7PUK

Crystal structure of Endoglycosidase E GH18 domain from Enterococcus faecalis in complex with Man5 product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of cooperative N-glycan processing by the multi-modular endoglycosidase EndoE.

Garcia-Alija, M.Du, J.J.Ordonez, I.Diz-Vallenilla, A.Moraleda-Montoya, A.Sultana, N.Huynh, C.G.Li, C.Donahue, T.C.Wang, L.X.Trastoy, B.Sundberg, E.J.Guerin, M.E.

(2022) Nat Commun 13: 1137-1137

  • DOI: https://doi.org/10.1038/s41467-022-28722-w
  • Primary Citation of Related Structures:  
    7PUJ, 7PUK, 7PUL

  • PubMed Abstract: 

    Bacteria produce a remarkably diverse range of glycoside hydrolases to metabolize glycans from the environment as a primary source of nutrients, and to promote the colonization and infection of a host. Here we focus on EndoE, a multi-modular glycoside hydrolase secreted by Enterococcus faecalis, one of the leading causes of healthcare-associated infections. We provide X-ray crystal structures of EndoE, which show an architecture composed of four domains, including GH18 and GH20 glycoside hydrolases connected by two consecutive three α-helical bundles. We determine that the GH20 domain is an exo-β-1,2-N-acetylglucosaminidase, whereas the GH18 domain is an endo-β-1,4-N-acetylglucosaminidase that exclusively processes the central core of complex-type or high-mannose-type N-glycans. Both glycoside hydrolase domains act in a concerted manner to process diverse N-glycans on glycoproteins, including therapeutic IgG antibodies. EndoE combines two enzyme domains with distinct functions and glycan specificities to play a dual role in glycan metabolism and immune evasion.


  • Organizational Affiliation

    Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903, Barakaldo, Bizkaia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-N-acetylhexosaminidaseA,
B [auth C]
435Enterococcus faecalisMutation(s): 0 
Gene Names: ndoE
EC: 3.2.1.52
UniProt
Find proteins for Q839P8 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q839P8 
Go to UniProtKB:  Q839P8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ839P8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B],
D
6N/A
Glycosylation Resources
GlyTouCan:  G28233ME
GlyCosmos:  G28233ME
GlyGen:  G28233ME
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.03α = 90
b = 54.55β = 110.36
c = 83.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI149297

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description