ArticleThe Journal of biological chemistry2008
Coupling between ATP binding and DNA cleavage by DNA topoisomerase II: A unifying kinetic and structural mechanism.
Article in The Journal of biological chemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
- Structural basis of chiral wrap and T-segment capture byProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations.Molecular microbiology · 2023Review
- How to measure and evaluate binding affinities.eLife · 2020Article
- A complex suite of loci and elements in eukaryotic type II topoisomerases determine selective sensitivity to distinct poisoning agents.Nucleic acids research · 2019Article
- Phenanthriplatin Acts As a Covalent Poison of Topoisomerase II Cleavage Complexes.ACS chemical biology · 2016Article
- Functional determinants of gate-DNA selection and cleavage by bacterial type II topoisomerases.Nucleic acids research · 2013Article
- The rate of opening and closing of the DNA gate for topoisomerase II.Theory in biosciences = Theorie in den Biowissenschaften · 2013Article
- DNA cleavage and opening reactions of human topoisomerase IIα are regulated via Mg2+-mediated dynamic bending of gate-DNA.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Direct observation of strand passage by DNA-topoisomerase and its limited processivity.PloS one · 2012Article
- Local sensing of global DNA topology: from crossover geometry to type II topoisomerase processivity.Nucleic acids research · 2011Article
- Article
- Dynamics of strand passage catalyzed by topoisomerase II.European biophysics journal : EBJ · 2010Article
- The use of divalent metal ions by type II topoisomerases.Metallomics : integrated biometal science · 2010Review
- DNA chirality-dependent stimulation of topoisomerase IV activity by the C-terminal AAA+ domain of FtsK.Nucleic acids research · 2010Article
- Metal ion interactions in the DNA cleavage/ligation active site of human topoisomerase IIalpha.Biochemistry · 2009Article
- The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Coordinating the two protomer active sites of human topoisomerase IIalpha: nicks as topoisomerase II poisons.Biochemistry · 2009Article
- The DNA cleavage reaction of topoisomerase II: wolf in sheep's clothing.Nucleic acids research · 2009Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
DNA topoisomerase II is a molecular machine that couples ATP hydrolysis to the transport of one DNA segment through a transient break in another segment. To learn about the energetic connectivity that underlies this coupling, we investigated how the ATPase domains exert control over DNA cleavage. We dissected the DNA cleavage reaction by measuring rate and equilibrium constants for the individual reaction steps utilizing defined DNA duplexes in the presence and absence of the nonhydrolyzable ATP analog 5'-adenylyl-beta,gamma-imidodiphosphate (AMPPNP). Our results revealed the existence of two enzyme conformations whose relative abundance is sensitive to the presence of nucleotides. The predominant species in the absence of nucleotides binds DNA at a diffusion limited rate but cannot efficiently cleave DNA. In the presence of AMPPNP, most of the enzyme is converted to a state in which DNA binding and release is extremely slow but which allows DNA cleavage. A minimal kinetic and thermodynamic framework is established that accounts for the cooperativity of cleavage of the two DNA strands in the presence and absence of bound AMPPNP and includes conformational steps revealed in the kinetic studies. The model unifies available kinetic, thermodynamic, and structural data to provide a description for the reaction in terms of the order and rate of individual reaction steps and the physical nature of the species on the reaction path. Furthermore, this reaction framework provides a foundation for a future in-depth analysis of energy transduction by topoisomerase II, for guiding and interpreting future structural studies, and for analyzing the mechanism of drugs that convert topoisomerase into a cellular poison.
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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.