December 2004 Molecule of the Month by David Goodsell
Keywords: protein ubiquitination, protein catabolism, ubiquitin ligase complex, ubiquitin cyle, proteasome
Nothing lasts forever. Many proteins, in fact, don't last more than a few minutes. Our cells are continually building proteins, using them for a single task, and then discarding them. For instance, proteins that are used for signaling or control, such as transcription regulators and the cyclins that control division of cells, lead very brief lives, carrying their messages and then being thrown away. Specialized enzymes are also built just when they are needed, allowing cells to keep up with their minute-by-minute synthetic needs. This approach of planned obsolescence may seem wasteful, but it allows each cell to respond quickly to its constantly changing requirements.
Out with the Old
Of course, cells need to control the destruction of their own proteins, making sure that they remove only proteins that aren't needed any more. The small protein ubiquitin plays a central role in this job. Ubiquitin is attached to obsolete proteins, signaling to the cell that they are ready to be disassembled. As shown in the figure, a string of ubiquitin molecules (colored pink and tan here, from PDB entry 1ubq) is attached to old proteins, such as the src protein shown here (colored blue, from PDB entry 2src). The ubiquitin is then recognized by the destruction machinery of the cell.
As its name implies, ubiquitin is found in all eukaryotic cells and in cells throughout your body. The Nobel Prize in Chemistry was awarded this year to the three researchers who discovered its essential function in 1980. In the subsequent years, it has become apparent that apart from its role in protein disposal, ubiquitin is also used for other tasks, such as directing the transport of proteins in and out of the cell. By connecting ubiquitin together in short or long chains, or using different types of linkages between the molecules, many different signals may be encoded. Because of the important roles it plays, ubiquitin has changed very little over the evolution of life, so you can find a similar form in yeast cells, plant cells, and in our own cells. For more information on ubiquitin from a genomic perspective, see the Protein of the Month at the European Bioinformatics Institute.
The tricky part of this whole process is making sure that ubiquitin is attached only to the proper proteins. Several specialized enzymes sort through the proteins in the cell and pick only the right ones. There are three types of these enzymes, called E1, E2, and E3. The E1 enzyme, shown at the top here from PDB entry 1r4n, is the ubiquitin-activating enzyme that starts the process. Powered by ATP (shown in red), it attaches the tail end of ubiquitin (shown here in light orange) to one of its own cysteine amino acids (shown in green--note, in this structure, the cysteine is mutated to alanine). Then, E1 passes the activated ubiquitin to one of several E2 enzymes, the ubiquitin-conjugating enzymes, shown here from PDB entry 1fxt. These E2 enzymes then work with a large number of different E3 enzymes to recognize obsolete proteins and attach the ubiquitin to them. The E3 enzyme shown here, from PDB entries 1ldk and 1fqv, is shaped like a big clamp. The target protein binds in the gap (shown with the star). The left side of the enzyme recognizes the protein and the right side positions E2 to allow transfer of its ubiquitin.
Once obsolete proteins are tagged with at least four ubiquitin molecules, they are destroyed by proteasomes. Proteasomes are voracious protein shredders, but the destructive machinery is carefully protected so that it can't attack all of the normal proteins in the cell. The proteasome, shown here from PDB entry 1fnt, is shaped like a cylinder, with its active sites sheltered inside the tube. The caps on the ends regulate entry into the destructive chamber, where the protein is chopped into pieces 3 to 23 amino acids long.
Exploring the Structure
PDB entry 1f9j
shows how ubiquitin molecules are strung together into chains. The
crystal was grown with tetraubiquitin (four proteins strung together), but the connection
was only observed between two ubiquitin molecules in the structure. If you look closely,
you can see the unusual connection between the last glycine amino acid in chain A and
the sidechain of lysine number 148 in the middle of chain B.
This illustration was created with RasMol. You can create similar illustrations by clicking on the accession codes here and picking one of the options under View Structure.
Further information on ubiquitin
A. P. VanDemark and C. P. Hill (2002) Structural Basis of Ubiquitylation. Current
Opinion in Structural Biology 12, 822-830.
M. H. Glickman and A. Ciechanover (2002) The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction. Physiological Reviews 82, 373-428.
C. M. Pickart (2000) Ubiquitin in Chains. Trends in Biochemical Sciences 25, 544-548.
© 2015 David Goodsell & RCSB Protein Data Bank