Nucleotide binding pockets, domains

The a subunit has two other important functional domains in addition to the P-binding domain. First, the a subunit interacts with the receptor through a domain that includes the last five amino acids of the C-terminus (Figure 7.3). Second, it bears the guanine nucleotide binding pocket and... 

Fig. 5.19. GTP and GDP structures of transducin. The Ga,t subunit of transducin possesses—in contrast to Ras protein and to other small regulatory GTPases —an a-hehcal domain that hides and closes the G-nucleotide binding pocket. The conformational changes that accompany the transition from the inactive G t GDP form (a) into the active G t GTP form (b), are restricted to three structural sections that are known as switches I, II and III. Switch I includes the link of the a-helical domain with P2, switch II affects in particular hehx a2, and switch III, the pS—a3 loop. Switch III includes a sequence that is characteristic for the a-subunits of the heterotrimeric G-proteins. The conformational changes of switches II and III affect structural sections that are assumed to be binding sites for the effector molecule adenylyl cyclase (AC) and the y-subunit of cGMP-dependent phosphodiesterase (PDEy), based on mutation experiments and biochemical investigations. MOLSKRIPT representation according to Krauhs, (1991).

Fig. 7. Two models also propose that R may use Gfly to catalyze GDP release. In the lever-arm model, the receptor uses the aN helix as a lever to pull G/ y away from Ga, thereby prying Switch II away from the nucleotide-binding pocket and causing GDP release. The alternative, gearshift model requires that the receptor pushes G/ y closer to Ga. This allows the N-terminus of Gy to engage the helical domain, thus forcing the binding pocket due to the reorientation of the two domains. FJ...

Fig. 4. The actin-binding cleft between the upper (red) and lower (gray) 50K domains (orientation as in Fig. 5A). In A (rigor-like), the cleft is shut. In B (pre-powerstroke), the outer end of the cleft (that forms the actin-binding site) is fully open, but the apex or inner end of the cleft (next to the nucleotide-binding pocket ATP is shown in B) is closed. This closure is brought about by the switch 2 element (SW2) being in the closed conformation. In C (post-rigor), both the outer end and the inner end are open. SW2 is open. In A and B the dispositions of SW2 are similar, but not identical. We refer to them as closed 1 (Cj) and closed 2 (C2), respectively.

The structure of the kinesin monomer is classified into the three subdomains—head, neck-linker, and tail (see Figure I.IA). The head domain (residue 1-323) contains a nucleotide-binding pocket, a catalytic site, which controls the conformational state of the neck-linker (residue 324-338) made of 15 amino acids. The neck-helix domain (residues from 339 to the C-terminus), extended from the neck-linker, forms an alpha-helical structure dimeric kinesins are made via coiled-coil interactions between the neck-helices from two monomers (see Figure I.IA). 

In the closed conformation (Fig. 5-10A) the two NBD domains bind to each other and, as shown in Figure 5-11, nucleotide binding occurs in pockets formed between these two domains. The stoichiometry and nucleotide selectivity of these binding pockets have been determined for an ABC transporter that functions to export peptides from yeast mitochondria [34]. The results of this study has led to the proposed reaction cycle diagrammed and described in Figure 5-12. 

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