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.

Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4

Abstract

The AAA+ ATPases are essential for various activities such as membrane trafficking, organelle biogenesis, DNA replication, intracellular locomotion, cytoskeletal remodelling, protein folding and proteolysis1. The AAA ATPase Vps4, which is central to endosomal traffic to lysosomes2,3, retroviral budding4 and cytokinesis5, dissociates ESCRT complexes (the endosomal sorting complexes required for transport) from membranes6,7,8,9,10,11,12,13,14,15. Here we show that, of the six ESCRT--related subunits in yeast, only Vps2 and Did2 bind the MIT (microtubule interacting and transport) domain of Vps4, and that the carboxy-terminal 30 residues of the subunits are both necessary and sufficient for interaction. We determined the crystal structure of the Vps2 C terminus in a complex with the Vps4 MIT domain, explaining the basis for selective ESCRT-III recognition. MIT helices α2 and α3 recognize a (D/E)xxLxxRLxxL(K/R) motif, and mutations within this motif cause sorting defects in yeast. Our crystal structure of the amino-terminal domain of an archaeal AAA ATPase of unknown function shows that it is closely related to the MIT domain of Vps4. The archaeal ATPase interacts with an archaeal ESCRT-III-like protein even though these organisms have no endomembrane system, suggesting that the Vps4/ESCRT-III partnership is a relic of a function that pre-dates the divergence of eukaryotes and Archaea.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Characterization of the Vps4–Vps2 complex.
Figure 2: A conserved MIT-interacting motif in ESCRT-III is critical for binding the Vps4 MIT domain.
Figure 3: MIT-interacting motifs in Vps2 and Did2 are important for function in vivo.
Figure 4: Conserved features of the MIT domain in ATPases.

References

  1. Ogura, T. & Wilkinson, A. J. AAA+ superfamily ATPases: common structure—diverse function. Genes Cells 6, 575–597 (2001)

    CAS  Article  Google Scholar 

  2. Slagsvold, T., Pattni, K., Malerod, L. & Stenmark, H. Endosomal and non-endosomal functions of ESCRT proteins. Trends Cell Biol. 16, 317–326 (2006)

    CAS  Article  Google Scholar 

  3. Williams, R. L. & Urbe, S. The emerging shape of the ESCRT machinery. Nature Rev. Mol. Cell Biol. 8, 355–368 (2007)

    CAS  Article  Google Scholar 

  4. Bieniasz, P. D. Late budding domains and host proteins in enveloped virus release. Virology 344, 55–63 (2006)

    CAS  Article  Google Scholar 

  5. Carlton, J. G. & Martin-Serrano, J. Parallels between cytokinesis and retroviral budding: a role for the ESCRT machinery. Science 316, 1908–1912 (2007)

    ADS  CAS  Article  Google Scholar 

  6. Nickerson, D. P., West, M. & Odorizzi, G. Did2 coordinates Vps4-mediated dissociation of ESCRT-III from endosomes. J. Cell Biol. 175, 715–720 (2006)

    CAS  Article  Google Scholar 

  7. Babst, M., Wendland, B., Estepa, E. J. & Emr, S. D. The Vps4p AAA ATPase regulates membrane association of a Vps protein complex required for normal endosome function. EMBO J. 17, 2982–2993 (1998)

    CAS  Article  Google Scholar 

  8. Howard, T. L., Stauffer, D. R., Degnin, C. R. & Hollenberg, S. M. CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins. J. Cell Sci. 114, 2395–2404 (2001)

    CAS  PubMed  Google Scholar 

  9. Amerik, A., Nowak, J., Swaminathan, S. & Hochstrasser, M. The Doa4 deubiquitinating enzyme is functionally linked to the vacuolar protein-sorting and endocytic pathways. Mol. Biol. Cell 11, 3365–3380 (2000)

    CAS  Article  Google Scholar 

  10. Tsang, H. T. et al. A systematic analysis of human CHMP protein interactions: Additional MIT domain-containing proteins bind to multiple components of the human ESCRT III complex. Genomics 88, 333–346 (2006)

    CAS  Article  Google Scholar 

  11. von Schwedler, U. K. et al. The protein network of HIV budding. Cell 114, 701–713 (2003)

    CAS  Article  Google Scholar 

  12. Bowers, K. et al. Protein–protein interactions of ESCRT complexes in the yeast Saccharomyces cerevisiae . Traffic 5, 194–210 (2004)

    CAS  Article  Google Scholar 

  13. Martin-Serrano, J., Yarovoy, A., Perez-Caballero, D. & Bieniasz, P. D. Divergent retroviral late-budding domains recruit vacuolar protein sorting factors by using alternative adaptor proteins. Proc. Natl Acad. Sci. USA 100, 12414–12419 (2003)

    ADS  CAS  Article  Google Scholar 

  14. Vajjhala, P. R., Catchpoole, E., Nguyen, C. H., Kistler, C. & Munn, A. L. Vps4 regulates a subset of protein interactions at the multivesicular endosome. FEBS J. 274, 1894–1907 (2007)

    CAS  Article  Google Scholar 

  15. Scott, A. et al. Structure and ESCRT-III protein interactions of the MIT domain of human VPS4A. Proc. Natl Acad. Sci. USA 102, 13813–13818 (2005)

    ADS  CAS  Article  Google Scholar 

  16. Bishop, N. & Woodman, P. ATPase-defective mammalian VPS4 localizes to aberrant endosomes and impairs cholesterol trafficking. Mol. Biol. Cell 11, 227–239 (2000)

    CAS  Article  Google Scholar 

  17. Scott, A. et al. Structural and mechanistic studies of VPS4 proteins. EMBO J. 24, 3658–3669 (2005)

    CAS  Article  Google Scholar 

  18. Babst, M., Katzmann, D. J., Estepa-Sabal, E. J., Meerloo, T. & Emr, S. D. ESCRT-III: an endosome-associated heterooligomeric protein complex required for MVB sorting. Dev. Cell 3, 271–282 (2002)

    CAS  Article  Google Scholar 

  19. Muziol, T. et al. Structural basis for budding by the ESCRT-III factor CHMP3. Dev. Cell 10, 821–830 (2006)

    CAS  Article  Google Scholar 

  20. Lin, Y., Kimpler, L. A., Naismith, T. V., Lauer, J. M. & Hanson, P. I. Interaction of the mammalian endosomal sorting complex required for transport (ESCRT) III protein hSnf7-1 with itself, membranes, and the AAA+ ATPase SKD1. J. Biol. Chem. 280, 12799–12809 (2005)

    CAS  Article  Google Scholar 

  21. Zamborlini, A. et al. Release of autoinhibition converts ESCRT-III components into potent inhibitors of HIV-1 budding. Proc. Natl Acad. Sci. USA 103, 19140–19145 (2006)

    ADS  CAS  Article  Google Scholar 

  22. Agromayor, M. & Martin-Serrano, J. Interaction of AMSH with ESCRT-III and deubiquitination of endosomal cargo. J. Biol. Chem. 281, 23083–23091 (2006)

    CAS  Article  Google Scholar 

  23. McCullough, J. et al. Activation of the endosome-associated ubiquitin isopeptidase AMSH by STAM, a component of the multivesicular body-sorting machinery. Curr. Biol. 16, 160–165 (2006)

    CAS  Article  Google Scholar 

  24. Whitley, P. et al. Identification of mammalian Vps24p as an effector of phosphatidylinositol 3,5-bisphosphate-dependent endosome compartmentalization. J. Biol. Chem. 278, 38786–38795 (2003)

    CAS  Article  Google Scholar 

  25. Yorikawa, C. et al. Human CHMP6, a myristoylated ESCRT-III protein, interacts directly with an ESCRT-II component EAP20 and regulates endosomal cargo sorting. Biochem. J. 387, 17–26 (2005)

    CAS  Article  Google Scholar 

  26. Takasu, H. et al. Structural characterization of the MIT domain from human Vps4b. Biochem. Biophys. Res. Commun. 334, 460–465 (2005)

    CAS  Article  Google Scholar 

  27. Scheuring, S. et al. Mammalian cells express two VPS4 proteins both of which are involved in intracellular protein trafficking. J. Mol. Biol. 312, 469–480 (2001)

    CAS  Article  Google Scholar 

  28. Reid, E. et al. The hereditary spastic paraplegia protein spastin interacts with the ESCRT-III complex-associated endosomal protein CHMP1B. Hum. Mol. Genet. 14, 19–38 (2005)

    CAS  Article  Google Scholar 

  29. Field, M. C., Gabernet-Castello, C. & Dacks, J. B. in Origins and Evolution of Eukaryotic Endomembranes and Cytoskeleton (ed. Jékely, G.) 84–96 (Eurekah/Landes Bioscience Press, Austin, TX, 2007)

    Google Scholar 

  30. Hartman, J. J. & Vale, R. D. Microtubule disassembly by ATP-dependent oligomerization of the AAA enzyme katanin. Science 286, 782–785 (1999)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank M. Babu for advice on the archaeal genome analysis. We acknowledge the European Synchrotron Radiation Facility for provision of synchrotron radiation facilities and we thank G. Cioci, D. Flot, I. Leiros and G. Leonard for assistance in using beamlines ID23-2 and ID23-1. T.O. was supported by a JSPS fellowship and S.S. by a fellowship from the Howard Hughes Medical Institute. This research was supported by the Howard Hughes Medical Institute (S.D.E.) and the Medical Research Council (R.L.W.).

The atomic coordinates of the yeast Vps2–Vps4 MIT-domain complex and the S. solfataricus MIT domain are deposited in the Protein Data Bank under accession numbers 2V6X and 2V6Y, respectively.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Roger L. Williams.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Tables 1-2, Supplementary Figures 1-2 with Legends, Supplementary Methods and additional references. Supplementary Tables 1 and 2 provide detailed statistics for the crystallographic structures. Supplementary Figure 1 provides a schematic of the process of Vps4-mediated disassembly of ESCRT-III lattices. Supplementary Figure 2 provides a dendrogram for archaeal ESCRT-III-like sequences and highlights the group of sequences that occur adjacent to the Vps4-like ATPase. (PDF 1324 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Obita, T., Saksena, S., Ghazi-Tabatabai, S. et al. Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4. Nature 449, 735–739 (2007). https://doi.org/10.1038/nature06171

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature06171

Further reading

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

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