ArticleDNA repair2014
The substrate binding interface of alkylpurine DNA glycosylase AlkD.
Article in DNA repair, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- DNA binding and lesion recognition by the bacterial interstrand DNA crosslink glycosylase AlkX.EMBO reports · 2026Article
- DNA binding and lesion recognition by the bacterial interstrand DNA crosslink glycosylase AlkX.bioRxiv : the preprint server for biology · 2025Article
- AlkD's Conformational Dynamics Regulated by Protein-DNA Interactions for Effective Target Recognition.The journal of physical chemistry letters · 2025Article
- Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway.Trends in biochemical sciences · 2019Review
- Insights into conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations.Theoretical chemistry accounts · 2018Article
- Toxicity and repair of DNA adducts produced by the natural product yatakemycin.Nature chemical biology · 2017Article
- A Catalytic Role for C-H/π Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD.Journal of the American Chemical Society · 2016Article
- Article
- A New Family of HEAT-Like Repeat Proteins Lacking a Critical Substrate Recognition Motif Present in Related DNA Glycosylases.PloS one · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Tandem helical repeats have emerged as an important DNA binding architecture. DNA glycosylase AlkD, which excises N3- and N7-alkylated nucleobases, uses repeating helical motifs to bind duplex DNA and to selectively pause at non-Watson-Crick base pairs. Remodeling of the DNA backbone promotes nucleotide flipping of the lesion and the complementary base into the solvent and toward the protein surface, respectively. The important features of this new DNA binding architecture that allow AlkD to distinguish between damaged and normal DNA without contacting the lesion are poorly understood. Here, we show through extensive mutational analysis that DNA binding and N3-methyladenine (3mA) and N7-methylguanine (7mG) excision are dependent upon each residue lining the DNA binding interface. Disrupting electrostatic or hydrophobic interactions with the DNA backbone substantially reduced binding affinity and catalytic activity. These results demonstrate that residues seemingly only involved in general DNA binding are important for catalytic activity and imply that base excision is driven by binding energy provided by the entire substrate interface of this novel DNA binding architecture.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.