PDBsum entry 7meh

Hydrolase/inhibitor

PDB id: 7meh

Contents

Protein chain

250 a.a.

Ligands

NXL

SO4 ×3

MPD ×2

IMD ×2

Waters ×190

PDB id:

7meh

Name:

Hydrolase/inhibitor

Title:

Cdd-1 beta-lactamase in imidazole/mpd 60 minute avibactam complex

Structure:

Beta-lactamase. Chain: a. Synonym: cdd-1 beta-lactamase. Engineered: yes. Mutation: yes. Other_details: double lysine to alanine mutant lys238ala and lys244ala

Source:

Clostridioides difficile. Peptoclostridium difficile. Organism_taxid: 1496. Gene: blar1_1, e5f32_07085, e5f39_11445, samea3374989_01677. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.186 R-free: 0.228

Authors:

C.A.Smith,S.B.Vakulenko

Key ref:

N.K.Stewart et al. (2021). 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, 7, 1765-1776. PubMed id: 33908775 DOI: 10.1021/acsinfecdis.1c00094

Date:

06-Apr-21 Release date: 16-Feb-22

Protein chain

A0A160YKM3  () -

Enzyme reactions

• Enzyme class: E.C.3.5.2.6 - beta-lactamase.
• Pathway: Penicillin Biosynthesis and Metabolism
• Reaction: a beta-lactam + H2O = a substituted beta-amino acid
• Cofactor: Zn(2+)

DOI no: 10.1021/acsinfecdis.1c00094

ACS Infect Dis 7:1765-1776 (2021)

PubMed id: 33908775

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.

N.K.Stewart, M.Toth, A.Stasyuk, S.B.Vakulenko, C.A.Smith.

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.