Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism

• Published in: Structure (London) Vol. 24; no. 11; pp. 1863 - 1875
• Main Authors: Batra, Vinod K., Beard, William A., Pedersen, Lars C., Wilson, Samuel H.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 01.11.2016
• Subjects: Catalytic Domain; Crystallography, X-Ray; DNA - chemistry; DNA - metabolism; DNA Polymerase beta - chemistry; DNA Polymerase beta - metabolism; Hydrogen Bonding; Kinetics; Models, Molecular; Nucleotides - chemistry; Protein Conformation; Substrate Specificity
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2016.08.006

High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase β with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions. The binary complex structures indicate an induced strain in the mismatched template nucleotide. Addition of a non-hydrolyzable incoming nucleotide stabilizes the templating nucleotide with concomitant strain in the primer terminus. Several dead-end ternary complex structures suggest that DNA synthesis might occur as the enzyme transitions from an open to a closed complex. The structures are consistent with an induced-fit mechanism where a mismatched terminus is misaligned relative to the correct incoming nucleotide to deter or delay further DNA synthesis. [Display omitted] •Structures (23) of a polymerase with DNA mismatched primer termini are analyzed•Binary DNA complexes with terminal DNA mismatches exhibit template distortion•Ternary DNA/dNTP complexes with terminal DNA mismatches exhibit primer distortion•Structures support an induced-fit mechanism enhancing base substitution fidelity Batra et al. uncover DNA polymerase molecular strategies that deter base substitution errors after a misinsertion event. Structures of binary DNA and ternary substrate complexes with mismatches reveal polymerase-induced strain at the primer terminus of the mismatched base pair as it transitions to a pre-catalytic complex, which deters further synthesis.