The proteasome (or macropain) (EC 3.4.25.1) [1,2,3,4,5,6] is a multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. The core of this 2.5 MDa enzyme complex is formed by the 20S proteasome, a barrel-shaped protease of about 700 KDa that associates with one or two 19S regulatory complexes. The 20S proteasome is ubiquitous in archaea and in eukaryotes. In bacteria, the 20S has been found only in actinomycetes.

The main difference between prokaryotic and eukaryotic proteasomes is one of complexity. Prokaryotic 20S proteasomes contain mostly only to different but related subunits, α and β (see <PDOC00668>), while eukaryotic proteasomes contain seven paralogous α-type and seven paralogous β-type subunits. Subunits that belong to the α-type group are proteins of from 210 to 290 amino acids that share a number of conserved sequence regions.

Some subunits that are known to belong to this family are listed below:

• Vertebrate subunits C2 (nu), C3, C8, C9, iota and zeta.
• Drosophila PROS-25, PROS-28.1, PROS-29 and PROS-35.
• Yeast C1 (PRS1), C5 (PRS3), C7-α (Y8) (PRS2), Y7, Y13, PRE5, PRE6 and PUP2.
• Arabidopsis thaliana subunits α and PSM30.
• Thermoplasma acidophilum α-subunit. In this archaebacteria the proteasome is composed of only two different subunits.
• Rhodococcus erythropolis 20S proteasome α subunit 1 (PrcA 1) and 2 (PrcA 2).

The core of the α subunit is a sandwich of two five-stranded antiparallel β-sheets. The β sandwich is flanked by the α helices H3, H4, and H5 on top and by H1 and H2 at the bottom (see <PDB:1PMA>) [7].

As a signature pattern for proteasome A-type subunits we selected the best conserved region, which is located in the N-terminal part of these proteins. We also have developed a profile which covers the whole conserved region.