Primary structure of the Thermoplasma proteasome and its implications for the structure, function, and evolution of the multicatalytic proteinase

Abstract

The proteasome or multicatalytic proteinase is a high molecular mass multisubunit complex ubiquitous in eukaryotes but also found in the archaebacterial proteasome is made of two different subunits only, and yet the complexes are almost identical in size and shape. Cloning and sequencing the gene encoding the small (beta) subunit of the T. acidophilum complex completes the primary structure of the archaebacterial proteasome. The similarity of the derived amino acid sequences of 233 (alpha) and 211 (beta) residues, respectively, indicates that they arose from a common ancestral gene. All the sequences of proteasomal subunits from eukaryotes available to date can be related to either the alpha-subunit or beta-subunit of the T. acidophilum "Urproteasome", and they can be distinguished by means of a highly conserved N-terminal extension, which is characteristic for alpha-type subunits. On the basis of circumstantial evidence we suggest that the alpha-subunits have regulatory and targeting functions, while the beta-subunits carry the active sites.

PRE3, highly homologous to the human major histocompatibility complex‐linked LMP2 (RING12) gene, codes for a yeast proteasome subunit necessary for the peptidylglutamyl‐peptide hydrolyzing activity

“…Molecular analysis of the Pre3 protein and proteins of yeast and higher eucaryotes identified as components of proteasomes demonstrate that the PRE3 gene product is a subunit of the yeast proteasome. The Pre3 protein can be classified as a member of the p-type proteasome gene family [38]. Thus the up to now identified subunits which can be linked to proteolytic activity of the complex are all of the /?-type [18,21,22].…”

“…3. Alignment of the/?-subunit from archaebacteriae Z acidophilum [38], the yeast Pre3 protein, the Hs6 subunit of the human proteasome [28], and the human MHC-encoded Lmp2 (Ring12) protein [12]. Gaps are inserted for optimal alignment.…”

Covalent modification of the active site threonine of proteasomal β subunits and theEscherichia colihomolog HslV by a new class of inhibitors

“…Initial attempts to classify the proteasome's catalytic mechanism into a category with known proteases were unsuccessful mainly due to a lack of homology with known peptidases (6). Mutational and structural studies uncovered a novel catalytic mechanism, involving an NH 2 -terminal threonine residue as the catalytic nucleophile (2,7): the free amino terminus or the amino group from a conserved, nearby lysine residue activates the threonine hydroxyl group for nucleophilic attack on the peptide bond (7).…”

cDNA cloning of rat proteasome subunit RC7‐I, a homologue of yeast PRE1 essential for chymotrypsin‐like activity

“…All the genes of the 20 S proteasome examined so far were found to encode previously unidentified proteins that have been highly conserved during evolution. The proteasomal subunits, which have considerably high inter-subunit homology, can be classified into two subgroups, a and /I, judging from their high similarities to the oz-and /?-subunit, respectively, of the archaebacterial proteasome [3]. For determining the functions of this proteasomal multisubunit complex, we are attempting to clarify the entire structure of the rat proteasome by recombinant DNA techniques, and so far we have isolated and sequenced cDNAs for 10 subunits [4-lo].…”

“…Proteasomal subunits, which have considerably high inter-subunit homology, can be classified into two subfamilies with high similarities to the 01-and ~-subunit, respectively, of the archaebacterial proteasome [3]. Table II shows computer-assisted homology analysis of the rat proteasomal subunits sequenced so far.…”