ArticleNucleic acids research2011
Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 39 citations in OpenAlex.
- Cytosine analogues as DNA methyltransferase substrates.Nucleic acids research · 2024Article
- Chemical Expansion of the Methyltransferase Reaction: Tools for DNA Labeling and Epigenome Analysis.Accounts of chemical research · 2023Article
- Base Dynamics in theThe journal of physical chemistry. B · 2023Article
- Unveiling the methyl transfer mechanisms in the epigenetic machinery DNMT3A-3 L: A comprehensive study integrating assembly dynamics with catalytic reactions.Computational and structural biotechnology journal · 2023Article
- The Differential Antitumor Activity of 5-Aza-2'-deoxycytidine in Prostate Cancer DU145, 22RV1, and LNCaP Cells.Journal of Cancer · 2021Article
- ATP Hydrolysis by the SNF2 Domain of Dnmt5 Is Coupled to Both Specific Recognition and Modification of Hemimethylated DNA.Molecular cell · 2020Article
- Functional Analysis of DNMT3A DNA Methyltransferase Mutations Reported in Patients with Acute Myeloid Leukemia.Biomolecules · 2019Article
- Single-molecule study on conformational dynamics of M.HhaI.RSC advances · 2019Article
- Kinetic Basis of the Bifunctionality of SsoII DNA Methyltransferase.Molecules (Basel, Switzerland) · 2018Article
- Archaeal fibrillarin-Nop5 heterodimer 2'-RNA (New York, N.Y.) · 2017Article
- Dynamics of Methylated Cytosine Flipping by UHRF1.Journal of the American Chemical Society · 2017Article
- Mechanisms of superoxide signaling in epigenetic processes: relation to aging and cancer.Aging and disease · 2015Review
- Local chromatin microenvironment determines DNMT activity: from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase.Epigenetics · 2015Review
- Article
- Dynamics of spontaneous flipping of a mismatched base in DNA duplex.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- New nucleophilic mechanisms of ros-dependent epigenetic modifications: comparison of aging and cancer.Aging and disease · 2014Review
- Metadynamics simulation study on the conformational transformation of HhaI methyltransferase: an induced-fit base-flipping hypothesis.BioMed research international · 2014Article
- CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Protein and nucleic acid methylating enzymes: mechanisms and regulation.Current opinion in chemical biology · 2012Review
- Structural origins of DNA target selection and nucleobase extrusion by a DNA cytosine methyltransferase.The Journal of biological chemistry · 2012Article
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 at 1 institution in 1 country.
Funding
Abstract
Methylation of the five position of cytosine in DNA plays important roles in epigenetic regulation in diverse organisms including humans. The transfer of methyl groups from the cofactor S-adenosyl-L-methionine is carried out by methyltransferase enzymes. Using the paradigm bacterial methyltransferase M.HhaI we demonstrate, in a chemically unperturbed system, the first direct real-time analysis of the key mechanistic events-the flipping of the target cytosine base and its covalent activation; these changes were followed by monitoring the hyperchromicity in the DNA and the loss of the cytosine chromophore in the target nucleotide, respectively. Combined with studies of M.HhaI variants containing redesigned tryptophan fluorophores, we find that the target base flipping and the closure of the mobile catalytic loop occur simultaneously, and the rate of this concerted motion inversely correlates with the stability of the target base pair. Subsequently, the covalent activation of the target cytosine is closely followed by but is not coincident with the methyl group transfer from the bound cofactor. These findings provide new insights into the temporal mechanism of this physiologically important reaction and pave the way to in-depth studies of other base-flipping systems.
Indexed as
Identifiers
What OpenQuestion holds
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.