2YL8

Inhibition of the pneumococcal virulence factor StrH and molecular insights into N-glycan recognition and hydrolysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis.

Pluvinage, B.Higgins, M.A.Abbott, D.W.Robb, C.Dalia, A.B.Deng, L.Weiser, J.N.Parsons, T.B.Fairbanks, A.J.Vocadlo, D.J.Boraston, A.B.

(2011) Structure 19: 1603

  • DOI: https://doi.org/10.1016/j.str.2011.08.011
  • Primary Citation of Related Structures:  
    2YL5, 2YL6, 2YL8, 2YL9, 2YLA, 2YLL

  • PubMed Abstract: 

    The complete degradation of N-linked glycans by the pathogenic bacterium Streptococcus pneumoniae is facilitated by the large multimodular cell wall-attached exo-β-D-N-acetylglucosaminidase StrH. Structural dissection of this virulence factor using X-ray crystallography showed it to have two structurally related glycoside hydrolase family 20 catalytic domains, which displayed the expected specificity for complex N-glycans terminating in N-acetylglucosamine but exhibited unexpected differences in their preferences for the substructures present in these glycans. The structures of the two catalytic domains in complex with unhydrolyzed substrates, including an N-glycan possessing a bisecting N-acetylglucosamine residue, revealed the specific architectural features in the active sites that confer their differential specificities. Inhibitors of StrH are demonstrated to be effective tools in modulating the interaction of StrH with components of the host, such as the innate immune system. Overall, new structural and functional insight into a carbohydrate-mediated component of the pneumococcus-host interaction is provided.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-N-ACETYLHEXOSAMINIDASE434Streptococcus pneumoniae TIGR4Mutation(s): 1 
EC: 3.2.1.52
UniProt
Find proteins for P49610 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P49610 
Go to UniProtKB:  P49610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49610
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G85856KC
GlyCosmos:  G85856KC
GlyGen:  G85856KC
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
N [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.57α = 90
b = 109.29β = 90
c = 112.93γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2011-11-23
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-05-08
    Changes: Data collection, Database references, Structure summary