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Published 7 July 2003. doi:10.1083/jcb.200302169
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© The Rockefeller University Press, 0021-9525/2003/7/71 $5.00
The Journal of Cell Biology, Volume 162, Number 1, 71-84

Article

 Function of the p97–Ufd1–Npl4 complex in retrotranslocation from the ER to the cytosol : dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains



Yihong Ye1, Hemmo H. Meyer2 and Tom A. Rapoport1

1 Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115
2 Department of Cell Biology, Yale Medical School, New Haven, CT, 06520

Address correspondence to Tom A. Rapoport, Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115. Tel.: (617) 432-0637. Fax: (617) 432-1190. E-mail: tom_rapoport{at}hms.harvard.edu

Amember of the family of ATPases associated with diverse cellular activities, called p97 in mammals and Cdc48 in yeast, associates with the cofactor Ufd1–Npl4 to move polyubiquitinated polypeptides from the endoplasmic reticulum (ER) membrane into the cytosol for their subsequent degradation by the proteasome. Here, we have studied the mechanism by which the p97–Ufd1–Npl4 complex functions in this retrotranslocation pathway. Substrate binding occurs when the first ATPase domain of p97 (D1 domain) is in its nucleotide-bound state, an interaction that also requires an association of p97 with the membrane through its NH2-terminal domain. The two ATPase domains (D1 and D2) of p97 appear to alternate in ATP hydrolysis, which is essential for the movement of polypeptides from the ER membrane into the cytosol. The ATPase itself can interact with nonmodified polypeptide substrates as they emerge from the ER membrane. Polyubiquitin chains linked by lysine 48 are recognized in a synergistic manner by both p97 and an evolutionarily conserved ubiquitin-binding site at the NH2 terminus of Ufd1. We propose a dual recognition model in which the ATPase complex binds both a nonmodified segment of the substrate and the attached polyubiquitin chain; polyubiquitin binding may activate the ATPase p97 to pull the polypeptide substrate out of the membrane.

Key Words: p97/Cdc48; ubiquitin; AAA ATPase; protein degradation; ER quality control

The online version of this article includes supplemental material.

* Abbreviations used in this paper: AAA, ATPase associated with diverse cellular activities; NZF, Npl4 zinc finger.


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