ArticleNucleic acids research2012
Residues of E. coli topoisomerase I conserved for interaction with a specific cytosine base to facilitate DNA cleavage.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 23 citations in OpenAlex.
- Investigation of potential hinge region forbioRxiv : the preprint server for biology · 2026Article
- Structural insights into human topoisomerase 3β DNA and RNA catalysis and nucleic acid gate dynamics.Nature communications · 2025Article
- Substrate binding of human and bacterial type IA topoisomerase: An experimentation with AlphaFold 3.0.Computational and structural biotechnology journal · 2025Article
- Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- What's on the Other Side of the Gate: A Structural Perspective on DNA Gate Opening of Type IA and IIA DNA Topoisomerases.International journal of molecular sciences · 2023Review
- Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β.Nature communications · 2022Article
- Interaction between transcribing RNA polymerase and topoisomerase I prevents R-loop formation in E. coli.Nature communications · 2022Article
- Mechanism of Type IA Topoisomerases.Molecules (Basel, Switzerland) · 2020Review
- Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains.Nucleic acids research · 2020Article
- Article
- Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site.Nucleic acids research · 2018Article
- Synthesizing topological structures containing RNA.Nature communications · 2017Article
- Identification of proximal sites for unwound DNA substrate in Escherichia coli topoisomerase I with oxidative crosslinking.FEBS letters · 2017Article
- RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals.Nucleic acids research · 2016Article
- Small-Molecule Inhibitors Targeting Topoisomerase I as Novel Antituberculosis Agents.Antimicrobial agents and chemotherapy · 2016Article
- Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I.Nucleic acids research · 2015Article
- Inhibition of Zn(II) binding type IA topoisomerases by organomercury compounds and Hg(II).PloS one · 2015Article
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2 authors at 1 institution in 1 country.
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Abstract
Bacterial and archaeal topoisomerase I display selectivity for a cytosine base 4 nt upstream from the DNA cleavage site. Recently, the solved crystal structure of Escherichia coli topoisomerase I covalently linked to a single-stranded oligonucleotide revealed that R169 and R173 interact with the cytosine base at the -4 position via hydrogen bonds while the phenol ring of Y177 wedges between the bases at the -4 and the -5 position. Substituting R169 to alanine changed the selectivity of the enzyme for the base at the -4 position from a cytosine to an adenine. The R173A mutant displayed similar sequence selectivity as the wild-type enzyme, but weaker cleavage and relaxation activity. Mutation of Y177 to serine or alanine rendered the enzyme inactive. Although mutation of each of these residues led to different outcomes, R169, R173 and Y177 work together to interact with a cytosine base at the -4 position to facilitate DNA cleavage. These strictly conserved residues might act after initial substrate binding as a Molecular Ruler to form a protein-DNA complex with the scissile phosphate positioned at the active site for optimal DNA cleavage by the tyrosine hydroxyl nucleophile to facilitate DNA cleavage in the reaction pathway.
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