ArticleThe Journal of biological chemistry2013
Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4.
Article in The Journal of biological chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 69 citations in OpenAlex.
- Human PMS1-dependent non-canonical mismatch repair engages with MBD4 to repair methylated CpG deamination.Nucleic acids research · 2026Article
- HM-DyadCap - capture and mapping of 5-hydroxymethylcytosine/5-methylcytosine CpG dyads in mammalian DNA.Nucleic acids research · 2026Article
- 8-Oxoguanine: A Lesion, an Epigenetic Mark, or a Molecular Signal?International journal of molecular sciences · 2025Review
- DNA-binding proteins from MBD through ZF to BEN: recognition of cytosine methylation status by one arginine with two conformations.Nucleic acids research · 2024Article
- Prognostic Significance ofPhenomics (Cham, Switzerland) · 2024Article
- Mechanistic model for epigenetic maintenance by methyl-CpG-binding domain proteins.bioRxiv : the preprint server for biology · 2024Article
- Micronutrient regulation of the DNA methylome.Frontiers in epigenetics and epigenomics · 2024Review
- DNA repair enzymes of the Antarctic Dry Valley metagenome.Frontiers in microbiology · 2023Article
- Crystal structure of the BAZ2B TAM domain.Heliyon · 2022Article
- Noncatalytic Domains in DNA Glycosylases.International journal of molecular sciences · 2022Review
- Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 fromACS omega · 2022Article
- Proteins That Read DNA Methylation.Advances in experimental medicine and biology · 2022Article
- Review
- Focus on DNA Glycosylases-A Set of Tightly Regulated Enzymes with a High Potential as Anticancer Drug Targets.International journal of molecular sciences · 2020Review
- Retracted Article: Divergent synthesis of 5-substituted pyrimidine 2'-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases.Chemical science · 2020Article
- The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex.Journal of molecular biology · 2020Review
- A novel sensitive detection method for DNA methylation in circulating free DNA of pancreatic cancer.PloS one · 2020Article
- Cytosine methylation of mitochondrial DNA at CpG sequences impacts transcription factor A DNA binding and transcription.Biochimica et biophysica acta. Gene regulatory mechanisms · 2019Article
- Detecting and interpreting DNA methylation marks.Current opinion in structural biology · 2018Review
- Zinc Finger Readers of Methylated DNA.Molecules (Basel, Switzerland) · 2018Review
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The methyl-CpG binding domain (MBD) protein MBD4 participates in DNA repair as a glycosylase that excises mismatched thymine bases in CpG sites and also functions in transcriptional repression. Unlike other MBD proteins, MBD4 recognizes not only methylated CpG dinucleotides ((5m)CG/(5m)CG) but also T/G mismatched sites generated by spontaneous deamination of 5-methylcytosine ((5m)CG/TG). The glycosylase activity of MBD4 is also implicated in active DNA demethylation initiated by the deaminase-catalyzed conversion of 5-methylcytosine to thymine. Here, we report the crystal structures of the MBD of MBD4 (MBDMBD4) complexed with (5m)CG/(5m)CG and (5m)CG/TG. The crystal structures show that the DNA interface of MBD4 has flexible structural features and harbors an extensive water network that supports its dual base specificities. Combined with the results of biochemical analyses, the crystal structure of MBD4 bound to 5-hydroxymethylcytosine further demonstrates that MBDMBD4 is able to recognize a wide range of 5-methylcytosine modifications through the unique water network. The versatile base recognition ability of MBDMBD4 implies multifunctional roles for MBD4 in the regulation of dynamic DNA methylation patterns coupled with deamination and/or oxidation of 5-methylcytosine.
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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.