Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase.

ABSTRACT: We have captured a preinsertion ternary complex of RB69 DNA polymerase (RB69pol) containing the 3' hydroxyl group at the terminus of an extendable primer (ptO3') and a nonhydrolyzable 2'-deoxyuridine 5'-?,?-substituted triphosphate, dUpXpp, where X is either NH or CH(2), opposite a complementary templating dA nucleotide residue. Here we report four structures of these complexes formed by three different RB69pol variants with catalytically inert Ca(2+) and four other structures with catalytically competent Mn(2+) or Mg(2+). These structures provide new insights into why the complete divalent metal-ion coordination complexes at the A and B sites are required for nucleotidyl transfer. They show that the metal ion in the A site brings ptO3' close to the ?-phosphorus atom (P?) of the incoming dNTP to enable phosphodiester bond formation through simultaneous coordination of both ptO3' and the nonbridging Sp oxygen of the dNTP's ?-phosphate. The coordination bond length of metal ion A as well as its ionic radius determines how close ptO3' can approach P?. These variables are expected to affect the rate of bond formation. The metal ion in the B site brings the pyrophosphate product close enough to P? to enable pyrophosphorolysis and assist in the departure of the pyrophosphate. In these dUpXpp-containing complexes, ptO3' occupies the vertex of a distorted metal ion A coordination octahedron. When ptO3' is placed at the vertex of an undistorted, idealized metal ion A octahedron, it is within bond formation distance to P?. This geometric relationship appears to be conserved among DNA polymerases of known structure.

SUBMITTER: Xia S 

PROVIDER: S-EPMC3760225 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature