ArticleNucleic acids research2011
The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1.
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 19 papers.
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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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Who cites it
19 citing papers in PubMed, 39 citations in OpenAlex.
- Epigenetic marks or not? The discovery of novel DNA modifications in eukaryotes.The Journal of biological chemistry · 2024Review
- Distant sequence regions of JBP1 contribute to J-DNA binding.Life science alliance · 2023Article
- Knockout of protein phosphatase 1 in Leishmania major reveals its role during RNA polymerase II transcription termination.Nucleic acids research · 2023Article
- Behind Base J: The Roles of JBP1 and JBP2 on Trypanosomatids.Pathogens (Basel, Switzerland) · 2023Review
- Article
- Chromatin-Associated Protein Complexes Link DNA Base J and Transcription Termination inmSphere · 2021Article
- Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes.PLoS genetics · 2020Article
- The domain architecture of the protozoan protein J-DNA-binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity.The Journal of biological chemistry · 2019Article
- Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling.Journal of molecular modeling · 2019Article
- Characterization and structure determination of a llama-derived nanobody targeting the J-base binding protein 1.Acta crystallographica. Section F, Structural biology communications · 2018Article
- A method for the efficient and selective identification of 5-hydroxymethyluracil in genomic DNA.Biology methods & protocols · 2017Article
- Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing.Nucleic acids research · 2015Article
- Quantitative mass spectrometry-based analysis of β-D-glucosyl-5-hydroxymethyluracil in genomic DNA of Trypanosoma brucei.Journal of the American Society for Mass Spectrometry · 2014Article
- Identification of the glucosyltransferase that converts hydroxymethyluracil to base J in the trypanosomatid genome.The Journal of biological chemistry · 2014Article
- Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania.Cell · 2012Article
- JBP1 and JBP2 proteins are Fe2+/2-oxoglutarate-dependent dioxygenases regulating hydroxylation of thymidine residues in trypanosome DNA.The Journal of biological chemistry · 2012Article
- The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications.Cell cycle (Georgetown, Tex.) · 2012Article
- Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction.Proteins · 2011Article
- CASP9 target classification.Proteins · 2011Article
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 3 countries.
Funding
Abstract
The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (β-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. We show that JBP1 recognizes J-containing DNA (J-DNA) through a 160-residue domain, DB-JBP1, with 10 000-fold preference over normal DNA. The crystal structure of DB-JBP1 revealed a helix-turn-helix variant fold, a 'helical bouquet' with a 'ribbon' helix encompassing the amino acids responsible for DNA binding. Mutation of a single residue (Asp525) in the ribbon helix abrogates specificity toward J-DNA. The same mutation renders JBP1 unable to rescue the targeted deletion of endogenous JBP1 genes in Leishmania and changes its distribution in the nucleus. Based on mutational analysis and hydrogen/deuterium-exchange mass-spectrometry data, a model of JBP1 bound to J-DNA was constructed and validated by small-angle X-ray scattering data. Our results open new possibilities for targeted prevention of J-DNA recognition as a therapeutic intervention for parasitic diseases.
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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.