4ZBE

Crystal structure of KPC-2 beta-lactamase complexed with avibactam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Inhibition of Klebsiella beta-Lactamases (SHV-1 and KPC-2) by Avibactam: A Structural Study.

Krishnan, N.P.Nguyen, N.Q.Papp-Wallace, K.M.Bonomo, R.A.van den Akker, F.

(2015) Plos One 10: e0136813-e0136813

  • DOI: 10.1371/journal.pone.0136813
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • β-Lactamase inhibition is an important clinical strategy in overcoming β-lactamase-mediated resistance to β-lactam antibiotics in Gram negative bacteria. A new β-lactamase inhibitor, avibactam, is entering the clinical arena and promising to be a maj ...

    β-Lactamase inhibition is an important clinical strategy in overcoming β-lactamase-mediated resistance to β-lactam antibiotics in Gram negative bacteria. A new β-lactamase inhibitor, avibactam, is entering the clinical arena and promising to be a major step forward in our antibiotic armamentarium. Avibactam has remarkable broad-spectrum activity in being able to inhibit classes A, C, and some class D β-lactamases. We present here structural investigations into class A β-lactamase inhibition by avibactam as we report the crystal structures of SHV-1, the chromosomal penicillinase of Klebsiella pneumoniae, and KPC-2, an acquired carbapenemase found in the same pathogen, complexed with avibactam. The 1.80 Å KPC-2 and 1.42 Å resolution SHV-1 β-lactamase avibactam complex structures reveal avibactam covalently bonded to the catalytic S70 residue. Analysis of the interactions and chair-shaped conformation of avibactam bound to the active sites of KPC-2 and SHV-1 provides structural insights into recently laboratory-generated amino acid substitutions that result in resistance to avibactam in KPC-2 and SHV-1. Furthermore, we observed several important differences in the interactions with amino acid residues, in particular that avibactam forms hydrogen bonds to S130 in KPC-2 but not in SHV-1, that can possibly explain some of the different kinetic constants of inhibition. Our observations provide a possible reason for the ability of KPC-2 β-lactamase to slowly desulfate avibactam with a potential role for the stereochemistry around the N1 atom of avibactam and/or the presence of an active site water molecule that could aid in avibactam desulfation, an unexpected consequence of novel inhibition chemistry.


    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbapenem-hydrolyzing beta-lactamase KPC
A
264Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bla (kpc, kpc1)
EC: 3.5.2.6
Find proteins for Q9F663 (Klebsiella pneumoniae)
Go to UniProtKB:  Q9F663
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
NXL
Query on NXL

Download SDF File 
Download CCD File 
A
(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
avibactam, bound form, NXL104, bound form
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.315α = 90.00
b = 66.695β = 90.00
c = 73.208γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release