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. 2019 Dec 20;9:19479. doi: 10.1038/s41598-019-55722-6

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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A conserved ion-binding site (Na2 site) in LeuT-fold transporters. (a) Overview of the structure of Mhp1 and the simulation system. (top) The simulation system. Mhp1 is rendered in cartoon, with the bound Na⁺ drawn in VDW. The POPE lipids and the solute ions are also drawn in VDW, and the water molecules are represented as semi-transparent surfaces. Lipids molecules overlapping with the protein are hidden for clarity. (bottom) A close view of the highly conserved Na⁺-binding site (Na2). Residues surrounding the Na⁺-binding site along with helices TM1 and TM8 are shown and labeled. (b) The Na2 site is a conserved motif shared by Na⁺-dependent transporters, namely, Mhp1, LeuT, DAT, BetP and vSGLT, and is replaced by a basic residue with a similar role in two Na⁺-independent transporters: CaiT and ApcT. The top panel shows four transporters in their OF states, with a well-coordinated Na2 site, while the bottom panel shows three transporters in either IF or occluded state with a more open Na2 site. TM1 and TM8 are represented in cartoon form, with the bound Na⁺ drawn in VDW. The two helical bundles are shown in transparent surface representation. The binding residues in Na2 site are shown in sticks. Bottom panel also includes a schematic summarizing the common architecture among the proteins shown, namely, a conserved site housing a positive charge and formed at the interface of the two helical bundles by TM1 and TM8 helices.