VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates

Ann Schirin Mirsanaye, Saskia Hoffmann, Melanie Weisser, Andreas Mund, Blanca Lopez Mendez, Dimitris Typas, Johannes Boom, Bente Benedict, Ivo A. Hendriks, Michael Lund Nielsen, Hemmo Meyer, Julien P. Duxin, Guillermo Montoya and Niels Mailand ()
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Ann Schirin Mirsanaye: University of Copenhagen
Saskia Hoffmann: University of Copenhagen
Melanie Weisser: University of Copenhagen
Andreas Mund: University of Copenhagen
Blanca Lopez Mendez: University of Copenhagen
Dimitris Typas: University of Copenhagen
Johannes Boom: University of Duisburg-Essen
Bente Benedict: University of Copenhagen
Ivo A. Hendriks: University of Copenhagen
Michael Lund Nielsen: University of Copenhagen
Hemmo Meyer: University of Duisburg-Essen
Julien P. Duxin: University of Copenhagen
Guillermo Montoya: University of Copenhagen
Niels Mailand: University of Copenhagen

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract The hexameric AAA+ ATPase p97/VCP functions as an essential mediator of ubiquitin-dependent cellular processes, extracting ubiquitylated proteins from macromolecular complexes or membranes by catalyzing their unfolding. p97 is directed to ubiquitylated client proteins via multiple cofactors, most of which interact with the p97 N-domain. Here, we discover that FAM104A, a protein of unknown function also named VCF1 (VCP/p97 nuclear Cofactor Family member 1), acts as a p97 cofactor in human cells. Detailed structure-function studies reveal that VCF1 directly binds p97 via a conserved α-helical motif that recognizes the p97 N-domain with unusually high affinity, exceeding that of other cofactors. We show that VCF1 engages in joint p97 complex formation with the heterodimeric primary p97 cofactor UFD1-NPL4 and promotes p97-UFD1-NPL4-dependent proteasomal degradation of ubiquitylated substrates in cells. Mechanistically, VCF1 indirectly stimulates UFD1-NPL4 interactions with ubiquitin conjugates via its binding to p97 but has no intrinsic affinity for ubiquitin. Collectively, our findings establish VCF1 as an unconventional p97 cofactor that promotes p97-dependent protein turnover by facilitating p97-UFD1-NPL4 recruitment to ubiquitylated targets.

Date: 2024
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DOI: 10.1038/s41467-024-46760-4

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