8PCI

Structure of serine-beta-lactamase CTX-M-14 following the time-resolved active site binding of boric acid, 5000 ms

Summary for 8PCI

• Entry DOI: 10.2210/pdb8pci/pdb
• Descriptor: Beta-lactamase, BORATE ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: catalytic activity, beta-lactamase activity, hydrolase activity, inhibitor, time-resolved, tape drive, hydrolase
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 28175.45

Authors

Prester, A.,Perbandt, M.,Galchenkova, M.,Oberthuer, D.,Yefanov, O.,Hinrichs, W.,Rohde, H.,Betzel, C. (deposition date: 2023-06-11, release date: 2024-06-26, Last modification date: 2024-11-06)

Primary citation

Prester, A.,Perbandt, M.,Galchenkova, M.,Oberthuer, D.,Werner, N.,Henkel, A.,Maracke, J.,Yefanov, O.,Hakanpaa, J.,Pompidor, G.,Meyer, J.,Chapman, H.,Aepfelbacher, M.,Hinrichs, W.,Rohde, H.,Betzel, C.
Time-resolved crystallography of boric acid binding to the active site serine of the beta-lactamase CTX-M-14 and subsequent 1,2-diol esterification.
Commun Chem, 7:152-152, 2024

PubMed Abstract: The emergence and spread of antibiotic resistance represent a growing threat to public health. Of particular concern is the appearance of β-lactamases, which are capable to hydrolyze and inactivate the most important class of antibiotics, the β-lactams. Effective β-lactamase inhibitors and mechanistic insights into their action are central in overcoming this type of resistance, and in this context boronate-based β-lactamase inhibitors were just recently approved to treat multidrug-resistant bacteria. Using boric acid as a simplified inhibitor model, time-resolved serial crystallography was employed to obtain mechanistic insights into binding to the active site serine of β-lactamase CTX-M-14, identifying a reaction time frame of 80-100 ms. In a next step, the subsequent 1,2-diol boric ester formation with glycerol in the active site was monitored proceeding in a time frame of 100-150 ms. Furthermore, the displacement of the crucial anion in the active site of the β-lactamase was verified as an essential part of the binding mechanism of substrates and inhibitors. In total, 22 datasets of β-lactamase intermediate complexes with high spatial resolution of 1.40-2.04 Å and high temporal resolution range of 50-10,000 ms were obtained, allowing a detailed analysis of the studied processes. Mechanistic details captured here contribute to the understanding of molecular processes and their time frames in enzymatic reactions. Moreover, we could demonstrate that time-resolved crystallography can serve as an additional tool for identifying and investigating enzymatic reactions.

PubMed: 38969718
DOI: 10.1038/s42004-024-01236-w

Experimental method

X-RAY DIFFRACTION (1.5 Å)