By SDS gelelectrophoresis, at least 15 different proteins can be distinguished in the 19 S cap complex which are called S1 to S15, starting with the largest protein (all subunits are conserved between yeast and man except S5b, which is absent in S. cerevisiae). Several components of the cap structures (S4, S6, S7, S8) have been characterized as members of the AAA superfamily belonging to the same family. In the phylogenetic tree, six eukaryotic subfamilies corresponding to different proteasome subunits can clearly be distinguished (S4, S6a, S6b, S7, S8, S10b). Each subfamily contains exactly one S. cerevisiae protein. They all contain an N-terminal coiled coil domain. A seventh subfamily consists of archebacterial proteins (PAN = proteasome activating nucleotidase), indicating that the archebacterial proteasome also has a regulatory cap in vivo. PAN can be isolated in a complex of 650 kDa containing full length and N-terminally shortened PAN forms (beginning at Met 74, within the coiled-coil domain). The complex stimulates proteolysis of the archebacterial and eukaryotic 20S proteasome, it utilizes CTP even better than ATP.
The RPTs appear to form a ring contacting the 20S core, it seems that every proteasome cap contains all six RPT species. Together with RPN1,2, and 10 (and subunit S5b in humans), they form the "base" of the 19S cap. RPN10 links to the "lid" consisting of the other RPNs. The lid may be responsible for preventing unubiquitinated proteins access to the base. The base alone is able to refold denaturated citrate synthase, its physiological role probably is unfolding substrate proteins and feeding them into the core. The AAA subunits appear to form dimers (S4>S7, S6a>S8, S6b>S10b) via the N-terminus, S4/S7 binds S5b and S2, forming a tetramer in vitro.
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