‘Enzyme ping-pong provides pointers for new antibiotics’ – Written by Charlotte Harrison, Science Writer
The specialized lipoproteins in bacteria are attractive targets for antibiotic drug discovery because of the lack of human counterparts. A new paper in Science Advances has produced high-resolution structural insights into a key bacterial lipoprotein enzyme, which will likely aid the rational design of new antibiotics.
The bacterial enzyme N-acyltransferase is a 57-kDa protein found in Gram-negative bacteria. The enzyme is the final one in the bacterial lipoprotein synthesis pathway, and is proposed to act by a ping-pong mechanism; that is, it catalyzes the acetylation of small molecules through a double displacement reaction.
In the current study, the researchers used X-ray crystallography and cryo-electron microscopy to determine the discrete structural states of the enzyme that occur as the N-acyltransferase reaction proceeded.
They obtained nine structures within the resolution range of 2.4–3.1 Å, which captured the enzyme in three states: the apo (substrate-free), Michaelis (substrate intermediate) and product complex states. The structures provided information on how N-acyltransferase engages with and transforms two substrates, and also produces and releases two products by a double-displacement mechanism.
Overall, the researchers showed that N-acyltransferase has a single active site that has evolved to sequentially bind substrates — in a way that meets structural and chemical criteria — so that the reactive parts are orientated next to the catalytic residues.
The authors note that the study validates the ping-pong mechanism and explains the molecular basis for the substrate promiscuity of N-acyltransferase. More importantly, though, they note that their findings should facilitate the structure-informed design of antibiotics with minimal off-target effects.
“New drugs are therefore badly needed and, while the journey can be a long one from providing a structural blueprint like this to developing a new drug, the precision to which we have resolved this potential target paints something of a ‘bullseye’ on that target,” said lead author Martin Caffrey in a press release.
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