Inward-facing conformation of a multidrug resistance MATE family transporter

Abstract

Multidrug and toxic compound extrusion (MATE) transporters mediate excretion of xenobiotics and toxic metabolites, thereby conferring multidrug resistance in bacterial pathogens and cancer cells. Structural information on the alternate conformational states and knowledge of the detailed mechanism of MATE transport are of great importance for drug development. However, the structures of MATE transporters are only known in V-shaped outward-facing conformations. Here, we present the crystal structure of a MATE transporter from Pyrococcus furiosus (PfMATE) in the long-soughtafter inward-facing state, which was obtained after crystallization in the presence of native lipids. Transition from the outward-facing state to the inward-facing state involves rigid body movements of transmembrane helices (TMs) 2-6 and 8-12 to form an inverted V, facilitated by a loose binding of TM1 and TM7 to their respective bundles and their conformational flexibility. The inward-facing structure of PfMATE in combination with the outward-facing one supports an alternating access mechanism for the MATE family transporters. multidrug resistance | membrane protein structure | MATE transporter | inward-facing conformation | lipids

Sequence and Structural Determinants of Ligand-dependent Alternating Access of a MATE Transporter

“…Although controversial 25,35 , this conformation of TM1 was also captured in a crystal structure of a H + -coupled MATE from V. cholerae suggesting a conserved element of alternating access 23 Prominent discrepancies between predicted and experimental distributions are noted for the intracellular side of TM1, which in the IF structure unwinds leading to distance changes relative to TMs 3, 6, 11 and 12 (Figs. 5A, 6A).…”

“…In the OF MATE structures, the putative central substrate binding cavities are shielded from the cytoplasm by highly ordered and packed protein regions, suggesting that transition to an IF conformation requires extensive structural rearrangements. A view of these rearrangements was recently captured from an IF crystal structure of PfMATE 25 . This structure, determined in the presence of native P. furiosus lipids, showed a change in the orientation of the central cavity that exposes its lumen to the intracellular side.…”

“…1), critical elements of the transport mechanism remain unresolved. Substrate/ion antiport entails differential stability of the conformations when either ligand is bound, yet Zakrzewska et al 25 found that the OF also crystallizes at low pH (pH 5-6.5), albeit in the absence of native lipids.…”

Sequence and structural determinants of ligand-dependent alternating access of a MATE transporter

“…1), critical elements of the transport mechanism remain unresolved. Substrate/ion antiport entails differential stability of the OF and IF conformations when either ligand is bound, yet Zakrzewska et al (25) found that the OF also crystallizes at low pH (pH 5 to 6.5), albeit in the absence of native lipids. This observation led the authors to question the role of protons in driving isomerization between OF and IF conformations.…”

“…In the OF MATE structures, the putative central substrate binding cavities are shielded from the cytoplasm by highly ordered and packed protein regions, suggesting that transition to an IF conformation requires extensive structural rearrangements. A view of these rearrangements was recently captured from an IF crystal structure of PfMATE (25). This structure, determined in the presence of native Pyrococcus furiosus lipids, showed a change in the orientation of the central cavity that exposes its lumen to the intracellular side.…”