5UTR

Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-butyryl-4,5,6-trihydroxyazepane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress beta-lactam antibiotic resistance.

Vadlamani, G.Stubbs, K.A.Desire, J.Bleriot, Y.Vocadlo, D.J.Mark, B.L.

(2017) Protein Sci. 26: 1161-1170

  • DOI: 10.1002/pro.3166
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NagZ is an N-acetyl-β-d-glucosaminidase that participates in the peptidoglycan (PG) recycling pathway of Gram-negative bacteria by removing N-acetyl-glucosamine (GlcNAc) from PG fragments that have been excised from the cell wall during growth. The 1 ...

    NagZ is an N-acetyl-β-d-glucosaminidase that participates in the peptidoglycan (PG) recycling pathway of Gram-negative bacteria by removing N-acetyl-glucosamine (GlcNAc) from PG fragments that have been excised from the cell wall during growth. The 1,6-anhydromuramoyl-peptide products generated by NagZ activate β-lactam resistance in many Gram-negative bacteria by inducing the expression of AmpC β-lactamase. Blocking NagZ activity can thereby suppress β-lactam antibiotic resistance in these bacteria. The NagZ active site is dynamic and it accommodates distortion of the glycan substrate during catalysis using a mobile catalytic loop that carries a histidine residue which serves as the active site general acid/base catalyst. Here, we show that flexibility of this catalytic loop also accommodates structural differences in small molecule inhibitors of NagZ, which could be exploited to improve inhibitor specificity. X-ray structures of NagZ bound to the potent yet non-selective N-acetyl-β-glucosaminidase inhibitor PUGNAc (O-(2-acetamido-2-deoxy-d-glucopyranosylidene) amino-N-phenylcarbamate), and two NagZ-selective inhibitors - EtBuPUG, a PUGNAc derivative bearing a 2-N-ethylbutyryl group, and MM-156, a 3-N-butyryl trihydroxyazepane, revealed that the phenylcarbamate moiety of PUGNAc and EtBuPUG completely displaces the catalytic loop from the NagZ active site to yield a catalytically incompetent form of the enzyme. In contrast, the catalytic loop was found positioned in the catalytically active conformation within the NagZ active site when bound to MM-156, which lacks the phenylcarbamate extension. Displacement of the catalytic loop by PUGNAc and its N-acyl derivative EtBuPUG alters the active site conformation of NagZ, which presents an additional strategy to improve the potency and specificity of NagZ inhibitors.


    Organizational Affiliation

    Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3T2N2.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-hexosaminidase
A, B
350Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)Mutation(s): 0 
Gene Names: nagZ1 (nagZ, nagZ2)
EC: 3.2.1.52
Find proteins for B4EA43 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Go to UniProtKB:  B4EA43
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8MP
Query on 8MP

Download SDF File 
Download CCD File 
A, B
N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]butanamide
C10 H20 N2 O4
SWEITPYHDWSHKI-AKEJEFCPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.139 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.660α = 90.00
b = 87.820β = 91.92
c = 66.970γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHASERphasing
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Author supporting evidence