Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

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

Nature volume 468, pages 717–720 (2010)Cite this article

Subjects

Abstract

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

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

References

  1. Rodionov, D. A. et al. A novel class of modular transporters for vitamins in prokaryotes. J. Bacteriol. 191, 42–51 (2009)

    Article  CAS  Google Scholar 

  2. Rodionov, D. A., Hebbeln, P., Gelfand, M. S. & Eitinger, T. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters. J. Bacteriol. 188, 317–327 (2006)

    Article  CAS  Google Scholar 

  3. Hollenstein, K., Dawson, R. J. & Locher, K. P. Structure and mechanism of ABC transporter proteins. Curr. Opin. Struct. Biol. 17, 412–418 (2007)

    Article  CAS  Google Scholar 

  4. Rees, D. C., Johnson, E. & Lewinson, O. ABC transporters: the power to change. Nature Rev. Mol. Cell Biol. 10, 218–227 (2009)

    Article  CAS  Google Scholar 

  5. Davidson, A. L., Dassa, E., Orelle, C. & Chen, J. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72, 317–364 (2008)

    Article  CAS  Google Scholar 

  6. Oldham, M. L., Davidson, A. L. & Chen, J. Structural insights into ABC transporter mechanism. Curr. Opin. Struct. Biol. 18, 726–733 (2008)

    Article  CAS  Google Scholar 

  7. Linton, K. J. Structure and function of ABC transporters. Physiology 22, 122–130 (2007)

    Article  CAS  Google Scholar 

  8. Dawson, R. J., Hollenstein, K. & Locher, K. P. Uptake or extrusion: crystal structures of full ABC transporters suggest a common mechanism. Mol. Microbiol. 65, 250–257 (2007)

    Article  CAS  Google Scholar 

  9. Davidson, A. L. & Maloney, P. C. ABC transporters: how small machines do a big job. Trends Microbiol. 15, 448–455 (2007)

    Article  CAS  Google Scholar 

  10. Locher, K. P. Review. Structure and mechanism of ATP-binding cassette transporters. Phil. Trans. R. Soc. B 364, 239–245 (2009)

    Article  CAS  Google Scholar 

  11. Jones, P. M., O’Mara, M. L. & George, A. M. ABC transporters: a riddle wrapped in a mystery inside an enigma. Trends Biochem. Sci. 34, 520–531 (2009)

    Article  CAS  Google Scholar 

  12. Hebbeln, P., Rodionov, D. A., Alfandega, A. & Eitinger, T. Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. Proc. Natl Acad. Sci. USA 104, 2909–2914 (2007)

    Article  ADS  Google Scholar 

  13. Burgess, C. M. et al. The riboflavin transporter RibU in Lactococcus lactis: molecular characterization of gene expression and the transport mechanism. J. Bacteriol. 188, 2752–2760 (2006)

    Article  CAS  Google Scholar 

  14. Duurkens, R. H., Tol, M. B., Geertsma, E. R., Permentier, H. P. & Slotboom, D. J. Flavin binding to the high affinity riboflavin transporter RibU. J. Biol. Chem. 282, 10380–10386 (2007)

    Article  CAS  Google Scholar 

  15. Vogl, C. et al. Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum . J. Bacteriol. 189, 7367–7375 (2007)

    Article  CAS  Google Scholar 

  16. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123–138 (1993)

    Article  CAS  Google Scholar 

  17. Lieberman, R. L. & Rosenzweig, A. C. Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane. Nature 434, 177–182 (2005)

    Article  ADS  CAS  Google Scholar 

  18. Hakemian, A. S. et al. The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b. Biochemistry 47, 6793–6801 (2008)

    Article  CAS  Google Scholar 

  19. Neubauer, O. et al. Two essential arginine residues in the T components of energy-coupling factor transporters. J. Bacteriol. 191, 6482–6488 (2009)

    Article  CAS  Google Scholar 

  20. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    Article  CAS  Google Scholar 

  21. Collaborative Computational Project, N. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  22. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  23. Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)

    Article  Google Scholar 

  24. DeLano, W. L. The PyMOL molecular graphics system. <http://www.pymol.org> (2002)

  25. Bandrin, S. V., Rabinovich, P. M. & Stepanov, A. I. Three linkage groups of the genes of riboflavin biosynthesis in Escherichia coli . Genetika 19, 1419–1925 (1983)

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, 08544, New Jersey, USA

    Peng Zhang

  2. State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084, China

    Jiawei Wang

  3. Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084, China

    Yigong Shi

Authors
  1. Peng Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiawei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yigong Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

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.

Corresponding author

Correspondence to Yigong Shi.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Table 1 and Supplementary Figures 1-15 with legends. (PDF 2565 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhang, P., Wang, J. & Shi, Y. Structure and mechanism of the S component of a bacterial ECF transporter. Nature 468, 717–720 (2010). https://doi.org/10.1038/nature09488

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature09488

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing