Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark.
Molecular Biology I, Faculty of Biology, University of Duisburg-Essen, 45117, Essen, Germany.
Nat Commun. 2024 Mar 19;15(1):2459. doi: 10.1038/s41467-024-46760-4.
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.
六聚体 AAA+ ATP 酶 p97/VCP 作为泛素依赖性细胞过程的重要介质发挥作用，通过催化其展开将泛素化蛋白从大分子复合物或膜中提取出来。p97 通过多种辅助因子被引导至泛素化的靶蛋白，其中大多数与 p97 N 结构域相互作用。在这里，我们发现 FAM104A（一种未知功能的蛋白质，也称为 VCF1（VCP/p97 核共因子家族成员 1））在人类细胞中作为 p97 的辅助因子发挥作用。详细的结构功能研究表明，VCF1 通过保守的α螺旋基序直接与 p97 结合，该基序以异常高的亲和力识别 p97 N 结构域，超过其他辅助因子。我们表明，VCF1 与异二聚体主要 p97 辅助因子 UFD1-NPL4 一起参与 p97 复合形成，并促进细胞中 p97-UFD1-NPL4 依赖性泛素化底物的蛋白酶体降解。从机制上讲，VCF1 通过与 p97 的结合间接刺激 UFD1-NPL4 与泛素缀合物的相互作用，但本身对泛素有内在亲和力。总之，我们的发现确立了 VCF1 作为一种非传统的 p97 辅助因子，通过促进 p97-UFD1-NPL4 募集到泛素化靶标，从而促进 p97 依赖性蛋白质周转。
