ArticleThe Journal of biological chemistry2012
Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Article in The Journal of biological chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 27 citations in OpenAlex.
- Entabolons: How Metabolites Modify the Biochemical Function of Proteins and Cause the Correlated Behavior of Proteins in Pathways.Journal of chemical information and modeling · 2025Review
- Cryo-EM uncovers a sequential mechanism for RNA polymerase I pausing and stalling at abasic DNA lesions.Nature communications · 2025Article
- Customized multiple sequence alignment as an effective strategy to improve performance of Taq DNA polymerase.Applied microbiology and biotechnology · 2023Article
- Abasic site-peptide cross-links are blocking lesions repaired by AP endonucleases.Nucleic acids research · 2023Article
- Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes.International journal of molecular sciences · 2022Article
- The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Review
- Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Plant organellar DNA polymerases are replicative and translesion DNA synthesis polymerases.Nucleic acids research · 2017Article
- Human DNA polymerase θ grasps the primer terminus to mediate DNA repair.Nature structural & molecular biology · 2015Article
- A conservative isoleucine to leucine mutation causes major rearrangements and cold sensitivity in KlenTaq1 DNA polymerase.Biochemistry · 2015Article
- C(α) torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation.Journal of molecular modeling · 2014Article
- Structural insights into DNA replication without hydrogen bonds.Journal of the American Chemical Society · 2013Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cleavage of the N-glycosidic bond that connects the nucleobase to the backbone in DNA leads to abasic sites, the most frequent lesion under physiological conditions. Several DNA polymerases preferentially incorporate an A opposite this lesion, a phenomenon termed "A-rule." Accordingly, KlenTaq, the large fragment of Thermus aquaticus DNA polymerase I, incorporates a nucleotide opposite an abasic site with efficiencies of A > G > T > C. Here we provide structural insights into constraints of the active site during nucleotide selection opposite an abasic site. It appears that these confines govern the nucleotide selection mainly by interaction of the incoming nucleotide with Tyr-671. Depending on the nucleobase, the nucleotides are differently positioned opposite Tyr-671 resulting in different alignments of the functional groups that are required for bond formation. The distances between the α-phosphate and the 3'-primer terminus increases in the order A < G < T, which follows the order of incorporation efficiency. Additionally, a binary KlenTaq structure bound to DNA containing an abasic site indicates that binding of the nucleotide triggers a remarkable rearrangement of enzyme and DNA template. The ability to resolve the stacking arrangement might be dependent on the intrinsic properties of the respective nucleotide contributing to nucleotide selection. Furthermore, we studied the incorporation of a non-natural nucleotide opposite an abasic site. The nucleotide was often used in studying stacking effects in DNA polymerization. Here, no interaction with Tyr-761 as found for the natural nucleotides is observed, indicating a different reaction path for this non-natural nucleotide.
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