwi

Crystallographic structure of a bacterial heparanase

• PDB DOI: https://doi.org/10.2210/pdb5BWI/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia pseudomallei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-08 Released: 2015-10-28 
• Deposition Author(s): Yu, X., Blanchard, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.192 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Functional and structural characterization of a heparanase.

Bohlmann, L., Tredwell, G.D., Yu, X., Chang, C.W., Haselhorst, T., Winger, M., Dyason, J.C., Thomson, R.J., Tiralongo, J., Beacham, I.R., Blanchard, H., von Itzstein, M.

(2015) Nat Chem Biol 11: 955-957

• PubMed: 26565989 
• DOI: https://doi.org/10.1038/nchembio.1956
• Primary Citation Related Structures: 
  5BWI


• PubMed Abstract: 
  

  We report the structural and functional characterization of a novel heparanase (BpHep) from the invasive pathogenic bacterium Burkholderia pseudomallei (Bp), showing ∼24% sequence identity with human heparanase (hHep). Site-directed mutagenesis studies confirmed the active site resi-dues essential for activity, and we found that BpHep has specificity for heparan sulfate. Finally, we describe the first heparanase X-ray crystal structure, which provides new insight into both substrate recognition and inhibitor design.

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Organizational Affiliation: 
• Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.09 kDa 
• Atom Count: 7,698 
• Modeled Residue Count: 880 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside Hydrolase Family 79	A, B	446	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: DP46_278, DP55_3260
UniProt
Find proteins for Q63T97 (Burkholderia pseudomallei (strain K96243)) Explore Q63T97  Go to UniProtKB:  Q63T97

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.192 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.03	α = 90
b = 125.03	β = 90
c = 125.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Yu, X., Blanchard, H.

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2015-11-11
  Changes: Structure summary
• Version 1.2: 2015-11-25
  Changes: Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary