Structural Basis for the Recognition of Mycolic Acid Precursors by KasA, a Condensing Enzyme and Drug Target from Mycobacterium Tuberculosis

Background: Although induced fit binding is central to molecular recognition, in most cases, the structural basis for this process remains to be elucidated. Results: We determined structural snapshots along the substrate binding reaction coordinate for the drug target Mycobacterium tuberculosis KasA. Conclusion: KasA binds acyl substrates via the induced fit concerted opening of a hydrophobic cavity. Significance: Improved understanding of induced fit binding is crucial for inhibitor design. The survival of Mycobacterium tuberculosis depends on mycolic acids, very long -alkyl--hydroxy fatty acids comprising 60-90 carbon atoms. However, despite considerable efforts, little is known about how enzymes involved in mycolic acid biosynthesis recognize and bind their hydrophobic fatty acyl substrates. The condensing enzyme KasA is pivotal for the synthesis of very long (C38-42) fatty acids, the precursors of mycolic acids. To probe the mechanism of substrate and inhibitor recognition by KasA, we determined the structure of this protein in complex with a mycobacterial phospholipid and with several thiolactomycin derivatives that were designed as substrate analogs. Our structures provide consecutive snapshots along the reaction coordinate for the enzyme-catalyzed reaction and support an induced fit mechanism in which a wide cavity is established through the concerted opening of three gatekeeping residues and several -helices. The stepwise characterization of the binding process provides mechanistic insights into the induced fit recognition in this system and serves as an excellent foundation for the development of high affinity KasA inhibitors.