2.2.1. Core proteases of UIPP and UPS

The term "20S proteasome" encompasses variant isoforms of compartmentalized, barrel shaped 700 kDa core proteases (CP) of α1–7β1–7β1–7α1–<sup>7</sup> stoichiometry [10]. Six active site β-subunits of the catalytic chamber are processed from zymogenic β1, β2, and β5 precursor subunits during standard (s20S) proteasome assembly, establishing the amino-(N)-terminal threonine nucleophiles central to the catalytic mechanism [11]. Proteasomes reveal cleavage site preferences for hydrophobic, basic, and acidic P1 residues resembling specificities of prototypic proteases (chymotrypsin-like (CHYT), trypsin-like (TRYP), caspase-like (CASP). Typically, for a compartmentalized protease, access to the active sites is regulated by gated pores, formed by the amino-terminal chains of α-ring subunits [12]. The narrow orifice formed by the α-rings restricts access of most native proteins. Therefore, unstructured protein regions or protein unfolding is a prerequisite for substrate channeling, conducted by 19S 11S proteasome activators [12–15].

Due to tissue-specific or cytokine-inducible expression of proteasomal active site subunits [16, 17], a high diversity of 20S proteasome complexes is principally available to associate with proteasome activators (PA) such as PA700 (19S), PA28αβ, or PA28γ (11S). As reviewed elsewhere [9, 10], proteasomes have been purified and biochemically characterized from various sources, most recently discovering the unique properties of 20S proteasomes from thymus (t20S) [18], a discovery highly relevant for the understanding of positive selection of T cells [19]. Constitutively, expressed standard 20S proteasomes (s20S) and immune proteasomes (i20S) have been compared with respect to their different assembly kinetics, half-lives, and catalytic capabilities [20].

The pro-inflammatory cytokine interferon-γ (IFN-γ) modulates the composition of the immunoproteasome (i20S), due to the expression of zymogens (pro-subunits) of inducible active site subunits (iβ1, iβ2, iβ5). During POMP-dependent proteasome assembly in proximity to the ER, active site subunits of constitutively expressed proteasomes (s20S) are replaced by the inducible subunits, forming immunoproteasomes (i20S). The i20S complexes reveal faster assembly (about 21 versus 80 min) and shorter half-lives (27 versus 133 h) and differ in activity and cleavage site preferences from s20S proteasomes [21, 22]. In concert with other intracellular proteases, combinations of both 20S isoforms, associated with 11S/19S activator complexes, contribute uniquely to processing of peptides for MHC class I antigen presentation of self or foreign antigens [23].
