Ubiquitin substrate interactions

Ubiquitin/Proteasome. Figure 2 Functional consequences of ubiquitin linkage. Substrates (blue bars) are linked via lysine residues (K) to ubiquitin or ubiquitin chains, (a) Attachment of chains connected via Lysines in position 48 of ubiquitin (K48) targets substrates for proteasomal degradation. In contrast modification of one (b) or multiple (c) lysines by a single ubiquitin molecule mediates novel protein interactions or initiates endocytosis. Conjugation of K63-linked polyubiquitin (d) alters protein function and can also serve as a signal for endocytosis. 

Fig. 4.1. Fundamentals of the ubiquitin system. Adapted from Ref [5]. Figure 4.1 shows the fundamentals of the ubiquitin system. (1) Ubiquitin is synthesized in linear chains or as the N-terminal fusion with small ribosomal subunits that are cleaved by de-ubiquitylating enzymes to form the active protein. Ubiquitin is then activated in an ATP-dependent manner by El where a thiolester linkage is formed. It is then transthiolated to the active-site cysteine of an E2. E2s interact with E3s and with substrates and mediate either the indirect (in the case of HECT E3s) or direct transfer of ubiquitin to substrate. A number of factors can affect this process. We know that interactions with Hsp70 can facilitate ubiquitylation in specific instances and competition for lysines on substrates with the processes of acetylation and sumoylation may be inhibitory in certain instances. (2) For efficient proteasomal targeting to occur chains of ubiquitin linked internally through K48 must be formed. This appears to involve multiple...

The essential components of the SCF ubiquitin E3 ligase include Skpl, Cul-1/ Cdc53, one of many F-box proteins, and the RINC-H2-finger protein Rod (Rbxl or Hrtl) (Figure 6.2). Although initial studies did not reveal the presence of a fourth component of the SCF complex [14, 15], later work showed that a RINC-H2-finger protein, Rod, is an essential subunit of the SCF complex [3]. The SCF complex thus contains three invariable components (Rod, Cull, and Skpl) which provide a core structure to which one of the many substrate-specific subunits (F-box proteins) binds. The Rocl-Cull-Skpl core also independently interacts with the ubiquitin E2-conjugating enzyme to couple ubiquitin transfer to the substrates [3]. One of the E-box proteins binds directly to a specific substrate and such interaction facilitates the polyubiquitination of the substrate by ubiquitin... 

Skpl serves as an adaptor protein that provides a molecular link between Cull/ Rod and the F-box proteins [4, 5]. The Skpl protein contains two separate protein-interaction domains that are conserved among its family members between species [21]. The N-terminal region of Skpl (- l-70 a.a.) interacts with Cull while the C-terminal half (100-163 a.a.) binds the F-box proteins [21]. The use of Skpl as an adaptor to link the core ubiquitin E3 ligase components of Cull/Rocl with numerous and diverse substrate-targeting subunits, the F-box proteins, represents a strategy to specifically target many proteins for ubiquitination... 

However, it is still possible that other mechanisms may exist to bridge the gap between substrate and E2 in the SCF-mediated ubiquitin-transfer reaction. For example, reports suggest that SCF may form higher order structures to facilitate the degradation of protein substrates. The S. pombe F-box proteins Popl and Pop2 have been shown to form heterodimers, and evidence suggests that these interactions may be important for the degradation of their in vivo substrates [62]. 

Another level of control is mediated through the control of F-box protein stabilities by the SCF complex using an auto-ubiquitination mechanism. Deletion of the F-box motif of various F-box proteins such as yeast Cdc4 or j5-Trcp abolishes the interaction between Skpl/Cull and the F-box proteins [66]. Consequently the F-box proteins become more stable. This regulation may provide a means to recycle the components of SCF complexes between different F-box proteins. In addition, the levels of a particular F-box protein may be in part regulated by the balance between autoubiquitination and substrate-specific ubiquitination and thus could be sensitive to the presence of the substrates. 

The F-box protein family is the largest substrate-recognition subunit family. It enables the eukaryotic cells to use the SCF E3 machinery to ubiquitinate a large number of diverse protein substrates. So far, over 70 F-box proteins have been identified in the human genome [57, 58]. F-box proteins all share an 40-amino acid F-box motif, which is usually followed by a C-terminal protein-protein interaction domain such as the WD40 repeats j5-propeller (Fbw subfamily) and /eucine-rich repeats (LRRs Fbl subfamily Figure 7.5) [59, 60]. F-box proteins interact with... 

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