Structure of the Replicating Complex of a Pol α Family DNA Polymerase

DNA polymerases, with the exception of DNA polymer-ase ␤ (pol ␤), have a common structural core, containing the two universally conserved aspartate residues (De-larue et al., 1990) which, together with the dNTP, bind and Biochemistry the two divalent metal ions that catalyze the polymerase Two structures of the DNA polymerase from the bacte-Yale University riophage RB69 (RB69 pol) have been described pre-New Haven, Connecticut 06511 viously: one of the apo enzyme (Wang et al., 1997), and one of an editing complex (Shamoo and Steitz, 1999). Comparison of these structures with those of thermo-Summary philic pol ␣ family polymerases (Hopfner et al., 1999; Rodriguez et al., 2000; Zhao et al., 1999) shows a high We describe the 2.6 A ˚ resolution crystal structure of degree of structural equivalence, suggesting that RB69 RB69 DNA polymerase with primer-template DNA and pol is a good structural model for other pol ␣ family dTTP, capturing the step just before primer extension. polymerases despite a low sequence similarity with This ternary complex structure in the human DNA poly-them (RB69 pol is 18% identical to the thermophilic pol merase ␣ family shows a 60؇ rotation of the fingers ␣ family polymerases, and about 15% identical to human domain relative to the apo-protein structure, similar pol ␣). RB69 pol is also closely related to T4 DNA poly-to the fingers movement in pol I family polymerases. merase (T4 pol, reviewed in Karam and Konigsberg, Minor groove interactions near the primer 3؅ terminus 2000). An interesting architectural difference between suggest a common fidelity mechanism for pol I and pol I and pol ␣ family polymerases is that the domain pol ␣ family polymerases. The duplex product DNA containing the site of the editing exonuclease lies on orientation differs by 40؇ between the polymerizing one side of the palm in the pol I family, and on the mode and editing mode structures. The role of the opposite side in the pol ␣ family, suggesting differences thumb in this DNA motion provides a model for editing in the mechanism by which the primer terminus is trans-in the pol ␣ family. ferred from the polymerase to the exonuclease active site (Wang et al., 1997). Introduction A structural model of the process of DNA polymeriza-tion has been generated by comparison of various binary DNA polymerases are the central element in the trans-(polymerase and DNA) and ternary (polymerase, primer-mission and maintenance of genetic information. While …