3spy | pdb_00003spy

RB69 DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA

spinqualitylabelsall models 3spy, resolution 2.14Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3spy is a 3 chain structure with sequence from Enterobacteria phage rb69. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MG, UPC Related: 3spz, 3sq0, 3sq1, 3sq2, 3sq4 Gene: 43 (Enterobacteria phage RB69) Activity: DNA-directed DNA polymerase, with EC number 2.7.7.7 Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed 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'-alpha,beta-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 alpha-phosphorus atom (Palpha) of the incoming dNTP to enable phosphodiester bond formation through simultaneous coordination of both ptO3' and the nonbridging Sp oxygen of the dNTP's alpha-phosphate. The coordination bond length of metal ion A as well as its ionic radius determines how close ptO3' can approach Palpha. 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 Palpha 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 Palpha. This geometric relationship appears to be conserved among DNA polymerases of known structure. Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase.,Xia S, Wang M, Blaha G, Konigsberg WH, Wang J Biochemistry. 2011 Oct 25;50(42):9114-24. Epub 2011 Sep 29. PMID:21923197 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also DNA polymerase

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