6V7I

Structure of KPC-2 bound to Vaborbactam at 1.25 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural Basis and Binding Kinetics of Vaborbactam in Class A beta-Lactamase Inhibition.

Pemberton, O.A.Tsivkovski, R.Totrov, M.Lomovskaya, O.Chen, Y.

(2020) Antimicrob Agents Chemother 64

  • DOI: https://doi.org/10.1128/AAC.00398-20
  • Primary Citation of Related Structures:  
    6V7H, 6V7I

  • PubMed Abstract: 

    Class A β-lactamases are a major cause of β-lactam resistance in Gram-negative bacteria. The recently FDA-approved cyclic boronate vaborbactam is a reversible covalent inhibitor of class A β-lactamases, including CTX-M extended-spectrum β-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity for these two enzymes, despite their similarity. A 1.0-Å crystal structure of CTX-M-14 demonstrated that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25-Å crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, as well as alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the β3 strand on the inactivation rate, as well as the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved β-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.


  • Organizational Affiliation

    Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbapenem-hydrolyzing beta-lactamase KPC290Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blakpckpc1
EC: 3.5.2.6
UniProt
Find proteins for Q9F663 (Klebsiella pneumoniae)
Explore Q9F663 
Go to UniProtKB:  Q9F663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F663
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.77α = 90
b = 59.97β = 90
c = 77.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI103158

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-08-26
    Changes: Database references
  • Version 1.3: 2020-09-30
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary