Structural Biochemistry/Enzyme/AAA+ Proteases

AAA+ proteases are a type of enzyme that performs as quality control for proteins, and are found the regulatory circuits of all cells. Proteins may need to be degraded for a variety of reasons, whether to remove damaged proteins or for the purpose of regulation. As the process is irreversible, AAA+ proteases must be highly specific in order to avoid wasteful destruction.

Structure
The AAA+ protease consists of a hexameric ring of ATPases surrounding the active site, which is located within an interior chamber, known as the AAA+ ring. There are as many as six potential binding sites within the ring, but studies have shown that there is only a maximum of four sites occupied even at complete saturation. In addition, even a single subunit is sufficient to drive the mechanism of protein unfolding.

Attached to the AAA+ ring is a sequestered degradation chamber of a protease. The very narrow entry portals to this chamber can only allow unfolded polypeptides to enter, allowing a high degree of specificity. Therefore, the degradation of the folded protein, then the polypeptide chain, requires collaboration between both the active sites of the AAA+ ring and the protease.

Mechanism
First, the AAA+ ring recognizes the proper protein to be degraded by binding to an exposed peptide of the substrate, called a degradation tag or a degron. Degrons are found in most substrates, and are simply short, unordered sequences of peptides recognized by the enzyme. As the degron is pulled in through the upper pore of the AAA+ ring, surrounding ATPases drive the conformational changes that result in the unfolding of the protein. The denatured polypeptides are then translocated through a narrow pore into the degradation chamber of a peptidase, where proteolysis occurs.

Cdc48
The ATPase Cdc48 is a principal ATP driven-machine that is active in eukaryotic cells. Its physiological functions are crucial to many cellular processes that include cellular progession, homotypic membrane fusion, chromatin reconstruction, and transcriptional management, and metabolic regulation. Cdc48 is best known for its endoplasmic reticulum protein degradation by the ubiquitin proteasome system.

ATPase Cdc48 is fairly associated with cellular activities (AAA) and maintains the homohexameric, ring-shaped complex. Typically, Cdc48 is initiated by the ubiquitin proteasome system, which leads to lysosomal degradation. However, Cdc48 is discovered to have significant functions in selective autophagy pathways. Cdc48 will guide proteins into the ubiquitin proteasome system or into the autophagy when protein degradation is in process. This task allows the cell to rid of incompetent and defective protein by either of the degradation pathways.

Human diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease are linked to protein degradation. Mutant Cdc48 induces defections in autophagy accounting for the accumulation of aggregates. Relatively, mutant Cdc48 proteins expose elevated ATPase activity and an immense number of conformational alterations of the N-terminal domain that may inflict an imbalance in cofactor binding along with ubiquitlated proteins affiliated with Cdc48.