Molecular determinants of Neu5Ac binding to a tripartite ATP independent periplasmic (TRAP) transporter

N -Acetylneuraminic acid (Neu5Ac) is a negatively charged nine-carbon amino-sugar that is often the peripheral sugar in human cell-surface glycoconjugates. Some bacteria scavenge, import, and metabolize Neu5Ac, or they redeploy it on their cell surfaces for immune evasion. The import of Neu5Ac by many bacteria is mediated by tripartite ATP-independent periplasmic (TRAP) transporters. We have previously reported the structures of SiaQM, a membrane-embedded component of the Haemophilus influenzae TRAP transport system (Currie, M J, et. al 2024). However, the published structures do not contain Neu5Ac bound to SiaQM. This information is critical for defining the mechanism of transport and for further structure-activity relationship studies. Here, we report the structure of Fusobacterium nucleatum SiaQM with and without Neu5Ac binding. Both structures are in an inward (cytoplasmic side) facing conformation. The Neu5Ac-bound structure reveals the interactions of Neu5Ac with the transporter and its relationship with the Na ⁺ binding sites. Two of the Na ⁺ -binding sites are similar to those described previously. We discover the presence of a third metal-binding site that is further away and buried in the elevator domain. Ser300 and Ser345 interact with the C1-carboxylate group of Neu5Ac. Proteoliposome-based transport assays showed that Ser300-Neu5Ac interaction is critical for transport, whereas Ser345 is dispensable. Neu5Ac primarily interacts with residues in the elevator domain of the protein, thereby supporting the elevator with an operator mechanism. The residues interacting with Neu5Ac are conserved, providing fundamental information required to design inhibitors against this class of proteins.