Crystal structure of Pseudomonas aeruginosa PBP3 in complex with vaborbactam

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Structural analysis of the boronic acid beta-lactamase inhibitor vaborbactam binding to Pseudomonas aeruginosa penicillin-binding protein 3.

Kumar, V.Viviani, S.L.Ismail, J.Agarwal, S.Bonomo, R.A.van den Akker, F.

(2021) PLoS One 16: e0258359-e0258359

  • DOI: https://doi.org/10.1371/journal.pone.0258359
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Antimicrobial resistance (AMR) mediated by β-lactamases is the major and leading cause of resistance to penicillins and cephalosporins among Gram-negative bacteria. β-Lactamases, periplasmic enzymes that are widely distributed in the bacterial world, protect penicillin-binding proteins (PBPs), the major cell wall synthesizing enzymes, from inactivation by β-lactam antibiotics. Developing novel PBP inhibitors with a non-β-lactam scaffold could potentially evade this resistance mechanism. Based on the structural similarities between the evolutionary related serine β-lactamases and PBPs, we investigated whether the potent β-lactamase inhibitor, vaborbactam, could also form an acyl-enzyme complex with Pseudomonas aeruginosa PBP3. We found that this cyclic boronate, vaborbactam, inhibited PBP3 (IC50 of 262 μM), and its binding to PBP3 increased the protein thermal stability by about 2°C. Crystallographic analysis of the PBP3:vaborbactam complex reveals that vaborbactam forms a covalent bond with the catalytic S294. The amide moiety of vaborbactam hydrogen bonds with N351 and the backbone oxygen of T487. The carboxyl group of vaborbactam hydrogen bonds with T487, S485, and S349. The thiophene ring and cyclic boronate ring of vaborbactam form hydrophobic interactions, including with V333 and Y503. The active site of the vaborbactam-bound PBP3 harbors the often observed ligand-induced formation of the aromatic wall and hydrophobic bridge, yet the residues involved in this wall and bridge display much higher temperature factors compared to PBP3 structures bound to high-affinity β-lactams. These insights could form the basis for developing more potent novel cyclic boronate-based PBP inhibitors to inhibit these targets and overcome β-lactamases-mediated resistance mechanisms.

  • Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan D,D-transpeptidase FtsI538Pseudomonas aeruginosaMutation(s): 0 
Gene Names: pbpBftsIftsI_2
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4D6 (Subject of Investigation/LOI)
Query on 4D6

Download Ideal Coordinates CCD File 
B [auth A]Vaborbactam
C12 H16 B N O5 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.095α = 90
b = 83.502β = 90
c = 88.419γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description