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:

Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains

Nature volume 415, pages 933–937 (2002)Cite this article

Abstract

Specific sorting signals direct transmembrane proteins to the compartments of the endosomal–lysosomal system1. Acidic-cluster-dileucine signals present within the cytoplasmic tails of sorting receptors, such as the cation-independent and cation-dependent mannose-6-phosphate receptors, are recognized by the GGA (Golgi-localized, γ-ear-containing, ADP-ribosylation-factor-binding) proteins2,3,4,5. The VHS (Vps27p, Hrs and STAM) domains6 of the GGA proteins are responsible for the highly specific recognition of these acidic-cluster-dileucine signals7,8,9,10. Here we report the structures of the VHS domain of human GGA3 complexed with signals from both mannose-6-phosphate receptors. The signals bind in an extended conformation to helices 6 and 8 of the VHS domain. The structures highlight an Asp residue separated by two residues from a dileucine sequence as critical recognition elements. The side chains of the Asp-X-X-Leu-Leu sequence interact with subsites consisting of one electropositive and two shallow hydrophobic pockets, respectively. The rigid spatial alignment of the three binding subsites leads to high specificity.

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: Structures of the GGA3-VHS domain bound to signal peptides.
Figure 2: Molecular details of the interactions between the acidic-cluster-dileucine motifs and their binding site on the VHS domain.
Figure 3: Functional analysis of interactions between the CI-MPR tail and GGA-VHS domains.

Similar content being viewed by others

References

  1. Kirchhausen, T. Clathrin. Annu. Rev. Biochem. 69, 699–727 (2000).

    Article  CAS  Google Scholar 

  2. Dell’Angelica, E. C. et al. GGAs: a family of ADP ribosylation factor-binding proteins related to adaptors and associated with the Golgi complex. J. Cell Biol. 149, 81–94 (2000).

    Article  Google Scholar 

  3. Hirst, J. et al. A family of proteins with gamma-adaptin and VHS domains that facilitate trafficking between the trans-Golgi network and the vacuole/lysosome. J. Cell Biol. 149, 67–80 (2000).

    Article  CAS  Google Scholar 

  4. Boman, A. L., Zhang, C.-J., Zhu, X. & Kahn, R. A. A family of ADP-ribosylation factor effectors that can alter membrane transport through the trans-Golgi. Mol. Biol. Cell 11, 1241–1255 (2000).

    Article  CAS  Google Scholar 

  5. Poussu, A., Lohi, O. & Lehto, V.-P. Vear, a novel Golgi-associated protein with VHS and gamma-adaptin ‘ear’ domains. J. Biol. Chem. 275, 7176–7183 (2000).

    Article  CAS  Google Scholar 

  6. Lohi, O. & Lehto, V.-P. VHS domain marks a group of proteins involved in endocytosis and vesicular trafficking. FEBS Lett. 440, 255–257 (1998).

    Article  ADS  CAS  Google Scholar 

  7. Puertollano, R., Aguilar, R. C., Gorshkova, I., Crouch, R. J. & Bonifacino, J. S. Sorting of mannose 6-phosphate receptors mediated by the GGAs. Science 292, 1712–1716 (2001).

    Article  ADS  CAS  Google Scholar 

  8. Zhu, Y., Doray, B., Poussu, A., Lehto, V.-P. & Kornfeld, S. Binding of GGA2 to the lysosomal enzyme sorting motif of the mannose 6-phosphate receptor. Science 292, 1716–1718 (2001).

    Article  ADS  CAS  Google Scholar 

  9. Takatsu, H., Katoh, Y., Shiba, Y. & Nakayama, K. GGA proteins interact with acidic di-leucine sequences within the cytoplasmic domains of sorting receptors through their VHS domains. J. Biol. Chem. 276, 28541–28545 (2001).

    Article  CAS  Google Scholar 

  10. Nielsen, M. S. et al. The sortilin cytoplasmic tail conveys Golgi-endosome transport and binds the VHS domain of the GGA2 sorting protein. EMBO J. 20, 2180–2190 (2001).

    Article  CAS  Google Scholar 

  11. Mao, Y. et al. Crystal structure of the VHS and FYVE tandem domains of Hrs, a protein involved in membrane trafficking and signal transduction. Cell 100, 447–456 (2000).

    Article  CAS  Google Scholar 

  12. Misra, S., Beach, B. M. & Hurley, J. H. Structure of the VHS domain of human Tom1 (target of myb 1): insights into interactions with proteins and membranes. Biochemistry 39, 11282–11290 (2000).

    Article  CAS  Google Scholar 

  13. Chen, H. J., Yuan, J. & Lobel, P. Systematic mutational analysis of the cation-independent mannose 6-phosphate/insulin-like growth factor II receptor cytoplasmic domain. An acidic cluster containing a key aspartate is important for function in lysosomal enzyme sorting. J. Biol. Chem. 272, 7003–7012 (1997).

    Article  CAS  Google Scholar 

  14. Johnson, K. F. & Kornfeld, S. The cytoplasmic tail of the mannose 6-phosphate/insulin-like growth factor-II receptor has two signals for lysosomal enzyme sorting in the Golgi. J. Cell. Biol. 119, 249–257 (1992).

    Article  CAS  Google Scholar 

  15. Meresse, S. & Hoflack, B. J. Phosphorylation of the cation-independent mannose 6-phosphate receptor is closely associated with its exit from the trans-Golgi network. J. Cell Biol. 120, 67–75 (1993).

    Article  CAS  Google Scholar 

  16. Owen, D. J. & Evans, P. R. A structural explanation for the recognition of tyrosine-based endocytotic signals. Science 282, 1327–1332 (1998).

    Article  ADS  CAS  Google Scholar 

  17. Gatto, G. J. Jr, Geisbrecht, B. V., Gould, S. J. & Berg, J. M. Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5. Nature Struct. Biol. 7, 1091–1095 (2000).

    Article  CAS  Google Scholar 

  18. Scheufler, C. et al. Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70–Hsp90 multichaperone machine. Cell 101, 199–210 (2000).

    Article  CAS  Google Scholar 

  19. Sheffield, P., Garrard, S. & Derewenda, Z. Overcoming expression and purification problems of RhoGDI using a family of ‘parallel’ expression vectors. Prot. Express. Purif. 15, 34–39 (1999).

    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. Terwilliger, T. C. & Berendzen., J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849–861 (1999).

    Article  CAS  Google Scholar 

  22. Terwilliger, T. C. Maximum-likelihood density modification. Acta Crystallogr. D 56, 965–972 (2000).

    Article  CAS  Google Scholar 

  23. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjelgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  24. Brünger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  Google Scholar 

  25. Esnouf, R. M. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr. D 55, 938–940 (1999).

    Article  CAS  Google Scholar 

  26. Merritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505–524 (1997).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank K. R. Rajashankar, U. Ramagopal, R. Trievel and E. Jones for assistance with data collection at beamline X9B, NSLS, D. E. Anderson for mass spectrometry, A. Peterkofsky for use of and assistance with the titration calorimeter, R. Ghirlando for analytical ultracentrifugation, X. Zhu for sequencing services, and H. Bernstein and P. Sun for comments on the manuscript.

Author information

Authors and Affiliations

  1. Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Saurav Misra & James H. Hurley

  2. Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Rosa Puertollano, Yukio Kato & Juan S. Bonifacino

Authors
  1. Saurav Misra
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rosa Puertollano
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yukio Kato
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Juan S. Bonifacino
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. James H. Hurley
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to James H. Hurley.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Misra, S., Puertollano, R., Kato, Y. et al. Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains. Nature 415, 933–937 (2002). https://doi.org/10.1038/415933a

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/415933a

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