Cleft domain

The catalytic subunit of cAPK contains two domains connected by a peptide linker. ATP binds in a deep cleft between the two domains. Presently, crystal structures showed cAPK in three different conformations, (1) in a closed conformation in the ternary complex with ATP or other tight-binding ligands and a peptide inhibitor PKI(5-24), (2) in an intermediate conformation in the binary complex with adenosine, and (3) in an open conformation in the binary complex of mammalian cAPK with PKI(5-24). Fig.l shows a superposition of the three protein kinase configurations to visualize the type of conformational movement. 

The catalytic subunit then catalyzes the direct transfer of the 7-phosphate of ATP (visible as small beads at the end of ATP) to its peptide substrate. Catalysis takes place in the cleft between the two domains. Mutual orientation and position of these two lobes can be classified as either closed or open, for a review of the structures and function see e.g. [36]. The presented structure shows a closed conformation. Both the apoenzyme and the binary complex of the porcine C-subunit with di-iodinated inhibitor peptide represent the crystal structure in an open conformation [37] resulting from an overall rotation of the small lobe relative to the large lobe. 

Another class of DNA-binding proteins are the polymerases. These have a nonspecific interaction with DNA because the same protein acts on all DNA sequences. DNA polymerase performs the dual function of DNA repHcation, in which nucleotides are added to a growing strand of DNA, and acts as a nuclease to remove mismatched nucleotides. The domain that performs the nuclease activity has an a/P-stmcture, a deep cleft that can accommodate double-stranded DNA, and a positively charged surface complementary to the phosphate groups of DNA. The smaller domain contains the exonuclease active site at a smaller cleft on the surface which can accommodate a single nucleotide. 

Figure 6.20 Space-filling diagram illustrating the structural changes of CDK2 upon cyclin binding, (a) The active site is in a cleft between the N-terminal domain (blue) and the C-terminal domain (purple). In the inactive form this site is blocked by the T-loop.

Figure 13.6 Schematic diagram of Go. from transducin with a bound GTP analog. The polypeptide chain is organized Into two domains a catalytic domain (light red) with a structure similar to Ras, and a helical domain (green) which is an Insert in the loop between al and P2. There are three switch regions (violet) that have different conformations in the different catalytic states of Go.. The GTP analog (brown) Is bound to the catalytic domain in a cleft between the two domains. (Adapted from J. Noel et al.. Nature 366 654-663, 1993.)...

Figure 14.15 Stmcture of the SI fragment of chicken myosin as a Richardson diagram (a) and a space-filling model (b). The two light chains are shown in magenta and yellow. The heavy chain is colored according to three proteolytic fragments produced by trypsin a 25-kDa N-terminal domain (green) a central 50-kDa fragment (red) divided by a cleft into a 50K upper and a 50K lower domain and a 20-kDa C-terminal domain (blue) that links the myosin head to the coiled-coil tail. The 50-kDa and 20-kDa domains both bind actin, while the 25-kDa domain binds ATP. [(b) Courtesy of 1. Rayment.]...

Citrate synthase in mammals is a dimer of 49-kD subunits (Table 20.1). On each subunit, oxaloacetate and acetyl-CoA bind to the active site, which lies in a cleft between two domains and is surrounded mainly by a-helical segments (Figure 20.6). Binding of oxaloacetate induces a conformational change that facilitates the binding of acetyl-CoA and closes the active site, so that the reactive carbanion of acetyl-CoA is protected from protonation by water. 

Conti et al. (1996) solved the crystal structure of the P. pyralis luciferase at 2.0 A resolution. The protein is folded into two compact domains, a large N-terminal portion and a small C-terminal portion. The former portion consists of a /1-barrel and two /1-sheets. The sheets are flanked by a-helices to form an aflafia five-layered structure. The C-terminal portion of the molecule forms a distinct domain, which is separated from the N-terminal domain by a wide cleft. It is suggested that the two domains will close up in the course of the luminescence reaction. 

Figure 3 shows the three-dimensional structure of the MoFe protein from Klebsiella pneumoniae, Kpl, obtained at 1.65-A resolution (7). The overall structure of the polypeptides is frilly consistent with that reported earlier for Avl (3). The a and /8 subunits exhibit similar polypeptide folds with three domains of parallel /3 sheet/a helical type. At the interface between the three domains in the a subunit is a wide shallow cleft with the FeMoco at the bottom of the cleft about 10 A from the solvent. FeMoco is enclosed within the a subunit. The P cluster, however, is buried within the protein at the interface between the a and /8 subunits, being bound by cysteine residues from each subunit. A pseudo-twofold rotation axis passes between the two halves of the P cluster and relates the a and (3 subunits. Each af3 pair of subunits contains one FeMoco and one P cluster and thus appears... 

And third, since virtually all enzymes [67], particularly those that catalyze phos-phoryl-transfer reactions [68 74], possess structures with at least two, discrete, relatively rigid structural domains, or lobes, separated by a deep cleft, the cytoplasmic portion of the H -ATPase polypeptide chain in the model of Fig. 2 is drawn in such a way as to suggest this situation. The proposed interdomain cleft is indicated by the arrow. No additional structural features of the ATPase molecule are implied in the model. In regard to comparisons with the Ca -ATPase, it is of interest to note that the two cytoplasmic domains proposed in Fig. 2 correspond to the Cl and C2 domains in the model of Andersen and Vilsen [53]. 

Further considerations here do not depend critically on the accuracy of the working model of Fig. 2. Indeed, the interdomain cleft may as well be at the side of the molecule near the surface of the membrane as can be imagined from inspection of the structures proposed by Taylor et al. [75] and Stokes and Green [76] for the Ca -ATPase. It is only important to stipulate that the molecule contains at least two domains and a cluster of membrane-embedded helices. 

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