Sliding DNA clamp

X.P. Kong, R. Onrust, M. OdonneU, J. Ktuiyan, 3-Dimensional Structure of the p Subunit of Escherichia coli DNA Polymerase-111 Holoenzyme - A Sliding DNA Clamp , Cell, 69,425(1992)... 

Kong XP, Onrust R, O Donnell M, Kuriyan J. Three-dimensional structure of the beta subunit of E. coli DNA polymerase m holoenzyme a sliding DNA clamp. Cell 1992 69 425-437. 

Bowman GD, O Donnell M, Kuriyan J. Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Nature 2004 429 724-730. 

Figure 28.26 Structure of a sliding DNA clamp. The dimeric (3 subunit...

Conserved residues among helicases Figure 28.25 A sliding DNA clamp Figure 28.26 DNA-repair enzyme AlkA Figure 28.43 Cre recombinase and topoisomerase I Figure 28.50 RNA polymerase Figure 29.1... 

Figure 16.1 Model of TLS across DNA lesions by specialized DNA polymerases. PCNA, the sliding DNA clamp, becomes monoubiquitinated in response to exposure to genotoxic agents. Binding of a TLS polymerase to the ubiquitinated PCNA via both ubiquitin- and PCNA-binding sites helps to recruit it to the damage site, and enables TLS. See text for details.

FIGURE 10.7 The dimer of 3-subunits of DNA polymerase III bound to DNA. One monomer is shown in yellow, the other in red. Note that the dimer forms a closed loop around the DNA (shown in blue). The rest of the polymerase III holoenzyme is not shown. The remainder of the holoenzyme consists of the core enzyme responsible for the polymerization and the 3 exonuclease activity (ot-, e-, and 0-subunits) and the y-complex (consisting of y-, 5-, 5, X t and /-subunits), which allows the 3-sub-units to form a clamp that surrounds the DNA and slides along it as polymerization proceeds. [Adapted from Kong, X. P., etal Three-Dimensional Structure of the Subunit ofE. Coli DNA Polymerase Holoenzyme A Sliding DNA Clamp. Cell 69, 425-437 (1992).]... 

DNA polymerase III is an asymmetric dimer. It contains two copies of the core polymerase, snbnnits a, e, and 0. The a subunit has polymerase activity while e is a 3 — 5 proofreading exonuclease. A 2 subunit is associated with one arm and a (55 i/)2 subunit with the other. These serve as the clamp-loading complex. The P2 subunits form ringlike structures that serve as sliding DNA clamps. 

Stukenberg, P. T., Studwell-Vaughan, P. S., and O Donnell, M. (1991). Mechanism of the sliding beta-clamp of DNA polymerase III holoenzyme. /. Biol. Ghem. 266, 11328-11334. 

Shamoo, Y. and Steitz, T. A. (1999). Building a replisome from interacting pieces sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell 99,155-166. 

DNA polymerase III can polymerize DNA, but with a much lower processivity than one would expect for the organized replication of an entire chromosome. The necessary increase in processivity is provided by the addition of the J8 subunits, four of which complete the DNA polymerase III holoenzyme. The J3 subunits associate in pairs to form donut-shaped structures that encircle the DNA and act like clamps (Fig. 25-10b). Each dimer associates with a core subassembly of polymerase III (one dimeric clamp per core subassembly) and slides along the DNA as replication proceeds. The J8 sliding clamp prevents the dissociation of DNA polymerase III from DNA, dramatically increasing processivity—to greater than 500,000 (Table 25-1). 

Indian C, Mclnerney P, Georgescu R, Goodman ME, O Donnell M. A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously. Mol. Cell 2005 19 805-815. Bunting KA, Roe SM, Pearl LH. Structural basis for recruitment of translesion DNA polymerase Pol JV/DinB to the beta-clamp. Embo. J. 2003 22 5883-5892. 

Majka J, Burgers PM. Yeast Radl7/Mec3/Ddcl a sliding clamp for the DNA damage checkpoint. Proc. Natl. Acad. Sci. U.S.A. 2003 100(5) 2249-2254. 

Figure 27.31. Structure of the Sliding Clamp. The dimeric P2 subunit of DNA polymerase III forms a ring that surrounds the DNA duplex. It allows the polymerase enzyme to move without falling off the DNA substrate. 

The polymerase holoenzyme assembles. The DNA polymerase ITT holoen-zyme assembles on the prepriming complex, initiated by interactions between DnaB and the sliding clamp subunit of DNA polymerase 111. These interactions also trigger ATP hydrolysis within the DnaA subunits, signaling the initiation of DNA replication. The breakup of the DnaA assembly prevents additional rounds of replication from beginning at the replication origin. 

The second functional difference between the DNA polymerases is the level of processivity, which refers to the number of nucleotides added before the polymerase dissociates from the template. Again, DNA pol III is the clear winner in this category, as might be expected based on its central role in DNA replication. The b subunit of DNA pol III is designated as the processivity subunit. Two b subunits form a "clamp" around the template strand, which then can slide along the DNA (Fig. 22.5). This arrangement ensures that an active holoenzyme (all the DNA pol III subunits combined) remains tightly associated with DNA to enhance processivity. 

Stukenberg P. T., Turner J., O Donnell M. (1994) An explanation for lagging strand replication Polymerase hopping among DNA sliding clamps. Cell 78 877. 

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