This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. In 2010, we have collected a number of X-ray diffraction data sets from crystals of ternary complexes (TCs) formed by the wild type and mutant bacteriophage RB69 DNA polymerase (RB69pol) at NE-CAT, APS, resulting in two publications (Wang et al., Insights into base selectivity from the 1.8 ? resolution structure of an RB69 DNA polymerase ternary complex, Biochemistry. in press;Xia et al., Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures. J. Mol. Biol. In press). In the first publication, we have extended the resolution of RB69pol TCs from our previously published 2.6 ?-resolution structure to the currently 1.8 ?-resolution structure, and revealed important functional roles of ordered-water molecules mediating the polymerase-DNA duplex interactions in incorporation efficiency of dNMPs. Using a strategically positioned mispair in DNA duplexes, we showed that primer-extension decreased by 100 fold after moving the mispair from the fourth to the third basepair, and sequentially by another 10 fold to the second and first basepair of the primer-terminus and finally to the nascent base pair position. In the second publication, we have captured the replication-competent TCs formed by an RB69pol mutant containing the dG/dTTP mispair at the polymerization insertion site. This is the first structure of the replication-competent TCs formed by any polymerases containing incorrect incoming dNTPs at the polymerization insertion site. This allows us to correlate crystal structures of a replicative polymerase to the kinetic behavior for incorporation of incorrect dNMPs as well as to correlate in vivo mutational rates with relevant in vitro kinetic parameters.
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