Crystal structure of Streptococcus pyogenes endo-beta-N-acetylglucosaminidase (EndoS2) with high-mannose glycan

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Molecular Basis of Broad SpectrumN-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2.

Klontz, E.H.Trastoy, B.Deredge, D.Fields, J.K.Li, C.Orwenyo, J.Marina, A.Beadenkopf, R.Gunther, S.Flores, J.Wintrode, P.L.Wang, L.X.Guerin, M.E.Sundberg, E.J.

(2019) ACS Cent Sci 5: 524-538

  • DOI: https://doi.org/10.1021/acscentsci.8b00917
  • Primary Citation of Related Structures:  
    6E58, 6MDS, 6MDV

  • PubMed Abstract: 

    Immunoglobulin G (IgG) glycosylation critically modulates antibody effector functions. Streptococcus pyogenes secretes a unique endo-β- N -acetylglucosaminidase, EndoS2, which deglycosylates the conserved N -linked glycan at Asn297 on IgG Fc to eliminate its effector functions and evade the immune system. EndoS2 and specific point mutants have been used to chemoenzymatically synthesize antibodies with customizable glycosylation for gain of functions. EndoS2 is useful in these schemes because it accommodates a broad range of N -glycans, including high-mannose, complex, and hybrid types; however, its mechanism of substrate recognition is poorly understood. We present crystal structures of EndoS2 alone and bound to complex and high-mannose glycans; the broad N -glycan specificity is governed by critical loops that shape the binding site of EndoS2. Furthermore, hydrolytic experiments, domain-swap chimeras, and hydrogen-deuterium exchange mass spectrometry reveal the importance of the carbohydrate-binding module in the mechanism of IgG recognition by EndoS2, providing insights into engineering enzymes to catalyze customizable glycosylation reactions.

  • Organizational Affiliation

    Institute of Human Virology, Department of Microbiology & Immunology, and Program in Molecular Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
802Streptococcus pyogenesMutation(s): 0 
Gene Names: ndoS2
Find proteins for T1WGN1 (Streptococcus pyogenes serotype M49)
Explore T1WGN1 
Go to UniProtKB:  T1WGN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1WGN1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G70903NP
GlyCosmos:  G70903NP
GlyGen:  G70903NP
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G50332IW
GlyCosmos:  G50332IW
GlyGen:  G50332IW
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.966α = 90
b = 105.353β = 90
c = 257.298γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary