Structural basis for amino acid export by DMT superfamily transporter YddG

• Published in: Nature (London) Vol. 534; no. 7607; pp. 417 - 420
• Main Authors: Tsuchiya, Hirotoshi, Doki, Shintaro, Takemoto, Mizuki, Ikuta, Tatsuya, Higuchi, Takashi, Fukui, Keita, Usuda, Yoshihiro, Tabuchi, Eri, Nagatoishi, Satoru, Tsumoto, Kouhei, Nishizawa, Tomohiro, Ito, Koichi, Dohmae, Naoshi, Ishitani, Ryuichiro, Nureki, Osamu
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16.06.2016; Nature Publishing Group
• Subjects: 631/535/1266; 631/92/577; 631/92/612/1237; Alphaproteobacteria - chemistry; Alphaproteobacteria - metabolism; Amino Acid Transport Systems, Neutral - chemistry; Amino Acid Transport Systems, Neutral - metabolism; Amino acids; Amino Acids - metabolism; Binding sites; Biological research; Biological Transport; Biology, Experimental; Carrier proteins; Crystal structure; Crystallography, X-Ray; Drugs; E coli; Escherichia coli - chemistry; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Humanities and Social Sciences; letter; Liposomes - chemistry; Liposomes - metabolism; Membranes; Metabolites; Models, Molecular; multidisciplinary; Properties; Protein Conformation; Proteins; Science; Structure; Structure-Activity Relationship; Topology
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature17991

The X-ray structure of the drug/metabolite transporter (DMT) protein YddG from Starkeya novella reveals a new membrane transport topology, with ten transmembrane segments in an outward-facing state and two pseudo-symmetric inverted structural repeats. An amino acid/metabolite exporter structure The drug/metabolite transporter (DMT) proteins form a superfamily of membrane transporters that includes exporters for a wide range of compounds, including the bacterial SMR (small multidrug resistance) proteins that can confer antibiotic resistance. YddG is a bacterial DMT protein that exports aromatic amino acids and exogenous toxic compounds. In this manuscript, the authors report the 2.4-Å resolution X-ray crystal structure of YddG from Starkeya novella . The topology of this membrane protein is unprecedented: it contains ten transmembrane segments and has two inverted structural repeats that are pseudo-symmetric. The protein is in an outward-facing state, with a large substrate-binding cavity at the centre of the protein. The drug/metabolite transporter (DMT) superfamily is a large group of membrane transporters ubiquitously found in eukaryotes, bacteria and archaea, and includes exporters for a remarkably wide range of substrates, such as toxic compounds and metabolites 1 . YddG is a bacterial DMT protein that expels aromatic amino acids and exogenous toxic compounds, thereby contributing to cellular homeostasis 2 , 3 . Here we present structural and functional analyses of YddG. Using liposome-based analyses, we show that Escherichia coli and Starkeya novella YddG export various amino acids. The crystal structure of S. novella YddG at 2.4 Å resolution reveals a new membrane transporter topology, with ten transmembrane segments in an outward-facing state. The overall structure is basket-shaped, with a large substrate-binding cavity at the centre of the molecule, and is composed of inverted structural repeats related by two-fold pseudo-symmetry. On the basis of this intramolecular symmetry, we propose a structural model for the inward-facing state and a mechanism of the conformational change for substrate transport, which we confirmed by biochemical analyses. These findings provide a structural basis for the mechanism of transport of DMT superfamily proteins.