Structure of endo-beta-N-acetylglucosaminidase A

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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This is version 2.2 of the entry. See complete history


Structural basis and catalytic mechanism for the dual functional endo-beta-N-acetylglucosaminidase A

Yin, J.Li, L.Shaw, N.Li, Y.Song, J.K.Zhang, W.Xia, C.Zhang, R.Joachimiak, A.Zhang, H.-C.Wang, L.X.Liu, Z.-J.Wang, P.

(2009) PLoS One 4: e4658-e4658

  • DOI: https://doi.org/10.1371/journal.pone.0004658
  • Primary Citation of Related Structures:  
    3FHA, 3FHQ

  • PubMed Abstract: 

    Endo-beta-N-acetylglucosaminidases (ENGases) are dual specificity enzymes with an ability to catalyze hydrolysis and transglycosylation reactions. Recently, these enzymes have become the focus of intense research because of their potential for synthesis of glycopeptides. We have determined the 3D structures of an ENGase from Arthrobacter protophormiae (Endo-A) in 3 forms, one in native form, one in complex with Man(3)GlcNAc-thiazoline and another in complex with GlcNAc-Asn. The carbohydrate moiety sits above the TIM-barrel in a cleft region surrounded by aromatic residues. The conserved essential catalytic residues - E173, N171 and Y205 are within hydrogen bonding distance of the substrate. W216 and W244 regulate access to the active site during transglycosylation by serving as "gate-keepers". Interestingly, Y299F mutation resulted in a 3 fold increase in the transglycosylation activity. The structure provides insights into the catalytic mechanism of GH85 family of glycoside hydrolases at molecular level and could assist rational engineering of ENGases.

  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C [auth D],
D [auth F]
621Glutamicibacter protophormiaeMutation(s): 4 
Find proteins for Q9ZB22 (Glutamicibacter protophormiae)
Explore Q9ZB22 
Go to UniProtKB:  Q9ZB22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZB22
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranoseE [auth C],
F [auth E],
Glycosylation Resources
GlyTouCan:  G72618IM
GlyCosmos:  G72618IM
GlyGen:  G72618IM
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.328α = 80.51
b = 79.265β = 83.84
c = 117.043γ = 64.33
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-04-16
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-11-10
    Changes: Database references, Structure summary
  • Version 2.2: 2023-11-01
    Changes: Data collection, Refinement description