In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D β-lactamases

ACS Infect Dis. 2021 Jun 11;7(6):1765-1776. doi: 10.1021/acsinfecdis.1c00094. Epub 2021 Apr 28.

Abstract

Class D β-lactamases have risen to notoriety due to their wide spread in bacterial pathogens, propensity to inactivate clinically important β-lactam antibiotics, and ability to withstand inhibition by the majority of classical β-lactamase inhibitors. Understanding the catalytic mechanism of these enzymes is thus vitally important for the development of novel antibiotics and inhibitors active against infections caused by antibiotic-resistant bacteria. Here we report an in crystallo time-resolved study of the interaction of the class D β-lactamase CDD-1 from Clostridioides difficile with the diazobicyclooctane inhibitor, avibactam. We show that the catalytic carboxylated lysine, a residue that is essential for both acylation and deacylation of β-lactams, is sequestered within an internal sealed pocket of the enzyme. Time-resolved snapshots generated in this study allowed us to observe decarboxylation of the lysine and movement of CO2 and water molecules through a transient channel formed between the lysine pocket and the substrate binding site facilitated by rotation of the side chain of a conserved leucine residue. These studies provide novel insights on avibactam binding to CDD-1 and into the catalytic mechanism of class D β-lactamases in general.

Keywords: avibactam; catalytic mechanism; crystal structure; inhibition; β-lactamase.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Azabicyclo Compounds
  • Clostridioides*
  • Models, Molecular
  • beta-Lactamases* / genetics

Substances

  • Azabicyclo Compounds
  • avibactam
  • beta-Lactamases