Clamp domain structure

The (t2 protein is a clamp attached to the 2,1 shell. The protein has three distinct binding sites on the shell, one of which is across a 2-fold axis. There are thus 150 copies of this protein. The 417 residues form a globular domain consisting mostly of helices (Fig. 13 see Color Insert). Most of the structure is formed by a repeated motif of about 150 residues. The motif starts with a strand and is followed by three helices, the last two of which are antiparallel. A loop region containing a two-stranded... 

Three structure-specific domains, mostly found in eukaryotic cells, have been identified for membrane association and activation of amphitropic proteins [21]. The Cl lipid clamp is a conserved cysteine-rich protein domain that binds lipids and is found in protein kinases... 

There are, however, minor differences on the enzymes surfaces caused by amino acid insertions and deletions. These differences are most likely responsible for conferring specificity toward the interaction with factors specific for Pol I, II, and III. In addition to the 12 subunits that are either identical or homologous, Pol I contains two specific subunits, A34.5 and A49, and Pol III contains a subcomplex of three specific subunits, called C82, C34, and C31, in yeast. The location of the two Pol I—specific subunits has been determined by electron microscopy and immunolabeling (Bischler et al., 2002). The Pol I subunit A49 binds to the top of the clamp, and subunit A34.5 is located near the jaws. The location of the specific C82/C34/C31 complex of Pol III can be inferred from subunit-subunit interaction studies (Ferri et al., 2000 Flores et al., 1999). These studies indicate that the specific subcomplex is located between the largest polymerase subunit and the Rpb4/7 complex counterpart C17/C25. The Cll subunit of Pol III contains a C-terminal domain that apparently corresponds structurally and functionally to domain III of TFIIS (Chedin et al., 1998 Kettenberger et al., 2003), which inserts into the polymerase pore. Thus, in Pol III, the RNA cleavage stimulatory activity is incorporated into a polymerase subunit, in contrast to Pol II, where it is provided by the additional factor TFIIS. 

Fig. 5. Structure of Dpo4 polymerase and of the Pol IV and 8 subunit /3-binding peptides bound to the clamp. (A) Crystal structure of Dpo4. The DNA and nucleotide in the ternary complex with Dpo4 are removed for clarity (Ling et al., 2001). The four structural domains common among Y polymerase are shown in red (palm), blue...

Although the role of RNA internal loops in the formation of RNA tertiary structure is only beginning to be understood, the crystal structure of the P4-P6 domain of the group I intron provides us with an instance of an internal loop which causes an approximately 180° bend between the two long helices which make up the three-dimensional structure and another internal loop which clamps down the two extended helices parallel to each other by forming a tertiary interaction with a tetraloop at the end of the other helbc (5)(7). The role of internal loops in stabilization of intermolecular RNA-RNA complexes has also been studied in several systems as discussed below. 

The interface between the helical domain and the remainder of the domain in the EF buries the 16 hydrophobic residues and 3600 A of surface area. None of these interactions are preserved in the EF-CaM complex when CaM inserts itself between Ca and the hehcal domain. In doing so, CaM occupies much of the same volume occupied by the helical domain in the structure of the EF alone. To accommodate CaM, the helical domain, acting as a unit, moves 15 A and rotates 30° such that Ca, the linker, and the helical domain form a large clamp that almost completely encircles CaM. 

Another feature common to all nonviral sialidases is the so-called Asp-box, a motif (S/T-X-D-[X]-G-X-T-W/F) that repeats one to five times along the sequences. Each Asp-box forms a clamp-like loop and they occur at topologically equivalent positions on the outside of the structure between the third and fourth p-strand of a propeller blade [12, 114, 115]. For example, in the sialidase Nani of Clostridium perfringens four Asp-boxes are located in the blades one to four (PDB ID 2BF6 [115]). However, in endosialidases only two Asp-boxes have been found in the first and fourth blade of the propeller [12], with the sequences S-G-D-D-G-Q/ K-T-W and S-X-D-X-G-X-X-W that are conserved in aU so far known endosialidases. Interestingly, in endoNF the p-barrel domain is inserted between the third and fourth p-sheet of the second blade, thereby replacing a potential Asp-box. Since the Asp-boxes are located on the back side of the propeller and remote from the active site, any functions other than structural folds have not been found as yet for these motifs. 

---