The proteasome (or macropain) (EC 3.4.25.1) [1,2,3,4,5,6,7] 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. All archaea and eukaryotes have a 20S proteasome as well as some actinobacteria , but most bacteria have a simpler homologous structure heat shock locus v (HslV) or ClpQ.

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 β-type group are proteins of from 190 to 290 amino acids that share a number of conserved sequence regions. The HslV subunit has sequence similarity with the β-type subunits of the 20S proteasome.

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

• Vertebrate subunits C5, β, delta, epsilon, theta (C10-II), LMP2/RING12, C13 (LMP7/RING10), C7-I and MECL-1.
• Yeast PRE1, PRE2 (PRG1), PRE3, PRE4, PRS3, PUP1 and PUP3.
• Drosophila L(3)73AI.
• Fission yeast pts1.
• Thermoplasma acidophilum β-subunit. In this archaebacteria the proteasome is composed of only two different subunits.
• Rhodococcus erythropolis 20S proteasome β subunit 1 (PrcB 1) and 2 (PrcB 2).
• Escherichia coli ATP-dependent protease subunit HslV (EC=3.4.25.2).

The proteasome β-type subunit structure consists of a core of two antiparallel β sheets that is flanked by α helices on both sides (see <PDB:1PMA>) [8].

As a signature pattern for proteasome B-type subunits we selected the best conserved region, which is located in the N-terminal part of these proteins. The pattern is specific for the 20S-subtype and does not detect the HslV-subtype. We also have developed a profile which covers the whole conserved region of both subtypes.