Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter

James S. Davies, Michael J. Currie, Rachel A. North (), Mariafrancesca Scalise, Joshua D. Wright, Jack M. Copping, Daniela M. Remus, Ashutosh Gulati, Dustin R. Morado, Sam A. Jamieson, Michael C. Newton-Vesty, Gayan S. Abeysekera, Subramanian Ramaswamy, Rosmarie Friemann, Soichi Wakatsuki, Jane R. Allison, Cesare Indiveri, David Drew, Peter D. Mace and Renwick C. J. Dobson ()
Additional contact information
James S. Davies: University of Canterbury
Michael J. Currie: University of Canterbury
Rachel A. North: University of Canterbury
Mariafrancesca Scalise: University of Calabria
Joshua D. Wright: University of Canterbury
Jack M. Copping: University of Auckland
Daniela M. Remus: University of Canterbury
Ashutosh Gulati: Stockholm University
Dustin R. Morado: Stockholm University
Sam A. Jamieson: University of Otago
Michael C. Newton-Vesty: University of Canterbury
Gayan S. Abeysekera: University of Canterbury
Subramanian Ramaswamy: Purdue University
Rosmarie Friemann: Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg
Soichi Wakatsuki: Biological Sciences Division, SLAC National Accelerator Laboratory
Jane R. Allison: University of Auckland
Cesare Indiveri: University of Calabria
David Drew: Stockholm University
Peter D. Mace: University of Otago
Renwick C. J. Dobson: University of Canterbury

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: Abstract In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 Å resolution. SiaM comprises a “transport” domain and a “scaffold” domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na+ and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an ‘elevator-with-an-operator’ mechanism.

Date: 2023
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DOI: 10.1038/s41467-023-36590-1

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