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| A Short Guide to the Proteolytic Pathway | ||||||
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Protein degradation is a critical regulatory process that allows cells to rapidly respond to intracellular signals and changing environmental conditions by adjusting the levels of key effector proteins. The major proteolytic pathway in plants and animals is the ubiquitin/26S proteasome pathway. Here, proteins destined for degradation become modified by the covalent attachment of multiple ubiquitins. These ubiquitinated substrates are then recognized and degraded by the 26S proteasome, a multisubunit protease complex that degrades the target but leaves the ubiquitins intact for reuse. This pathway is comprised of several steps which require ubiquitin, ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), ubiquitin-protein ligases (E3), and the 26S proteasome. Accumulating genetic analyses indicate that the ubiquitin/26S proteasome pathway plays a major role in a variety of physiological processes in plants, including the cell cycle, embryogenesis, hormone responses, floral homeosis, photomorphogenesis, circadian rhythms, senescence, the stress response and pathogen invasion. Ubiquitin and Ubiquitin-like Proteins
E1: Ubiquitin-activating Enzymes
E2: Ubiquitin-conjugating Enzymes
E3: Ubiquitin-Protein Ligases
26S Proteasome
Suggested Reading
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Ubiquitin is a 76 residue protein that is critical to several cell processes, notably targeted protein
degradation.
To date, ubiquitin genes have been found only in
eukaryotic organisms and these genes are highly conserved across species. Most organisms contain several
genes that encode ubiquitin (and ubiquitin-like proteins, such as SUMO/Smt3 and RUB/Nedd8).
This small
protein is attached to a target protein through a series of ATP-dependent steps.
At the end of the pathway, the target protein will
have a linear chain of several ubiquitins attached to it. This chain is recognized by the 26S proteasome
which degrades the target protein while leaving the ubiquitins intact.
E2 proteins are involved in the second step of the ubiquitin conjugation cascade.
E2 proteins effect an ATP-dependent transfer
of a ubiquitin molecule from a ubiquitin-E1 complex to itself, again covalently attaching the ubiquitin to
a cysteine residue. There are many E2 isoforms in plants and some have specialized functions.
These proteins contain an active site cysteine residue
and generally a Dbox motif 
E3 enzymes facilitate the formation of an isopeptide linkage between the ubiquitin bound to an E2 enzyme
and the target protein that is bound to the E3 enzyme. Additional ubiquitins monomers are added to the
initial ubiquitin to form a poly-ubiquitin chain. This chain is recognized by the proteasome which
subsequently degrades the target protein, leaving the ubiquitin molecules intact for reuse in the
proteolytic pathway. These enzymes are believed to be primarily responsible for substrate selectivity and
thus comprise a diverse and complex family.
The 26S proteasome is a huge, multi-subunit protein complex that is found in all eukaryotic
cells. The proteasome consists of a proteolytically active 20S core complex and the 19S regulatory
complex. The 20S complex is a cylinder made up of four stacked heptameric rings whose active sites are on
the inside of the cylinder. These sites can only be reached through openings at either end of the
cylinder. Access to one or both of these openings is regulated by the 19S complex which is attached to the
end(s) of the cylinder. The 19S complex also participates in unfolding the target protein so it can
interact with the active sites inside the core of the 20S complex.![[Condensed tree]](/images/F-Box-condensed-tree.png){kind=link}
![[Enlarged Tree]](/images/Enlarged_FBox_tree.png){kind=link}