6MDV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

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: 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 ...

    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

    Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-beta-N-acetylglucosaminidaseA, B802Streptococcus pyogenesMutation(s): 0 
Gene Names: ndoS2
UniProt
Find proteins for T1WGN1 (Streptococcus pyogenes)
Explore T1WGN1 
Go to UniProtKB:  T1WGN1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC8N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G70903NP
GlyCosmos:  G70903NP
GlyGen:  G70903NP
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD7N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G50332IW
GlyCosmos:  G50332IW
GlyGen:  G50332IW
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], F [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




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