ArticleJournal of chemical theory and computation2019
Structural Analysis of the Active Site and DNA Binding of Human Cytidine Deaminase APOBEC3B.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed, 25 citations in OpenAlex.
- Regulatory Interactions between APOBEC3B N- and C-Terminal Domains.Journal of chemical information and modeling · 2025Article
- Regulatory interactions between APOBEC3B N- and C-terminal domains.bioRxiv : the preprint server for biology · 2024Article
- A real-time biochemical assay for quantitative analyses of APOBEC-catalyzed DNA deamination.The Journal of biological chemistry · 2024Article
- A real-time biochemical assay for quantitative analyses of APOBEC-catalyzed DNA deamination.bioRxiv : the preprint server for biology · 2024Article
- Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A.Beilstein journal of organic chemistry · 2024Article
- Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A.Organic & biomolecular chemistry · 2023Article
- Design, Synthesis, and Evaluation of a Cross-Linked Oligonucleotide as the First Nanomolar Inhibitor of APOBEC3A.Biochemistry · 2022Article
- Human activation-induced deaminase lacks strong replicative strand bias or preference for cytosines in hairpin loops.Nucleic acids research · 2022Article
- The current toolbox for APOBEC drug discovery.Trends in pharmacological sciences · 2022Review
- Interactions of APOBEC3s with DNA and RNA.Current opinion in structural biology · 2021Review
- A cross-reactive human IgA monoclonal antibody blocks SARS-CoV-2 spike-ACE2 interaction.Nature communications · 2020Article
- Review
- Computational Investigation of APOBEC3H Substrate Orientation and Selectivity.The journal of physical chemistry. B · 2020Article
- Understanding the structural details of APOBEC3-DNA interactions using graph-based representations.Current research in structural biology · 2020Article
- APOBEC3A Loop 1 Is a Determinant for Single-Stranded DNA Binding and Deamination.Biochemistry · 2019Article
- APOBEC3s: DNA-editing human cytidine deaminases.Protein science : a publication of the Protein Society · 2019Review
- Evaluation of APOBEC3B Recognition Motifs by NMR Reveals Preferred Substrates.ACS chemical biology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
APOBEC3 (A3) proteins, a family of human cytidine deaminases, protect the host from endogenous retro-elements and exogenous viral infections by introducing hypermutations. However, overexpressed A3s can modify genomic DNA to promote tumorigenesis, especially A3B. Despite their overall similarity, A3 proteins have distinct deamination activity. Recently determined A3 structures have revealed the molecular determinants of nucleotide specificity and DNA binding. However, for A3B, the structural basis for regulation of deamination activity and the role of active site loops in coordinating DNA had remained unknown. Using advanced molecular modeling followed by experimental mutational analysis and dynamics simulations, we investigated the molecular mechanism of DNA binding by A3B-CTD. We modeled fully native A3B-DNA structure, and we identified Arg211 in loop 1 as the gatekeeper coordinating DNA and critical residue for nucleotide specificity. We also identified a unique autoinhibited conformation in A3B-CTD that restricts access and binding of DNA to the active site. Our results reveal the structural basis for DNA binding and relatively lower catalytic activity of A3B and provide opportunities for rational design of specific inhibitors to benefit cancer therapeutics.
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.