Structure and mechanism of a eukaryotic ceramide synthase complex

Abstract

Ceramide synthases (CerS) catalyze ceramide formation via N‐acylation of a sphingoid base with a fatty acyl‐CoA and are attractive drug targets for treating numerous metabolic diseases and cancers. Here, we present the cryo‐EM structure of a yeast CerS complex, consisting of a catalytic Lac1 subunit and a regulatory Lip1 subunit, in complex with C26‐CoA substrate. The CerS holoenzyme exists as a dimer of Lac1‐Lip1 heterodimers. Lac1 contains a hydrophilic reaction chamber and a hydrophobic tunnel for binding the CoA moiety and C26‐acyl chain of C26‐CoA, respectively. Lip1 interacts with both the transmembrane region and the last luminal loop of Lac1 to maintain the proper acyl chain binding tunnel. A lateral opening on Lac1 serves as a potential entrance for the sphingoid base substrate. Our findings provide a template for understanding the working mechanism of eukaryotic ceramide synthases and may facilitate the development of therapeutic CerS modulators.

Structural basis of the mechanism and inhibition of a human ceramide synthase

“…In addition, while this manuscript was under review, the cryo-EM structure of yeast Lac1p bound to an acyl-CoA was reported. That structure revealed a small lateral opening in Lac1p adjacent to the active site 56 . This observation led the authors to hypothesize that it could potentially correspond to the entry route for sphingoid base substrates 56 .…”

“…That structure revealed a small lateral opening in Lac1p adjacent to the active site 56 . This observation led the authors to hypothesize that it could potentially correspond to the entry route for sphingoid base substrates 56 . However, this lateral opening is not present in our cryo-EM structures of CerS6 or in our molecular dynamics simulations.…”