6K35

Crystal structure of GH20 exo beta-N-acetylglucosaminidase from Vibrio harveyi in complex with NAG-thiazoline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

NAG-thiazoline is a potent inhibitor of the Vibrio campbellii GH20 beta-N-Acetylglucosaminidase.

Meekrathok, P.Stubbs, K.A.Aunkham, A.Kaewmaneewat, A.Kardkuntod, A.Bulmer, D.M.van den Berg, B.Suginta, W.

(2020) FEBS J 287: 4982-4995

  • DOI: https://doi.org/10.1111/febs.15283
  • Primary Citation of Related Structures:  
    6K35

  • PubMed Abstract: 

    Vibrio spp. play a vital role in the recycling of chitin in oceans, but several Vibrio strains are highly infectious to aquatic animals and humans. These bacteria require chitin for growth; thus, potent inhibitors of chitin-degrading enzymes could serve as candidate drugs against Vibrio infections. This study examined NAG-thiazoline (NGT)-mediated inhibition of a recombinantly expressed GH20 β-N-acetylglucosaminidase, namely VhGlcNAcase from Vibrio campbellii (formerly V. harveyi) ATCC BAA-1116. NGT strongly inhibited VhGlcNAcase with an IC 50 of 11.9 ± 1.0 μm and K i 62 ± 3 µm, respectively. NGT was also found to completely inhibit the growth of V. campbellii strain 650 with an minimal inhibitory concentration value of 0.5 µm. ITC data analysis showed direct binding of NGT to VhGlcNAcase with a K d of 32 ± 1.2 μm. The observed ΔG° binding of -7.56 kcal·mol -1 is the result of a large negative enthalpy change and a small positive entropic compensation, suggesting that NGT binding is enthalpy-driven. The structural complex shows that NGT fully occupies the substrate-binding pocket of VhGlcNAcase and makes an exclusive hydrogen bond network, as well as hydrophobic interactions with the conserved residues around the -1 subsite. Our results strongly suggest that NGT could serve as an excellent scaffold for further development of antimicrobial agents against Vibrio infections. DATABASE: Structural data are available in PDB database under the accession number 6K35.


  • Organizational Affiliation

    School of Chemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-N-acetylglucosaminidase Nag2
A, B
652Vibrio harveyiMutation(s): 0 
EC: 3.2.1.52
UniProt
Find proteins for D9ISE0 (Vibrio harveyi)
Explore D9ISE0 
Go to UniProtKB:  D9ISE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9ISE0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGT (Subject of Investigation/LOI)
Query on NGT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
C8 H13 N O4 S
DRHXTSWSUAJOJZ-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.34α = 90
b = 145.04β = 109.66
c = 88.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description