4WYY

Crystal Structure of P. aeruginosa AmpC

• PDB DOI: https://doi.org/10.2210/pdb4WYY/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Pseudomonas aeruginosa PAO1
• Mutation(s): No 


• Deposited: 2014-11-18 Released: 2015-08-05 
• Deposition Author(s): Ferguson, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.194 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

4,5-Disubstituted 6-Aryloxy-1,3-dihydrobenzo[c][1,2]oxaboroles Are Broad-Spectrum Serine beta-Lactamase Inhibitors.

McKinney, D.C., Zhou, F., Eyermann, C.J., Ferguson, A.D., Prince, D.B., Breen, J., Giacobbe, R.A., Lahiri, S., Verheijen, J.C.

(2015) ACS Infect Dis 1: 310-316

• PubMed: 27622821 
• DOI: https://doi.org/10.1021/acsinfecdis.5b00031
• Primary Citation of Related Structures:  
  4WYY, 4WZ4, 4WZ5


• PubMed Abstract: 
  

  Bacterially expressed β-lactamases are rapidly eroding the clinical utility of the important β-lactam class of antibacterials, significantly impairing our ability to fight serious bacterial infections. This paper describes a study of oxaborole-derived β-lactamase inhibitors in which crystal structures and computational modeling aided in the rational design of analogues with improved spectrum of activity against class A, C, and D enzymes. Crystal structures of two of these inhibitors covalently bound to two different serine β-lactamases, class C Pseudomonas aeruginosa AmpC and class D OXA-10, are described herein. Improved physicochemical properties as well as increased activity against an array of β-lactamases resulted in substantial restoration of susceptibility to ceftazidime in Escherichia coli and Klebsiella pneumoniae.

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Organizational Affiliation: 

Infection Innovative Medicines, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham Massachusetts 02451, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.26 kDa 
• Atom Count: 3,248 
• Modelled Residue Count: 360 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	360	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: ampC, PA4110 EC: 3.5.2.6
UniProt
Find proteins for P24735 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P24735  Go to UniProtKB:  P24735

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3VT	G [auth A]	[(3R)-1-hydroxy-4,5-dimethyl-6-(pyrazin-2-yloxy)-1,3-dihydro-2,1-benzoxaborol-3-yl]acetic acid C15 H15 B N2 O5 MTHDAYXINWUJNY-GFCCVEGCSA-N
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.194 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.745	α = 90
b = 70.824	β = 90
c = 106.23	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-05 
Deposition Author(s): Ferguson, A.D.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2018-04-25
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description