ArticleJournal of molecular biology2006
Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase.
Article in Journal of molecular biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 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.
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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
65 citing papers in PubMed, 139 citations in OpenAlex.
- Genome-wide chromatin recording resolves dynamic cell state changes.Cell systems · 2026Article
- Lineage-associated differences in adenine methylation patterns of mammalian-associatedMicrobiology spectrum · 2026Article
- Genome-wide chromatin recording resolves dynamic cell state changes.bioRxiv : the preprint server for biology · 2026Article
- MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.Nature structural & molecular biology · 2026Article
- Inhibition ofACS omega · 2025Article
- Mapping SET1B chromatin interactions with DamID using DamMapper, a comprehensive Snakemake workflow.BMC genomics · 2025Article
- Inhibition ofbioRxiv : the preprint server for biology · 2025Article
- A nomogram for predicting 3-year total weight loss percentage following LSG: insights from visceral adipose tissue inflammatory methylation sites.BMC surgery · 2025Article
- Targeted DamID detects cell-type-specific histone modifications in intact tissues or organisms.PLoS biology · 2025Article
- Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout.Nucleic acids research · 2025Article
- Quinoline-based compounds can inhibit diverse enzymes that act on DNA.Cell chemical biology · 2024Article
- Article
- Comparative Study of Adenosine Analogs as Inhibitors of Protein Arginine Methyltransferases and aACS chemical biology · 2023Article
- Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression.Communications biology · 2023Article
- Systematic Design of Adenosine Analogs as Inhibitors of aJournal of medicinal chemistry · 2023Article
- Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria.Frontiers in microbiology · 2023Review
- Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing.Nature communications · 2022Article
- Diverse Roles for a Conserved DNA-Methyltransferase in the Entomopathogenic BacteriumInternational journal of molecular sciences · 2022Article
- Repurposing epigenetic inhibitors to target theEpigenetics · 2022Article
- Energy Landscapes for Base-Flipping in a Model DNA Duplex.The journal of physical chemistry. B · 2022Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
The structure of the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase in complex with cognate DNA was determined at 1.89 A resolution in the presence of S-adenosyl-L-homocysteine. DNA recognition and the dynamics of base-flipping were studied by site-directed mutagenesis, DNA methylation kinetics and fluorescence stopped-flow experiments. Our data illustrate the mechanism of coupling of DNA recognition and base-flipping. Contacts to the non-target strand in the second (3') half of the GATC site are established by R124 to the fourth base-pair, and by L122 and P134 to the third base-pair. The aromatic ring of Y119 intercalates into the DNA between the second and third base-pairs, which is essential for base-flipping to occur. Compared to previous published structures of bacteriophage T4 Dam, three major new observations are made in E.coli Dam. (1) The first Gua is recognized by K9, removal of which abrogates the first base-pair recognition. (2) The flipped target Ade binds to the surface of EcoDam in the absence of S-adenosyl-L-methionine, which illustrates a possible intermediate in the base-flipping pathway. (3) The orphaned Thy residue displays structural flexibility by adopting an extrahelical or intrahelical position where it is in contact to N120.
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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.