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.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 

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This is version 2.0 of the entry. See complete history. 


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

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

  • 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 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FUCOLECTIN-RELATED PROTEINA581Streptococcus pneumoniae TIGR4Mutation(s): 1 
Gene Names: SP_2159
UniProt
Find proteins for A0A0H2US34 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2US34 
Go to UniProtKB:  A0A0H2US34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2US34
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranoseB 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G00052MO
GlyCosmos:  G00052MO
GlyGen:  G00052MO
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.86α = 90
b = 90.87β = 90
c = 116.23γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary