On the function of TRAP substrate-binding proteins: Conformational variation of the sialic acid binding protein SiaP.

Autor: King-Hudson TJ; Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand., Davies JS; Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Computational and Structural Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia. Electronic address: j.davies@victorchang.edu.au., Quan S; Biomolecular Interaction Centre, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of Auckland, Auckland, New Zealand., Currie MJ; Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand., Tillett ZD; Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand., Copping J; Biomolecular Interaction Centre, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of Auckland, Auckland, New Zealand., Panjikar S; Australian Synchrotron, ANSTO, Clayton, Victoria, Australia; Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Victoria, Australia., Friemann R; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden., Allison JR; Biomolecular Interaction Centre, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of Auckland, Auckland, New Zealand., North RA; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia., Dobson RCJ; Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia. Electronic address: renwick.dobson@canterbury.ac.nz.
Jazyk: angličtina
Zdroj: The Journal of biological chemistry [J Biol Chem] 2024 Sep 30; Vol. 300 (11), pp. 107851. Date of Electronic Publication: 2024 Sep 30.
DOI: 10.1016/j.jbc.2024.107851
Abstrakt: Tripartite ATP-independent periplasmic (TRAP) transporters are analogous to ABC transporters in that they use a substrate-binding protein to scavenge metabolites (e.g., N-acetylneuraminate) and deliver them to the membrane components for import. TRAP substrate-binding proteins are thought to bind the substrate using a two-state (open and closed) induced-fit mechanism. We solved the structure of the TRAP N-acetylneuraminate substrate-binding protein from Aggregatibacter actinomycetemcomitans (AaSiaP) in both the open ligand-free and closed liganded conformations. Surprisingly, we also observed an intermediate conformation, where AaSiaP is mostly closed and is bound to a non-cognate ligand, acetate, which hints at how N-acetylneuraminate binding stabilizes a fully closed state. AaSiaP preferentially binds N-acetylneuraminate (K D  = 0.4 μM) compared to N-glycolylneuraminate (K D  = 4.4 μM), which is explained by the closed-N-acetylneuraminate bound structure. Small-angle X-ray scattering data alongside molecular dynamics simulations suggest the AaSiaP adopts a more open state in solution than in a crystal. However, the open unliganded conformation can also sample closed conformations. Molecular dynamics simulations also demonstrate the importance of water molecules for stabilizing the closed conformation. Although our data is consistent with an induced fit model of binding, we suggest that the open unliganded conformation may sample multiple states capable of binding substrate. The mechanism by which the ligand is released for import remains to be determined.
Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article.
(Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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