4FK2

RB69 DNA polymerase ternary complex with dTTP/dG

Summary for 4FK2

• Entry DOI: 10.2210/pdb4fk2/pdb
• Related: 4FJ5 4FJ7 4FJ8 4FJ9 4FJG 4FJH 4FJI 4FJJ 4FJK 4FJL 4FJM 4FJN 4FJX 4FK0 4FK4
• Descriptor: DNA polymerase, DNA template, DNA primer, ... (6 entities in total)
• Functional Keywords: dttp/dg, rb69, rb69 pol, quadruple, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage RB69
• Total number of polymer chains: 3
• Total formula weight: 114320.41

Authors

Xia, S.,Wang, J.,Konigsberg, W.H. (deposition date: 2012-06-12, release date: 2012-12-19, Last modification date: 2024-02-28)

Primary citation

Xia, S.,Wang, J.,Konigsberg, W.H.
DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase.
J.Am.Chem.Soc., 135:193-202, 2013

PubMed Abstract: 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 12 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 wild-type (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 dNTPs are incorporated so inefficiently by wt 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; and (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.

PubMed: 23214497
DOI: 10.1021/ja3079048

Experimental method

X-RAY DIFFRACTION (1.98 Å)