Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 67499.44 
• Atom Count: 4544 
• Residue Count: 581 
• Unique protein chains: 1

2WMG

Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae TIGR4 (Sp4GH98) in complex with the LewisY pentasaccharide blood group antigen.

• DOI: 10.2210/pdb2WMG/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2009-06-30 Released: 2009-07-14 
• Deposition Author(s): Higgins, M.A., Whitworth, G.E., El Warry, N., Randriantsoa, M., Samain, E., Burke, R.D., Vocadlo, D.J., Boraston, A.B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.227 
• R-Value Work: 0.156 

Literature

Differential Recognition and Hydrolysis of Host Carbohydrate-Antigens by Streptococcus Pneumoniae Family 98 Glycoside Hydrolases.

Higgins, M.A., Whitworth, G.E., El Warry, N., Randriantsoa, M., Samain, E., Burke, R.D., Vocadlo, D.J., Boraston, A.B.

(2009) J.Biol.Chem. 284: 26161

• PubMed: 19608744 
• DOI: 10.1074/jbc.M109.024067
• Primary Citation of Related Structures:  
  2WMK, 2WMJ, 2WMI, 2WMH, 2WMF


• PubMed Abstract: 
  

The presence of a fucose utilization operon in the Streptococcus pneumoniae genome and its established importance in virulence indicates a reliance of this bacterium on the harvesting of host fucose-containing glycans. The identities of these glycans, however, and how they are harvested is presently unknown. The biochemical and high resolution x-ray crystallographic analysis of two family 98 glycoside hydrolases (GH98s) from distinctive forms of the fucose utilization operon that originate from different S. pneumoniae strains reveal that one enzyme, the predominant type among pneumococcal isolates, has a unique endo-beta-galactosidase activity on the LewisY antigen. Altered active site topography in the other species of GH98 enzyme tune its endo-beta-galactosidase activity to the blood group A and B antigens. Despite their different specificities, these enzymes, and by extension all family 98 glycoside hydrolases, use an inverting catalytic mechanism. Many bacterial and viral pathogens exploit host carbohydrate antigens for adherence as a precursor to colonization or infection. However, this is the first evidence of bacterial endoglycosidase enzymes that are known to play a role in virulence and are specific for distinct host carbohydrate antigens. The strain-specific distribution of two distinct types of GH98 enzymes further suggests that S. pneumoniae strains may specialize to exploit host-specific antigens that vary from host to host, a factor that may feature in whether a strain is capable of colonizing a host or establishing an invasive infection.

---

Organizational Affiliation: 

Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
FUCOLECTIN-RELATED PROTEIN	A	581	Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)	Mutation(s): 1
Find proteins for A0A0H2US34 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Go to UniProtKB:  A0A0H2US34

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FUC	A	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
GAL	A	BETA-D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.227 
• R-Value Work: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 50.860	α = 90.00
b = 90.870	β = 90.00
c = 116.230	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-30 
• Released Date: 2009-07-14 
• Deposition Author(s): Higgins, M.A., Whitworth, G.E., El Warry, N., Randriantsoa, M., Samain, E., Burke, R.D., Vocadlo, D.J., Boraston, A.B.

Revision History 

• Version 1.0: 2009-07-14
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance