Special enzyme drives new class of antibiotics

Understanding how antibiotic scaffolds are constructed in nature can help scientists prospect for new classes of antibiotics through DNA sequencing and genome mining. Researchers have used this knowledge to help solve the X-ray crystal structure of the enzyme that makes obafluorin -- a broad spectrum antibiotic agent made by a fluorescent strain of soil bacteria. The new work is from Washington University in St. Louis and the University at Buffalo.

A multi-part enzyme called a nonribosomal peptide synthetase produces the highly reactive beta-lactone ring that is responsible for obafluorin's antimicrobial activity. These chemicals could be used as next-generation antibiotics for humans, or even to benefit the agriculture sector.

The new work provides a useful road map that shows how individual protein domains in the ObiF1 enzyme are stitched together in three-dimensional space. An enzyme's structure is fundamental to almost every function it performs.

Obafluorin is made by a fluorescent strain of soil bacteria that forms biofilms on plant roots. Like penicillin, obafluorin has a four-membered ring -- sometimes called an enchanted ring. A four-membered ring puts strain on bond angles that carbon prefers to adopt. But because a four-member ring is unstable, these molecules are also short-lived and difficult to make. For example, it took years for chemists to learn how to synthesize penicillin from chemicals and then figure out how fungi make it. This ultimately led to the global production of penicillin by fermentation.

Researchers were able to fast-track the discovery process using genetics to zero in on the biosynthetic machinery that bacteria use to make obafluorin, and then to reconstruct that multi-step, enzyme-catalyzed process in the laboratory.

The result is a comprehensive, detailed molecular structure at 3 Angstrom resolution that allows one to identify the atoms in the protein chain, see their location and points of contact along the chain, and determine how the pieces are assembled to produce useful molecules from start to finish.

One particular component -- something called an MbtH-like protein, or MLP, because it was first identified in a related system to produce mycobactin in the bacteria that causes tuberculosis -- was shown to play a critical role in facilitating protein-to-protein interactions between catalytic domains.

See:

Dale F. Kreitler, Erin M. Gemmell, Jason E. Schaffer, Timothy A. Wencewicz, Andrew M. Gulick. The structural basis of N-acyl-α-amino-β-lactone formation catalyzed by a nonribosomal peptide synthetase. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-11383-7

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology