3FHA

Structure of endo-beta-N-acetylglucosaminidase A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-beta-N-acetylglucosaminidase
A, B, C, D
621Glutamicibacter protophormiaeMutation(s): 3 
EC: 3.2.1.96
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B],
K [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
L [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.892α = 84.23
b = 78.972β = 80.77
c = 117.267γ = 64.01
Software Package:
Software NamePurpose
HKL-2000data collection
OASISmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
OASISphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-29
    Changes: Data collection