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Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP


Betaine and Na+ symport has been extensively studied in the osmotically regulated transporter BetP from Corynebacterium glutamicum, a member of the betaine/choline/carnitine transporter family, which shares the conserved LeuT-like fold of two inverted structural repeats1. BetP adjusts its transport activity by sensing the cytoplasmic K+ concentration as a measure for hyperosmotic stress via the osmosensing carboxy-terminal domain2,3. BetP needs to be in a trimeric state for communication between individual protomers through several intratrimeric interaction sites4. Recently, crystal structures of inward-facing BetP trimers have contributed to our understanding of activity regulation on a molecular level5,6. Here we report new crystal structures, which reveal two conformationally asymmetric BetP trimers7, capturing among them three distinct transport states. We observe a total of four new conformations at once: an outward-open apo and an outward-occluded apo state, and two closed transition states—one in complex with betaine and one substrate-free. On the basis of these new structures, we identified local and global conformational changes in BetP that underlie the molecular transport mechanism, which partially resemble structural changes observed in other sodium-coupled LeuT-like fold transporters, but show differences we attribute to the osmolytic nature of betaine, the exclusive substrate specificity and the regulatory properties of BetP.

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Figure 1: Conformational states and substrate-binding sites observed in BetP and BetP(G153D) asymmetric trimers.
Figure 2: Conformational changes during the alternating-access cycle.
Figure 3: Opening and closing of the periplasmic and cytoplasmic gates in BetP.
Figure 4: Conformational changes of the sodium-binding sites.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors for the structures presented here have been deposited in the Protein Data Bank under accession 4DOJ and 4AIN.


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We thank L. Forrest and R. Krämer for careful reading of the manuscript and suggestions and discussions. This work was supported by the International Max-Planck Research School (C.K. and C.P.), and by the DFG (German Research Foundation), Collaborative Research Center 807 “Transport and Communication across Biological Membranes” (C.Z.).

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Authors and Affiliations



C.P. performed mutations, activity and binding measurements in cells and proteoliposomes, crystallization, collection and processing of data for PDB accession 4DOJ; C.K. performed crystallization for PDB accession 4AIN; C.K. and Ö.Y. performed collection and processing of data for PDB accession 4AIN; C.P., C.K. and C.Z. analysed the data; C.Z. directed the research; and C.P. and C.Z. wrote the manuscript.

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Correspondence to Christine Ziegler.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, a Supplementary Discussion, Supplementary Tables 1-3, Supplementary Figures 1-10, a legend for Supplementary Movie 1 and Supplementary References. (PDF 6018 kb)

Supplementary Movie 1

The movie represents structural morphs of the conformational changes in BetP during transition from the outward-open to closed and inward-open states – see Supplementary Information file for full legend. (MP4 30132 kb)

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Perez, C., Koshy, C., Yildiz, Ö. et al. Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP. Nature 490, 126–130 (2012).

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