5G5K

Crystal structure of NagZ from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa.

Acebron, I.Mahasenan, K.V.De Benedetti, S.Lee, M.Artola-Recolons, C.Hesek, D.Wang, H.Hermoso, J.A.Mobashery, S.

(2017) J. Am. Chem. Soc. 139: 6795-6798

  • DOI: 10.1021/jacs.7b01626
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The N-acetylglucosaminidase NagZ of Pseudomonas aeruginosa catalyzes the first cytoplasmic step in recycling of muropeptides, cell-wall-derived natural products. This reaction regulates gene expression for the β-lactam resistance enzyme, β-lactamase. ...

    The N-acetylglucosaminidase NagZ of Pseudomonas aeruginosa catalyzes the first cytoplasmic step in recycling of muropeptides, cell-wall-derived natural products. This reaction regulates gene expression for the β-lactam resistance enzyme, β-lactamase. The enzyme catalyzes hydrolysis of N-acetyl-β-d-glucosamine-(1→4)-1,6-anhydro-N-acetyl-β-d-muramyl-peptide (1) to N-acetyl-β-d-glucosamine (2) and 1,6-anhydro-N-acetyl-β-d-muramyl-peptide (3). The structural and functional aspects of catalysis by NagZ were investigated by a total of seven X-ray structures, three computational models based on the X-ray structures, molecular-dynamics simulations and mutagenesis. The structural insights came from the unbound state and complexes of NagZ with the substrate, products and a mimetic of the transient oxocarbenium species, which were prepared by synthesis. The mechanism involves a histidine as acid/base catalyst, which is unique for glycosidases. The turnover process utilizes covalent modification of D244, requiring two transition-state species and is regulated by coordination with a zinc ion. The analysis provides a seamless continuum for the catalytic cycle, incorporating large motions by four loops that surround the active site.


    Organizational Affiliation

    Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid, Spain.,Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-HEXOSAMINIDASE
A, B
352Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: nagZ
EC: 3.2.1.52
Find proteins for Q9HZK0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HZK0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NOK
Query on NOK

Download SDF File 
Download CCD File 
A, B
2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN
C8 H16 N2 O4
GBRAQQUMMCVTAV-LXGUWJNJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.224α = 90.00
b = 67.607β = 97.83
c = 74.064γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-05-24
    Type: Database references
  • Version 1.2: 2017-05-31
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Data collection