Structure of the SLC4 transporter Bor1p in an inward-facing conformation

Nicolas Coudray, Sean L. Seyler, Ralph Lasala, Zhening Zhang, Kathy M. Clark, Mark E. Dumont, Alexis Rohou, Oliver Beckstein, David L. Stokes

Research output: Contribution to journalArticle

13 Scopus citations

Abstract

Bor1p is a secondary transporter in yeast that is responsible for boron transport. Bor1p belongs to the SLC4 family which controls bicarbonate exchange and pH regulation in animals as well as borate uptake in plants. The SLC4 family is more distantly related to members of the Amino acid-Polyamine-organoCation (APC) superfamily, which includes well studied transporters such as LeuT, Mhp1, AdiC, vSGLT, UraA, SLC26Dg. Their mechanism generally involves relative movements of two domains: a core domain that binds substrate and a gate domain that in many cases mediates dimerization. To shed light on conformational changes governing transport by the SLC4 family, we grew helical membrane crystals of Bor1p from Saccharomyces mikatae and determined a structure at ∼6 Å resolution using cryo-electron microscopy. To evaluate the conformation of Bor1p in these crystals, a homology model was built based on the related anion exchanger from red blood cells (AE1). This homology model was fitted to the cryo-EM density map using the Molecular Dynamics (MD) Flexible Fitting method and then relaxed by all-atom MD simulation in explicit solvent and membrane. Mapping of water accessibility indicates that the resulting structure represents an inward-facing conformation. Comparisons of the resulting Bor1p model with the X-ray structure of AE1 in an outward-facing conformation, together with MD simulations of inward-facing and outward-facing Bor1p models, suggest rigid body movements of the core domain relative to the gate domain. These movements are consistent with the rocking-bundle transport mechanism described for other members of the APC superfamily.

Original languageEnglish (US)
Pages (from-to)130-145
Number of pages16
JournalProtein Science
Volume26
Issue number1
DOIs
StatePublished - Jan 1 2017

Keywords

  • 2D crystallization
  • alternating access mechanism
  • anion exchanger family
  • boron transporter
  • cryo-EM
  • helical reconstruction
  • homology modeling
  • molecular dynamics
  • rocking-bundle mechanism
  • secondary transport

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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    Coudray, N., L. Seyler, S., Lasala, R., Zhang, Z., Clark, K. M., Dumont, M. E., Rohou, A., Beckstein, O., & Stokes, D. L. (2017). Structure of the SLC4 transporter Bor1p in an inward-facing conformation. Protein Science, 26(1), 130-145. https://doi.org/10.1002/pro.3061