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PDB:1RYP

Protein Name

20S proteasome

Species

Saccharomyces cerevisiae (Baker's yeast)

Biological Context

The proteasome is a multifunctional enzyme complex which is found in the cytosol and the nucleus. In eukaryotic cells the proteasome is mainly involved in the removal of abnormal or misfolded protein. Furthermore it plays an important role in stress response (by processing or degrading transcriptional regulators), cell-cycle control (by degradation of cyclins), cell differentiation and metabolic adaptation (by destruction of transcription factors or metabolic enzymes), and the cellular immune response (by generating antigenic peptide presented by major histocompatibility complex (MHC) class I molecules). All these functions are linked to the degradation of polyubiquitinated proteins (ubiquitin-proteasome system). The activated proteasomes are called 26S proteasomes. They are constructed from the core region 20S proteasomes and the regulatory particles (RP, another name PA700; 19S particle) which are connected to both ends of the 20S proteasomes and have ATPase activity. In addition the 20S proteasomes are connected to the other activation factor, PA28, forming the football-like shaped proteasomes.

Structure Description

1ryp1ryp_x1ryp_y

The 20S proteasomes have cylindrical structures composed of the 28 subunits, in which the regions containing the seven different alpha-type subunits (alpha1-7) and the regions containing seven different beta-type subunits (beta1-7) are arranged (alpha)(beta)(beta)(alpha). Five of the seven types of beta-subunits assemble as proproteins, which are proteins in a functional matured state, after proteolysis. Three of them, beta1/PRE3, beta2/PUP1 and beta5/PRE2 (catalytic subunits) are cleaved between the threonine at position 1 (Thr1) and the last glycine of the pro-sequence, which releases the active-site residue Thr1. The mature enzymes beta1, beta2 and beta3 have activity to cleave polypeptides at the C-terminal side of acidic residues (PGPH activity or Caspase-like activity), at the C-terminal side of basic residues (Trypsin-like activity), and at the C-terminal side of hydrophobic residues (Chymotrypsin-like activity), respectively. In mammalian cells, highly homologous isozymes exist in which each catalytic subunit of the three beta-type subunits is replaced by LMP2, LMP7 or MECL2. These exchangeable catalytic subunits are induced by T-cell-derived antiviral cytokines such as interferon-gamma. The induced enzymes are called "immuno-proteasomes", since their function is changed to generate the antigen epitopes of MHC class I. Although Archaea also have archaeal proteasomes composed of (alpha)7(beta)7(beta)7(alpha)7 and are difficult to distinguish from eukaryotic 20S proteasomes, they have no activation factor. The first X-ray structural analysis of a proteasome was carried out for the Thermoplasma acidophilum enzyme. This is the crystal structure of the yeast 20S proteasome. All alpha- and beta-type subunits have the beta-sandwich structure typical for the Ntn (N-terminal nucleophile) family of hydrolases. It is formed by five-stranded antiparallel beta-sheets wedged between an upper layer formed by helices H3, H4, H5 and a lower layer formed by helices H1 and H2. The overall quaternary structure of the yeast proteasome is similar to that of T. acidophilum.

Protein Data Bank (PDB)

References

Source

  • Groll, M. Ditzel, L. Lowe, J. Stock, D. Bochtler, M. Bartunik, H.D. Huber, R.; "Structure of 20S proteasome from yeast at 2.4 angstroms resolution."; Nature; (1997) 386:463-471 PubMed:9087403.

Others

author: Tomoki Matsuda


Japanese version:PDB:1RYP