Interdomain-linkers control conformational transitions in the SLC23 elevator transporter UraA

• Published in: Nature communications Vol. 15; no. 1; pp. 7518 - 12
• Main Authors: Kuhn, Benedikt T., Zöller, Jonathan, Zimmermann, Iwan, Gemeinhardt, Tim, Özkul, Dogukan H., Langer, Julian D., Seeger, Markus A., Geertsma, Eric R.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.08.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/45/173; 631/45/535; 82/1; 82/58; 82/80; 82/83; Ascorbic acid; Ascorbic Acid - chemistry; Ascorbic Acid - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Bases (nucleic acids); Biological Transport; Deuterium; Humanities and Social Sciences; Hydrogen Deuterium Exchange-Mass Spectrometry; Hydrogen-deuterium exchange; Mass spectrometry; Mass spectroscopy; Membrane Transport Proteins - chemistry; Membrane Transport Proteins - metabolism; Models, Molecular; multidisciplinary; Nanobodies; Protein Conformation; Protein Domains; Protein transport; Proteins; Science; Science (multidisciplinary); Solutes; Substrate preferences; Substrates; Tethers; Transport rate
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-51814-8

Uptake of nucleobases and ascorbate is an essential process in all living organisms mediated by SLC23 transport proteins. These transmembrane carriers operate via the elevator alternating-access mechanism, and are composed of two rigid domains whose relative motion drives transport. The lack of large conformational changes within these domains suggests that the interdomain-linkers act as flexible tethers. Here, we show that interdomain-linkers are not mere tethers, but have a key regulatory role in dictating the conformational space of the transporter and defining the rotation axis of the mobile transport domain. By resolving a wide inward-open conformation of the SLC23 elevator transporter UraA and combining biochemical studies using a synthetic nanobody as conformational probe with hydrogen-deuterium exchange mass spectrometry, we demonstrate that interdomain-linkers control the function of transport proteins by influencing substrate affinity and transport rate. These findings open the possibility to allosterically modulate the activity of elevator proteins by targeting their linkers. Elevator transporters, like SLC23 proteins, transport solutes by a mechanism involving a reorientation of two rigid domains. Here, the authors show that linkers connecting these domains control the carrier’s conformational space and thus its function.