9LR5 | pdb_00009lr5

Crystal structure of Bacteroides thetaiotaomicron GH84 O-GlcNAcase D243N mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.297 (Depositor), 0.297 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

beta 1,6-Selective Enzymatic N-Acetylglucosamination Catalyzed by the Family GH84 N-Acetyl-beta-D-glucosaminidase from Bacteroides thetaiotaomicron and its Glycosyl Acceptor Specificity.

Okuno, R.Nakada, S.Tonomura, K.Aso, Y.Takeshita, D.Ohnuma, T.Tanaka, T.

(2025) Chem Asian J 20: e202500142-e202500142

  • DOI: https://doi.org/10.1002/asia.202500142
  • Primary Citation of Related Structures:  
    9LR5

  • PubMed Abstract: 

    The chemoenzymatic synthesis of oligosaccharides presents a highly attractive methodology with significant potential for diverse applications, particularly through using various glycosidases. In this study, the O-glycan core 6 disaccharide moiety, GlcNAcβ1-6GalNAc, was successfully synthesized via enzymatic glycosylation using an N-acetyl-β-D-glucosaminidase from Bacteroides thetaiotaomicron (BtOGA), a member of glycoside hydrolase family 84 (GH84), alongside an N-acetyl-D-glucosamine oxazoline derivative (GlcNAc-oxa) as the glycosyl donor. Furthermore, an investigation into glycosyl acceptor recognition in BtOGA-catalyzed enzymatic glycosylation indicated that the presence of an aromatic group at the anomeric position and an axial hydroxy group at the 4-position of the saccharide moiety is crucial for effective recognition of BtOGA as a glycosyl acceptor. The protecting-group-free chemoenzymatic synthesis of the core 6 disaccharide moiety was achieved by integrating the direct synthesis of GlcNAc-oxa thorough Shoda activation method using a water-soluble dehydration condensing agent in an aqueous medium, followed by BtOGA-catalyzed enzymatic glycosylation.


  • Organizational Affiliation
    • Department of Biobased Materials Science, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-GlcNAcase BT_4395723Bacteroides thetaiotaomicron VPI-5482Mutation(s): 1 
Gene Names: BT_4395
EC: 3.2.1.169
UniProt
Find proteins for Q89ZI2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q89ZI2 
Go to UniProtKB:  Q89ZI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89ZI2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.297 (Depositor), 0.297 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.136α = 90
b = 52.787β = 97.44
c = 79.827γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Database references