8URA | pdb_00008ura

Crystal structure of Corynebacterium ulcerans endo-beta-N-acetylglucosaminidase catalytically inactive CU43 D187A-E189A at 2.6 A resolution (space group P21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8URA

This is version 1.2 of the entry. See complete history

Literature

Potent efficacy of an IgG-specific endoglycosidase against IgG-mediated pathologies.

Sastre, D.E.Bournazos, S.Du, J.Boder, E.J.Edgar, J.E.Azzam, T.Sultana, N.Huliciak, M.Flowers, M.Yoza, L.Xu, T.Chernova, T.A.Ravetch, J.V.Sundberg, E.J.

(2024) Cell 187: 6994

  • DOI: https://doi.org/10.1016/j.cell.2024.09.038
  • Primary Citation Related Structures: 
    8UEN, 8URA

  • PubMed Abstract: 

    Endo-β-N-acetylglucosaminidases (ENGases) that specifically hydrolyze the Asn297-linked glycan on immunoglobulin G (IgG) antibodies, the major molecular determinant of fragment crystallizable (Fc) γ receptor (FcγR) binding, are exceedingly rare. All previously characterized IgG-specific ENGases are multi-domain proteins secreted as an immune evasion strategy by Streptococcus pyogenes strains. Here, using in silico analysis and mass spectrometry techniques, we identified a family of single-domain ENGases secreted by pathogenic corynebacterial species that exhibit strict specificity for IgG antibodies. By X-ray crystallographic and surface plasmon resonance analyses, we found that the most catalytically efficient IgG-specific ENGase family member recognizes both protein and glycan components of IgG. Employing in vivo models, we demonstrated the remarkable efficacy of this IgG-specific ENGase in mitigating numerous pathologies that rely on FcγR-mediated effector functions, including T and B lymphocyte depletion, autoimmune hemolytic anemia, and antibody-dependent enhancement of dengue disease, revealing its potential for treating and/or preventing a wide range of IgG-mediated diseases in humans.


  • Organizational Affiliation
    • Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA. Electronic address: dsastre@emory.edu.

Macromolecule Content 

  • Total Structure Weight: 92.21 kDa 
  • Atom Count: 5,145 
  • Modeled Residue Count: 647 
  • Deposited Residue Count: 830 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Corynebacterial protease CP40
A, B
415Corynebacterium ulceransMutation(s): 2 
Gene Names: cppCULC0211_20780

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.514α = 90
b = 70.897β = 92.53
c = 73.734γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Database references
  • Version 1.2: 2024-12-11
    Changes: Database references