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Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains

Nature Structural & Molecular Biology volume 10, pages 856–863 (2003)Cite this article

Abstract

The ATPase p97/VCP affects multiple events within the cell. These events include the alteration of both nuclear and mitotic Golgi membranes, the dislocation of ubiquitylated proteins from the endoplasmic reticulum and regulation of the NF-κb pathway. Here we present the crystal structure of full-length Mus musculus p97/VCP in complex with a mixture of ADP and ADP–AlFx at a resolution of 4.7 Å. This is the first complete hexameric structure of a protein containing tandem AAA (ATPases associated with a variety of cellular activities) domains. Comparison of the crystal structure and cryo-electron microscopy (EM) reconstructions reveals large conformational changes in the helical subdomains during the hydrolysis cycle. Structural and functional data imply a communication mechanism between the AAA domains. A Zn2+ occludes the central pore of the hexamer, suggesting that substrate does not thread through the pore of the molecule.

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Figure 1: Domain diagram and electron density maps for selected regions.
Figure 2: p97/VCP protomer and pore schematic.
Figure 3: Protomer views and schematic.
Figure 4: Primary sequence alignment of D1 to D2, with secondary structural elements assigned.
Figure 5: ADP titration and fit to cryo-EM densities.

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Acknowledgements

We thank G. Warren for supplying the initial p97/VCP clones, P. Adams, C. Chaudhry, I. Rouiller, P. Strop, W. Weis and L. Wilson-Kubalek for stimulating discussions, A. Joachimiak for generous access to beamline ID-19 at Advanced Photon Source, M. Boulanger for expert assistance with ITC experiments and C. Garcia for generous access to ITC equipment, E. Gabriel for assistance with crystal production and A. May and N. Gassner for a critical reading of the manuscript. Portions of this research were carried out at the Stanford Synchrotron Radiation Laboratory (SSRL), a national user facility operated by Stanford University on behalf of the US Department of Energy, Office of Basic Energy Sciences. The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, and by the US National Institutes of Health, National Center for Research Resources, Biomedical Technology Program, and the National Institute of General Medical Sciences.

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  1. Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and Stanford Synchrotron Radiation Laboratory, Stanford University, James H. Clark Center E300-C, 318 Campus Drive, Stanford, 94305-5432, California, USA

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DeLaBarre, B., Brunger, A. Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nat Struct Mol Biol 10, 856–863 (2003). https://doi.org/10.1038/nsb972

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