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Journal of Biological Chemistry
Article . 2002 . Peer-reviewed
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Journal of Biological Chemistry
Article
License: CC BY
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Loss of DNA Polymerase β Stacking Interactions with Templating Purines, but Not Pyrimidines, Alters Catalytic Efficiency and Fidelity

Authors: William A, Beard; David D, Shock; Xiao-Ping, Yang; Saundra F, DeLauder; Samuel H, Wilson;

Loss of DNA Polymerase β Stacking Interactions with Templating Purines, but Not Pyrimidines, Alters Catalytic Efficiency and Fidelity

Abstract

Structures of DNA polymerases bound with DNA reveal that the 5'-trajectory of the template strand is dramatically altered as it exits the polymerase active site. This distortion provides the polymerase access to the nascent base pair to interrogate proper Watson-Crick geometry. Upon binding a correct deoxynucleoside triphosphate, alpha-helix N of DNA polymerase beta is observed to form one face of the binding pocket for the new base pair. Asp-276 and Lys-280 stack with the bases of the incoming nucleotide and template, respectively. To determine the role of Lys-280, site-directed mutants were constructed at this position, and the proteins were expressed and purified, and their catalytic efficiency and fidelity were assessed. The catalytic efficiency for single-nucleotide gap filling with the glycine mutant (K280G) was strongly diminished relative to wild type for templating purines (>15-fold) due to a decreased binding affinity for the incoming nucleotide. In contrast, catalytic efficiency was hardly affected by glycine substitution for templating pyrimidines (<4-fold). The fidelity of the glycine mutant was identical to the wild type enzyme for misinsertion opposite a template thymidine, whereas the fidelity of misinsertion opposite a template guanine was modestly altered. The nature of the Lys-280 side-chain substitution for thymidine triphosphate insertion (templating adenine) indicates that Lys-280 "stabilizes" templating purines through van der Waals interactions.

Keywords

Models, Molecular, Aspartic Acid, Binding Sites, Dose-Response Relationship, Drug, Base Pair Mismatch, Lysine, Glycine, Hydrogen Bonding, DNA, Arginine, Catalysis, Protein Structure, Secondary, Protein Structure, Tertiary, Kinetics, Models, Chemical, Mutation, Mutagenesis, Site-Directed, Humans, DNA Polymerase beta, Protein Binding

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
75
Top 10%
Top 10%
Top 10%
gold