Structure of an endogenous mycobacterial MCE lipid transporter

To replicate inside human macrophages and cause the disease tuberculosis, Mycobacterium tuberculosis (Mtb) must scavenge a variety of nutrients from the host(1,2). The Mammalian Cell Entry (MCE) proteins are important virulence factors in Mtb(1,3), where they are encoded in large gene clusters and have been implicated in the transport of fatty acids(4–7) and cholesterol(1,4,8) across the impermeable mycobacterial cell envelope. Very little is known about how cargos are transported across this barrier, and how the ~10 proteins encoded in a mycobacterial mce gene cluster might assemble to transport cargo across the cell envelope remains unknown. Here we report the cryo-EM structure of the endogenous Mce1 fatty acid import machine from Mycobacterium smegmatis, a non-pathogenic relative of Mtb. The structure reveals how the proteins of the Mce1 system assemble to form an elongated ABC transporter complex, long enough to span the cell envelope. The Mce1 complex is dominated by a curved, needle-like domain that appears to be unrelated to previously described protein structures, and creates a protected hydrophobic pathway for lipid transport across the periplasm. Unexpectedly, our structural data revealed the presence of a previously unknown subunit of the Mce1 complex, which we identified using a combination of cryo-EM and AlphaFold2, and name LucB. Our data lead to a structural model for Mce1-mediated fatty acid import across the mycobacterial cell envelope.