ArticleProceedings of the National Academy of Sciences of the United States of America2009
The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- AssessingbioRxiv : the preprint server for biology · 2026Article
- DNA deformability in sequence-dependent capture of E. coli gyrase.Nature communications · 2026Article
- Different propensities for gate opening in gyrases and topoisomerase IV.Nucleic acids research · 2025Article
- What makes a type IIA topoisomerase a gyrase or a Topo IV?Nucleic acids research · 2021Review
- Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors.Molecules (Basel, Switzerland) · 2021Review
- Article
- Functional interactions between gyrase subunits are optimized in a species-specific manner.The Journal of biological chemistry · 2020Article
- Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.Nature communications · 2018Article
- Gyrase containing a single C-terminal domain catalyzes negative supercoiling of DNA by decreasing the linking number in steps of two.Nucleic acids research · 2018Article
- Why Two? On the Role of (A-)Symmetry in Negative Supercoiling of DNA by Gyrase.International journal of molecular sciences · 2018Review
- DNA gyrase with a single catalytic tyrosine can catalyze DNA supercoiling by a nicking-closing mechanism.Nucleic acids research · 2016Article
- Structural Dynamics and Mechanochemical Coupling in DNA Gyrase.Journal of molecular biology · 2016Article
- The acidic C-terminal tail of the GyrA subunit moderates the DNA supercoiling activity of Bacillus subtilis gyrase.The Journal of biological chemistry · 2014Article
- Studying DNA-protein interactions with single-molecule Förster resonance energy transfer.Protoplasma · 2014Review
- Comparative Molecular docking analysis of DNA Gyrase subunit A in Pseudomonas aeruginosaPAO1.Bioinformation · 2013Article
- The GyrA-box determines the geometry of DNA bound to gyrase and couples DNA binding to the nucleotide cycle.Nucleic acids research · 2012Article
- Potassium ions are required for nucleotide-induced closure of gyrase N-gate.The Journal of biological chemistry · 2012Article
- 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
- Guiding strand passage: DNA-induced movement of the gyrase C-terminal domains defines an early step in the supercoiling cycle.Nucleic acids research · 2011Article
- DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gyrase is the only type II topoisomerase that introduces negative supercoils into DNA. Supercoiling is catalyzed via a strand-passage mechanism, in which the gate DNA (gDNA) is transiently cleaved, and a second DNA segment, the transfer DNA (tDNA), is passed through the gap before the gDNA is religated. Strand passage requires an opening of the so-called DNA-gate by approximately 2 nm. A single-molecule FRET study reported equal populations of open and closed DNA-gate in topoisomerase II. We present here single-molecule FRET experiments that monitor the conformation of DNA bound to the DNA-gate of Bacillus subtilis gyrase and the conformation of the DNA-gate itself. DNA bound to gyrase adopts two different conformations, one slightly, one severely distorted. DNA distortion requires cleavage, but neither ATP nor the presence of a tDNA. At the same time, the DNA-gate of gyrase is predominantly in the closed conformation. In agreement with the single molecule data and with the danger of dsDNA breaks for genome integrity, <5% of cleavage complexes are detected in equilibrium. Quinolone inhibitors favor DNA cleavage by B. subtilis gyrase, but disfavor DNA distortion, and the DNA-gate remains in the closed conformation. Our results demonstrate that DNA binding, distortion and cleavage, and gate-opening are mechanistically distinct events. During the relaxation and supercoiling reactions, gyrase with an open DNA-gate is not significantly populated, consistent with gate-opening as a very rare event that only occurs briefly to allow for strand passage.
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.