ATP-dependent chaperone which probably uses the energy provided by ATP hydrolysis to generate mechanical force to unfold substrate proteins, disassemble protein complexes, and disaggregate protein aggregates. By recruiting and promoting the degradation of ubiquitinated proteins, plays a role in the ubiquitin fusion degradation (UFD) pathway. Has a role in the endoplasmic reticulum-associated degradation (ERAD) pathway which mediates the cytoplasmic elimination of misfolded proteins exported from the ER. Involved in spindle disassembly. Component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation. CDC48 may provide the mechanical force that dislodges the polyubiquitinated nascent peptides from the exit channel. Required for ribophagy, a process which relocalizes ribosomal particles into the vacuole for degradation in response to starvation. ATP + H2O = ADP + H(+) + phosphate The first ATP-binding region has low ATPase activity. The second ATP-binding region is responsible for ATPase activity. ATP binding to the first ATP-binding region induces intrinsic activity of the second ATP-binding region. While ATP binding to the first ATP-binding region appears to prevent ATP hydrolysis by the second ATP-binding region, ADP-binding to first region promotes the coordinate and cooperative ATPase cycle of the second ATP-binding region. ATP binding to the first ATP-binding region induces a conformational change, promoting the rotation of the first ATP-binding region relative to the second ATP-binding region in the hexamer. Component of the ribosome quality control complex (RQC), composed of the E3 ubiquitin ligase rkr1/ltn1, rqc1 and mtr1/rqc2, as well as cdc48 and its ubiquitin-binding cofactors. RQC forms a stable complex with 60S ribosomal subunits (By similarity). Interacts with ubx2 and ubx3 (PubMed:15120077). Interacts with lub1 (PubMed:14993272). Belongs to the AAA ATPase family.