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PROSITE documentation PDOC00668

Proteasome beta-type subunit signature and profile


The proteasome (or macropain) (EC [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=

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.


These proteins belong to family T1 in the classification of peptidases [9,E2].

Last update:

July 2013 / Text and profile revised.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

PROTEASOME_BETA_2, PS51476; Proteasome beta-type subunit profile  (MATRIX)

PROTEASOME_BETA_1, PS00854; Proteasome beta-type subunits signature  (PATTERN)


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PubMed ID7682410

2AuthorsRivett A.J.
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TitleCrystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly.
SourceJ. Mol. Biol. 335:233-245(2004).
PubMed ID14659753

7AuthorsBochtler M. Ditzel L. Groll M. Huber R.
TitleCrystal structure of heat shock locus V (HslV) from Escherichia coli.
SourceProc. Natl. Acad. Sci. U.S.A. 94:6070-6074(1997).
PubMed ID9177170

8AuthorsLoewe J. Stock D. Jap B. Zwickl P. Baumeister W. Huber R. "Crystal structure of the 20S proteasome from the archaeon T.
Titleacidophilum at 3.4 A resolution.
SourceScience 268:533-539(1995).
PubMed ID7725097

9AuthorsRawlings N.D. Barrett A.J.
TitleFamilies of serine peptidases.
SourceMethods Enzymol. 244:19-61(1994).
PubMed ID7845208


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