7KCY

Crystal structure of S. aureus penicillin-binding protein 4 (PBP4) with cefoxitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

PBP4-mediated beta-lactam resistance among clinical strains of Staphylococcus aureus.

Satishkumar, N.Alexander, J.A.N.Poon, R.Buggeln, E.Argudin, M.A.Strynadka, N.C.J.Chatterjee, S.S.

(2021) J Antimicrob Chemother 76: 2268-2272

  • DOI: https://doi.org/10.1093/jac/dkab201
  • Primary Citation of Related Structures:  
    7KCV, 7KCW, 7KCX, 7KCY

  • PubMed Abstract: 

    PBP4, a low-molecular-weight PBP in Staphylococcus aureus, is not considered to be a classical mediator of β-lactam resistance. Previous studies carried out by our group with laboratory strains of S. aureus demonstrated the ability of PBP4 to produce β-lactam resistance through mutations associated with the pbp4 promoter and/or gene. Recent studies of β-lactam-resistant clinical isolates of S. aureus have reported similar mutations associated with pbp4. To determine if pbp4-associated mutations reported among clinical strains of S. aureus mediate β-lactam resistance. The pbp4 promoters and genes bearing mutations from clinical isolates were cloned into a heterologous host. Reporter, growth and Bocillin assays were performed to assess their role in β-lactam resistance. X-ray crystallography was used to obtain acyl-enzyme intermediate structures of the WT and mutant PBP4 with nafcillin and cefoxitin. Of the five strains that contained pbp4 promoter mutations, three strains exhibited enhanced expression of PBP4. The R200L mutation in pbp4 resulted in increased survival in the presence of the β-lactams nafcillin and cefoxitin. Further, introduction of either a promoter or a gene mutation into the genome of a WT host increased the ability of the strains to resist the action of β-lactams. The four high-resolution X-ray structures presented demonstrate the binding pose of the β-lactams tested and provide hints for further drug development. Mutations associated with the pbp4 promoter and pbp4 gene altered protein activity and mediated β-lactam resistance among the clinically isolated strains that were studied.


  • Organizational Affiliation

    Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 4367Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: pbp4SACOL0699
UniProt
Find proteins for A0A0H2WY27 (Staphylococcus aureus (strain COL))
Explore A0A0H2WY27 
Go to UniProtKB:  A0A0H2WY27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2WY27
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1S7 (Subject of Investigation/LOI)
Query on 1S7

Download Ideal Coordinates CCD File 
B [auth A](2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
C15 H16 N2 O5 S2
BMQDZZSQSZJJQV-CABCVRRESA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.16α = 90
b = 83.01β = 90
c = 103.64γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2021-09-29
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary