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

Nature volume 449, pages 735–739 (2007)Cite this article

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.

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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.

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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.

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Authors and Affiliations

  1. MRC Laboratory of Molecular Biology, Medical Research Council Centre, Cambridge CB2 0QH, UK

    Takayuki Obita, Sara Ghazi-Tabatabai, David J. Gill, Olga Perisic & Roger L. Williams

  2. Department of Molecular Biology and Genetics and Institute for Cell and Molecular Biology, Biotechnology Building, Cornell University, Ithaca, New York 14853, USA,

    Suraj Saksena & Scott D. Emr

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Correspondence to Roger L. Williams.

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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)

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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

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