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PreprintCited by 20Drug Transport and Resistance MechanismsAdvanced Electron Microscopy Techniques and ApplicationsBacterial Genetics and Biotechnology

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Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter

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Currie, Michael J., Davies, James S., Scalise, Mariafrancesca, Gulati, Ashutosh, Wright, Joshua D., Newton-Vesty, Michael C., Abeysekera, Gayan S., Subramanian, Ramaswamy, Wahlgren, Weixiao Y., Friemann, Rosmarie, Allison, Jane R., Mace, Peter D., Griffin, Michael D.W., Demeler, Borries, Wakatsuki, Soichi, Drew, David, Indiveri, Cesare, Dobson, Renwick C.J., North, Rachel A.·2023·eLife
DOI 10.1101/2023.08.28.549404PMC PMC10942642

Preprint — published as 10.7554/elife.92307.3 · Paper page

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Abstract

Tripartite ATP-independent periplasmic (TRAP) transporters are secondary-active transporters that receive their substrates via a soluble binding protein to move bioorganic acids across bacterial or archaeal cell membranes. Recent cryo-EM structures of TRAP transporters provide a broad framework to understand how they work, but the mechanistic details of transport are not yet defined. Here we report the cryo-EM structure of the Haemophilus influenzae N -acetylneuraminate TRAP transporter ( Hi SiaQM) at 2.99 Å resolution (extending to 2.2 Å at the core), revealing new features. The improved resolution (the previous Hi SiaQM structure is 4.7 Å resolution) permits accurate assignment of two Na + sites and the architecture of the substrate binding site, consistent with mutagenic and functional data. Moreover, rather than a monomer, the Hi SiaQM structure is a homodimer. We observe lipids at the dimer interface, as well as a lipid trapped within the fusion that links the SiaQ and SiaM subunits. We show that the affinity ( K D ) for the complex between the soluble Hi SiaP protein and Hi SiaQM is in the micromolar range and that a related SiaP can bind Hi SiaQM. This work provides key data that enhances our understanding of the ‘elevator-with-an-operator’ mechanism of TRAP transporters.

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Metadata

Authors
Currie, M. J., Davies, J. S., Scalise, M., Gulati, A., Wright, J. D., Newton-Vesty, M. C., Abeysekera, G. S., Subramanian, R., Wahlgren, W. Y., Friemann, R., Allison, J. R., Mace, P. D., Griffin, M. D. W., Demeler, B., Wakatsuki, S., Drew, D., Indiveri, C., Dobson, R. C. J., & North, R. A.
Affiliations
  • University of Canterbury (NZ)
  • Stockholm University (SE)
  • University of Calabria (IT)
  • University of Gothenburg (SE)
  • University of Auckland (NZ)
  • University of Otago (NZ)
  • The University of Melbourne (AU)
  • University of Lethbridge (CA)
  • Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IT)
  • The University of Sydney (AU)
Corresponding author
  • Dobson, Renwick C.J.
  • North, Rachel A.
ORCID
Venue
eLife
Publisher
openRxiv
Published
2023-08-29
Volume
12
ISSN
2050-084X (ISSN-L)
DOI
10.1101/2023.08.28.549404
PMC
PMC10942642
OpenAlex
W4388099794
Cited by
20
References
1
Citations by year
2026: 5 · 2025: 4 · 2024: 10 · 2023: 1
FWCI
2.43
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • eLife (publishedVersion, cc-by)
  • eLife (acceptedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Archive of Doctoral Theses and Digital Collections (University of Calabria) (submittedVersion)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
Funders
  • Australian Nuclear Science and Technology Organisation
  • Kempe Foundation
  • Australian Cancer Research Foundation
  • Australian Institute of Nuclear Science and Engineering
  • Australian Synchrotron
  • Royal Society Te Apārangi (UOC1506)
  • Canterbury Medical Research Foundation
  • Ministry of Business, Innovation and Employment (UOCX1706)
  • Knut och Alice Wallenbergs Stiftelse
  • Umeå Universitet
  • Kempestiftelserna
  • Stockholms Universitet
  • Science for Life Laboratory
  • Biomolecular Interaction Centre, University of Canterbury
  • Marsden Fund (UOC1506)
  • National Institute of General Medical Sciences (R01GM120600)
Topics
  • Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
TRAP transporter, Haemophilus influenzae, secondary active transport, homodimer structure, Na+ binding site, substrate binding site
MeSH terms
Adenosine Triphosphate, Bacterial Proteins, Haemophilus influenzae, N-Acetylneuraminic Acid, Cryoelectron Microscopy, Membrane Transport Proteins

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