4fjk | pdb_00004fjk

RB69 DNA polymerase ternary complex with dATP/dA

spinqualitylabelsall models 4fjk, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4fjk is a 3 chain structure with sequence from Escherichia phage RB69. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, DTP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function DPOL_BPR69 This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Publication Abstract from PubMed Current hypotheses that attempt to rationalize the high degree of base selectivity exhibited by replicative DNA polymerases (pols) concur that ternary complexes formed with incorrect dNTPs are destabilized. Knowing what accounts for this destabilization is likely to be the key to understanding base discrimination. To address this issue, we have determined crystal structures of ternary complexes with all twelve mismatches using an engineered RB69 pol quadruple mutant (qm, L415A/L561A/S565G/Y567A) that enabled us to capture nascent mispaired dNTPs. These structures show that mismatches in the Nascent base-pair Binding Pocket (NBP) of the qm pol differ markedly from mismatches embedded in binary pol-DNA complexes. Surprisingly only 3 of 12 mismatches clash with the NBP when they are modeled into the wt pol. The remaining can fit into a wt pol ternary complex but deviate from normal Watson-Crick base-pairs. Repositioning of the templating nucleotide residue and the enlarged NBP in qm ternary complex play important roles in accommodating incorrect incoming dNTPs. From these structures, we propose additional reasons as to why incorrect dNTP are incorporated so inefficiently by wild type RB69 pol: (i) steric clashes with side chains in the NBP after Fingers closing; (ii) weak interactions or large gaps between the incoming dNTP and the templating base; (iii) burying a protonated base in the hydrophobic environment of the NBP. All of these possibilities would be expected to destabilize the closed ternary complex so that incorporation of incorrect dNTP would be a rare event. DNA Mismatch Synthesis Complexes Provide Insights into Base Selectivity of a B Family DNA Polymerase.,Xia S, Wang J, Konigsberg WH J Am Chem Soc. 2012 Dec 6. PMID:23214497 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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