Structure
Volume 19, Issue 6, 8 June 2011, Pages 833-843
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Article
Hierarchical Binding of Cofactors to the AAA ATPase p97

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Summary

The hexameric AAA ATPase p97 is involved in several human proteinopathies and mediates ubiquitin-dependent protein degradation among other essential cellular processes. Via its N-terminal domain (N domain), p97 interacts with multiple regulatory cofactors including the UFD1/NPL4 heterodimer and members of the “ubiquitin regulatory X” (UBX) domain protein family; however, the principles governing cofactor selectivity remain to be deciphered. Our crystal structure of the FAS-associated factor 1 (FAF1)UBX domain in complex with the p97N domain reveals that the signature Phe-Pro-Arg motif known to be crucial for interactions of UBX domains with p97 adopts a cis-proline configuration, in contrast to a cis-trans mixture we derive for the isolated FAF1UBX domain. Biochemical studies confirm that binding critically depends on a proline at this position. Furthermore, we observe that the UBX proteins FAF1 and UBXD7 only bind to p97-UFD1/NPL4, but not free p97, thus demonstrating for the first time a hierarchy in p97-cofactor interactions.

Highlights

► FAF1UBX binds into the p97N domain hydrophobic interdomain CLEFT ► The conserved R…FPR signature of FAF1UBX features a cis-proline in the p97 complex ► A conserved binding mode for p97N adaptor proteins ► Hierarchical binding of cofactors to p97

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