Figure 3–71 The structure and mode of action of an SCF ubiquitin ligase. (A) The structure of the five-protein ubiquitin ligase complex that includes an E2 ubiquitinconjugating enzyme. Four proteins form the E3 portion. The protein denoted here as adaptor protein 1 is the Rbx1/Hrt1 protein, adaptor protein 2 is the Skp1 protein, and the cullin is the Cul1 protein. One of the many different F-box proteins completes the complex. (B) Comparison of the same complex with two different substrate-binding arms, the F-box proteins Skp2 (top) and β-trCP1 (bottom), respectively. (C) The binding and ubiquitylation of a target protein by the SCF ubiquitin ligase. If, as indicated, a chain of ubiquitin molecules is added to the same lysine of the target protein, that protein is marked for rapid destruction by the proteasome. (D) Comparison of SCF (bottom) with a low-resolution electron microscopy structure of a ubiquitin ligase called the anaphase-promoting complex (APC/C; top) at the same scale. The APC/C is a large, 15-protein complex. As discussed in Chapter 17, its ubiquitylations control the late stages of mitosis. It is distantly related to SCF and contains a cullin subunit (green) that lies along the side of the complex at right, only partly visible in this view. E2 proteins are not shown here, but their binding sites are indicated in orange, along with substrate-binding sites in purple. (A and B, adapted from G. Wu et al., Mol. Cell 11:1445–1456, 2003. With permission from Elsevier; D, adapted from
P. da Fonseca et al., Nature 470:274–278, 2011. With permission from Macmillan Publishers Ltd.)
Figure 3–72 The large conformational change in eF-Tu caused by GTP hydrolysis. (A and B) The three-dimensional structure of EF-Tu with GTP bound. The domain at the top has a structure similar to the Ras protein, and its red α helix is the switch helix, which moves after GTP hydrolysis. (C) The change in the conformation of the switch helix in domain 1 allows domains 2 and 3 to rotate as a single unit by about 90 degrees toward the viewer, which releases the tRNA that was bound to this structure (see also Figure 3–73). (A, adapted from H. Berchtold et al., Nature 365:126–132, 1993. With permission from Macmillan Publishers Ltd. B, courtesy of Mathias Sprinzl and Rolf Hilgenfeld. PDB code: 1EFT.) (B) domain 1 P P P GTP-binding site switch helix domain 3 domain 2 PP bound GDP release of tRNA GTP hydrolysis site of tRNA binding G G HOOC NH2 switch helix GTP (A) polypeptide chain only after the GTP bound to EF-Tu is hydrolyzed, dissociating the EF-Tu. Since this GTP hydrolysis is triggered by a proper fit of the tRNA to the mRNA molecule on the ribosome, the EF-Tu serves as a factor that discriminates between correct and incorrect mRNA–tRNA pairings (see Figure 6–65).