Identification of a Second Substrate Binding Site in Solute:Sodium Symporters [Computational Biology]

November 14th, 2014 by Li, Z., Lee, A. S. E., Bracher, S., Jung, H., Paz, A., Kumar, J. P., Abramson, J., Quick, M., Shi, L.

The structure of the sodium/galactose transporter (vSGLT), a solute:sodium symporter (SSS) from Vibrio parahaemolyticus, shares a common structural fold with LeuT of the neurotransmitter:sodium symporter (NSS) family. Structural alignments between LeuT and vSGLT reveal that the crystallographically identified galactose binding site in vSGLT is located in a more extracellular location relative to the central substrate binding (S1) site in LeuT. Our computational analyses suggest the existence of an additional galactose binding site in vSGLT that aligns to the S1 site of LeuT. Radiolabeled galactose saturation binding experiments indicate that, like LeuT, vSGLT can simultaneously bind two substrate molecules under equilibrium conditions. Mutating key residues in the individual substrate binding sites reduced the molar substrate-to-protein binding stoichiometry to ~1. In addition, the related and more experimentally tractable SSS member PutP (the Na+/proline transporter) also exhibits a binding stoichiometry of 2. Targeting residues in the proposed sites with mutations results in the reduction of the binding stoichiometry and is accompanied with severely impaired translocation of proline. Our data suggest that substrate transport by SSS members requires both substrate binding sites, thereby implying that SSSs and NSSs share common mechanistic elements in substrate transport.