Figure 3–69 The marking of proteins by ubiquitin. (A) The three-dimensional structure of ubiquitin, a small protein of 76 amino acids. A family of special enzymes couples its carboxyl end to the amino group of a lysine side chain in a target protein molecule, forming an isopeptide bond. (B) Some modification patterns that have specific meanings to the cell. Note that the two types of polyubiquitylation differ in the way the ubiquitin molecules are linked together. Linkage through Lys48 signifies degradation by the proteasome (see Figure 6–84), whereas that through Lys63 has other meanings. Ubiquitin markings are “read” by proteins that specifically recognize each type of modification.
Figure 3–70 The marking of proteins with ubiquitin. (A) The C-terminus of ubiquitin is initially activated by being linked via a high-energy thioester bond to a cysteine side chain on the E1 protein. This reaction requires ATP, and it proceeds via a covalent AMP-ubiquitin intermediate. The activated ubiquitin on E1, also known as the ubiquitin-activating enzyme, is then transferred to the cysteine on an E2 molecule. (B) The addition of a polyubiquitin chain to a target protein. In a mammalian cell, there are several hundred distinct E2–E3 complexes. The E2s are called ubiquitinconjugating enzymes. The E3s are referred to as ubiquitin ligases. (Adapted from D.R. Knighton et al., Science 253:407–414, 1991.) two of many polyubiquitylated possible protein targeted substrate-binding for destruction arms
In this manner, specific proteins are targeted for rapid destruction in response to specific signals, thereby helping to drive the cell cycle (discussed in Chapter 17). The timing of the destruction often involves creating a specific pattern of phosphorylation on the target protein that is required for its recognition by the F-box subunit. It also requires the activation of an SCF ubiquitin ligase that carries the appropriate substrate-binding arm. Many of these arms (the F-box subunits) are interchangeable in the protein complex (see Figure 3–71B), and there are more than 70 human genes that encode them.
As emphasized previously, once a successful protein has evolved, its genetic information tends to be duplicated to produce a family of related proteins. Thus, for example, not only are there many F-box proteins—making possible the recognition of different sets of target proteins—but there is also a family of scaffolds (known as cullins) that give rise to a family of SCF-like ubiquitin ligases.
A protein machine like the SCF ubiquitin ligase, with its interchangeable parts, makes economical use of the genetic information in cells. It also creates opportunities for “rapid” evolution, inasmuch as new functions can evolve for the entire complex simply by producing an alternative version of one of its subunits.
Ubiquitin ligases form a diverse family of protein complexes. Some of these complexes are far larger and more complicated than SCF, but their underlying enzymatic function remains the same (Figure 3–71D).
Detailed structures obtained for one of the GTP-binding protein family members, the EF-Tu protein, provide a good example of how allosteric changes in protein conformations can produce large movements by amplifying a small, local conformational change. As will be discussed in Chapter 6, EF-Tu is an abundant molecule that serves as an elongation factor (hence the EF) in protein synthesis, loading each aminoacyl-tRNA molecule onto the ribosome. EF-Tu contains a Ras-like domain (see Figure 3–67), and the tRNA molecule forms a tight complex with its GTP-bound form. This tRNA molecule can transfer its amino acid to the growing