Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates

The crystal structures of the Klenow fragment of the Thermus aquaticus DNA polymerase I (Klentaql) complexed with four deoxyribonucleoside triphosphates (dNTP) have been determined to 2.5 Angstrom resolution. The dNTPs bind adjacent to the O helix of Klentaql. The triphosphate moieties are at nearly identical positions in all four complexes and are anchored by three positively charged residues, Arg659, Lys663, and Arg587, and by two polar residues, His639 and Gln613. The configuration of the base moieties in the Klentaql/dNTP complexes demonstrates variability suggesting that dNTP binding is primarily determined by recognition and binding of the phosphate moiety. However, when superimposed on the Tag polymerase/blunt end DNA complex structure (Eom et al., 1996), two of the dNTP/Klentaql structures demonstrate appropriate stacking of the nucleotide base with the 3' end of the DNA primer strand, suggesting that at least in these two binary complexes, the observed dNTP conformations are functionally relevant.