A Numbering System for MFS Transporter Proteins

Joanna Lee,Zara A Sands,Philip C Biggin

doi:10.3389/fmolb.2016.00021

Abstract

The Major Facilitator Superfamily (MFS) is one of the largest classes of secondary active transporters and is widely expressed in many domains of life. It is characterized by a common 12-transmembrane helix motif that allows the selective transport of a vast range of diverse substrates across the membrane. MFS transporters play a central role in many physiological processes and are increasingly recognized as potential drug targets. Despite intensive efforts, there are still only a handful of crystal structures and therefore homology modeling is likely to be a necessary process for providing models to interpret experiments for many years to come. However, the diversity of sequences and the multiple conformational states these proteins can exist in makes the process significantly more complicated, especially for sequences for which there is very little sequence identity to known templates. Inspired by the approach adopted many years ago for GPCRs, we have analyzed the large number of MFS sequences now available alongside the current structural information to propose a series of conserved contact points that can provide additional guidance for the homology modeling process. To enable cross-comparison across MFS models we also present a numbering scheme that can be used to provide a point of reference within each of the 12 transmembrane regions.

Highlights

The Major Facilitator Superfamily (MFS) is the largest known superfamily of secondary transporters (Marger and Saier, 1993) expanding in recent years to contain 74 distinct families according to the Transporter Classification Database (TCDB; Saier et al, 2014)
We initially explored the use of Pfam (Finn et al, 2014), but this turned out to be too diverse in terms of clan members, as has been discussed when compared to the Transporter Classification Database (Chiang et al, 2015)
Two of the conserved sites highlighted by the multiple sequence alignment (MSA) analysis are the glycine residues on transmembrane helices (TMH) 4 and its symmetrically equivalent helix in domain 2, TMH 10

Summary

Introduction

The Major Facilitator Superfamily (MFS) is the largest known superfamily of secondary transporters (Marger and Saier, 1993) expanding in recent years to contain 74 distinct families according to the Transporter Classification Database (TCDB; Saier et al, 2014) These transporters operate by uniport, symport, or antiport mechanisms that take advantage of the electrochemical gradient of the co-transported ion (in the case of symport or antiport) or the concentration of the ligand to instigate the transport cycle (Pao et al, 1998). MFS proteins have a conserved 12 transmembrane (TM) α-helix fold (Figure 1A; Reddy et al, 2012) that is comprised of two 6-TM helix bundles that are related by a pseudo two-fold axis of symmetry The presence of both domains is thought to be functionally important for the transport mechanism, as the ligand binds to the central TM cavity at the interface between the two domains (Pazdernik et al, 1997; Figures 1B,C). The 12-TM topology appears to be the core fold, though the presence of additional helices is sometimes observed as for example seen in peptide transporters

Methods

Results

Conclusion