9FZP

Pseudomonas aeruginosa penicillin binding protein 3 in complex with cefepime


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Structural basis of Pseudomonas aeruginosa penicillin binding protein 3 inhibition by the siderophore-antibiotic cefiderocol.

Smith, H.G.Basak, S.Aniebok, V.Beech, M.J.Alshref, F.M.Allen, M.D.Farley, A.J.M.Schofield, C.J.

(2024) Chem Sci 

  • DOI: https://doi.org/10.1039/d4sc04937c
  • Primary Citation of Related Structures:  
    9FZ7, 9FZ8, 9FZE, 9FZO, 9FZP

  • PubMed Abstract: 

    The breakthrough cephalosporin cefiderocol, approved for clinical use in 2019, has activity against many Gram-negative bacteria. The catechol group of cefiderocol enables it to efficiently enter bacterial cells via the iron/siderophore transport system thereby reducing resistance due to porin channel mutations and efflux pump upregulation. Limited information is reported regarding the binding of cefiderocol to its key proposed target, the transpeptidase penicillin binding protein 3 (PBP3). We report studies on the reaction of cefiderocol and the related cephalosporins ceftazidime and cefepime with Pseudomonas aeruginosa PBP3, including inhibition measurements, protein observed mass spectrometry, and X-ray crystallography. The three cephalosporins form analogous 3-exomethylene products with P. aeruginosa PBP3 following elimination of the C3' side chain. pIC 50 and k inact / K i measurements with isolated PBP3 imply ceftazidime and cefiderocol react less efficiently than cefepime and, in particular, meropenem with P. aeruginosa PBP3. Crystal structures inform on conserved and different interactions involved in binding of the three cephalosporins and meropenem to P. aeruginosa PBP3. The results will aid development of cephalosporins with improved PBP3 inhibition properties.


  • Organizational Affiliation

    Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK christopher.schofield@chem.ox.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan D,D-transpeptidase FtsI517Pseudomonas aeruginosaMutation(s): 0 
Gene Names: ftsIpbpBPA4418
EC: 3.4.16.4
UniProt
Find proteins for G3XD46 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD46 
Go to UniProtKB:  G3XD46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3XD46
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CEF (Subject of Investigation/LOI)
Query on CEF

Download Ideal Coordinates CCD File 
B [auth A]CEFOTAXIME, C3' cleaved, open, bound form
C14 H15 N5 O5 S2
NRYMPLKBKFIWQC-YVCCLBOHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.303α = 90
b = 88.467β = 90
c = 82.008γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateIneos Oxford Institute (UK)

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release