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Structure and mechanism of the S component of a bacterial ECF transporter


The energy-coupling factor (ECF) transporters, responsible for vitamin uptake in prokaryotes, are a unique family of membrane transporters1,2. Each ECF transporter contains a membrane-embedded, substrate-binding protein (known as the S component), an energy-coupling module that comprises two ATP-binding proteins (known as the A and A′ components) and a transmembrane protein (known as the T component). The structure and transport mechanism of the ECF family remain unknown. Here we report the crystal structure of RibU, the S component of the ECF-type riboflavin transporter from Staphylococcus aureus at 3.6-Å resolution. RibU contains six transmembrane segments, adopts a previously unreported transporter fold and contains a riboflavin molecule bound to the L1 loop and the periplasmic portion of transmembrane segments 4–6. Structural analysis reveals the essential ligand-binding residues, identifies the putative transport path and, with sequence alignment, uncovers conserved structural features and suggests potential mechanisms of action among the ECF transporters.

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Figure 1: The overall structure of RibU.
Figure 2: Sequence alignment and structural fold of RibU.
Figure 3: Conserved amino acids map to the binding site and transport path of riboflavin.
Figure 4: Recognition of riboflavin by RibU.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates of RibUare deposited in ProteinDataBank under accession code 3P5N.


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We thank H. Yan for technical advice, A. Schmedel for administrative assistance and E. coli Genetic Resources at Yale Coli Genetic Stock Center for providing mutant E. coli strains. This work was supported by the National Institutes of Health (R01 GM084964), funds from the Ministry of Science and Technology of China (grant number 2009CB918801) and Project 30888001 supported by National Natural Science Foundation of China.

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P.Z. and Y.S. designed all experiments. P.Z. performed the bulk of the experiments. P.Z., J.W. and Y.S. analysed the data and contributed to manuscript preparation. Y.S. wrote the manuscript.

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Correspondence to Yigong Shi.

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The authors declare no competing financial interests.

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Zhang, P., Wang, J. & Shi, Y. Structure and mechanism of the S component of a bacterial ECF transporter. Nature 468, 717–720 (2010).

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