Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Cdc48 ATPase (p97/VCP) and Ufd1/Npl4 extract ubiquitinated proteins for proteasomal degradation.
• The mechanism by which Cdc48 processes diverse and folded substrates remains poorly understood.

Purpose of the Study:

• To elucidate the structural mechanism of Cdc48-mediated substrate processing.
• To understand how the Cdc48-Ufd1/Npl4 complex handles various protein substrates.

Main Methods:

• Cryo-electron microscopy (cryo-EM) was used to determine the structures of the Cdc48 complex bound to Ufd1/Npl4 and a polyubiquitinated substrate.
• Structural analysis focused on the interaction between Cdc48, its cofactors, and the substrate during extraction.

Main Results:

• The study reveals that the Cdc48 complex initiates substrate processing by unfolding a ubiquitin molecule.
• Structural data show the unfolded ubiquitin's N-terminal segment threading through the Cdc48 hexameric rings.
• A staircase-like structure formed by pore loops in the second ring acts as a polypeptide conveyer belt.

Conclusions:

• The unfolding of ubiquitin is a key step enabling the Cdc48 ATPase complex to process a wide array of substrates.
• This mechanism provides insight into the molecular basis of Cdc48's role in protein degradation pathways.