STRUCTURES OF TERNARY COMPLEXES OF RAT DNA-POLYMERASE-BETA, A DNA TEMPLATE-PRIMER, AND DDCTP

Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA tem plate-primer, and dideoxycytidine triphosphate (ddCTP) have been deter mined at 2.9 Angstrom and 3.6 Angstrom resolution, respectively, ddCTP is the triphosphate of dideoxycytidine (ddC), a nucleoside analog tha t targets the reverse transcriptase of human immunodeficiency virus (H IV) and is at present used to treat AIDS, Although crystals of the two complexes belong to different space groups, the structures are simila r, suggesting that the polymerase-DNA-ddCTP interactions are not affec ted by crystal packing forces. In the pol beta active site, the attack ing 3'-OH of the elongating primer, the ddCTP phosphates, and two Mg2 ions are all clustered around Asp(190), Asp(192), and Asp(256). Two o f these residues, Asp(190) and Asp(256), are present in the amino acid sequences of all polymerases so far studied and are also spatially si milar in the four polymerases-the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta-whose crystal structures are now known. A two-metal i on mechanism is described for the nucleotidyl transfer reaction and ma y apply to all polymerases. In the ternary complex structures analyzed , pol beta binds to the DNA template-primer in a different manner from that recently proposed for other polymerase-DNA models.