GTP-binding proteins are controlled by regulatory proteins that determine whether GTP or GDP is bound, just as phosphorylated proteins are turned on and off by protein kinases and protein phosphatases. Thus, Ras is inactivated by a GTPase-activating protein (GAP), which binds to the Ras protein and induces Ras to hydrolyze its bound GTP molecule to GDP—which remains tightly bound— and inorganic phosphate (Pi), which is rapidly released. The Ras protein stays in its inactive, GDP-bound conformation until it encounters a guanine nucleotide exchange factor (GEF), which binds to GDP-Ras and causes Ras to release its GDP. Because the empty nucleotide-binding site is immediately filled by a GTP molecule (GTP is present in large excess over GDP in cells), the GEF activates Ras by indirectly adding back the phosphate removed by GTP hydrolysis. Thus, in a sense, the roles of GAP and GEF are analogous to those of a protein phosphatase and a protein kinase, respectively (Figure 3–68).
Proteins Can Be Regulated by the Covalent Addition of Other Proteins
Cells contain a special family of small proteins whose members are covalently attached to many other proteins to determine the activity or fate of the second protein. In each case, the carboxyl end of the small protein becomes linked to the amino group of a lysine side chain of a “target” protein through an isopeptide bond. The first such protein discovered, and the most abundantly used, is ubiquitin (Figure 3–69A). Ubiquitin can be covalently attached to target proteins in a variety of ways, each of which has a different meaning for cells. The major form of ubiquitin addition produces polyubiquitin chains in which—once the first ubiquitin molecule is attached to the target—each subsequent ubiquitin molecule links to Lys48 of the previous ubiquitin, creating a chain of Lys48-linked ubiquitins that are attached to a single lysine side chain of the target protein. This form of polyubiquitin directs the target protein to the interior of a proteasome, where it is digested to small peptides (see Figure 6–84). In other circumstances, only single molecules of ubiquitin are added to proteins. In addition, some target proteins are has this binding been disrupted? has this phosphate been added? has this phosphate been removed? P P
Src-type protein kinase activity turns on fully only if the answers to all of the above questions are yes
Figure 3–66 GTP-binding proteins as molecular switches. The activity of a GTP-binding protein (also called a GTPase) generally requires the presence of a tightly bound GTP molecule (switch “on”). Hydrolysis of this GTP molecule by the GTP-binding protein produces GDP and inorganic phosphate (Pi), and it causes the protein to convert to a different, usually inactive, conformation (switch “off”). Resetting the switch requires that the tightly bound GDP dissociates. This is a slow step that is greatly accelerated by specific signals; once the GDP has dissociated, a molecule of GTP is quickly rebound.
modified with a different type of polyubiquitin chain. These modifications have different functional consequences for the protein that is targeted (Figure 3–69B).
Related structures are created when a different member of the ubiquitin family, such as SUMO (small ubiquitin-related modifier), is covalently attached to a lysine side chain of target proteins. Not surprisingly, all such modifications are reversible. Cells contain sets of ubiquitylating and deubiquitylating (and sumoylating and desumoylating) enzymes that manipulate these covalent adducts, thereby playing roles analogous to the protein kinases and phosphatases that add and remove phosphates from protein side chains.
An Elaborate Ubiquitin-Conjugating System Is Used to Mark Proteins