DNA transport by a type II DNA topoisomerase: Evidence in favor of a two-gate mechanism

@article{Roca1994DNATB,
  title={DNA transport by a type II DNA topoisomerase: Evidence in favor of a two-gate mechanism},
  author={Joaquim Roca and James C. Wang},
  journal={Cell},
  year={1994},
  volume={77},
  pages={609-616}
}

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  • 2001
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The single-step DNA transport preferences of the yeast type II topoisomerase bound to positively and negatively supercoiled DNA rings are examined and it is found that negative supercoiling favors decatenation of DNA rings more than positive super coiling.
Coupling between ATP Binding and DNA Cleavage by DNA Topoisomerase II
TLDR
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.
Topoisomerase II drives DNA transport by hydrolyzing one ATP.
TLDR
Evidence is presented that hydrolysis of one ATP by topoisomerase II precedes, and accelerates, DNA transport, indicating that important features of this enzyme's mechanism previously have been overlooked because of the reliance on nonhydrolyzable analogs for studying a single reaction turnover.
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References

SHOWING 1-10 OF 39 REFERENCES
On the coupling between ATP usage and DNA transport by yeast DNA topoisomerase II.
Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers.
TLDR
It is proposed that eukaryotic topoisomerases I and II recognize underwound or overwound substrates by interacting preferentially with DNA crossovers, which may represent a general mechanism for the recognition of DNA topology by proteins.
DNA gyrase: structure and function.
TLDR
In this review, the current knowledge concerning DNA gyrase is summarized by addressing a wide range of aspects of the study of this enzyme.
Topological complexes between DNA and topoisomerase II and effects of polyamines.
TLDR
At relatively high concentrations, spermine (1 mM) enhances topoisomerase II induced cleavage at certain sites on the SV40 genome that could have regulatory significance.
Cleavage of DNA by mammalian DNA topoisomerase II.
On the simultaneous binding of eukaryotic DNA topoisomerase II to a pair of double-stranded DNA helices.
TLDR
Binding of yeast DNA topoisomerase II to DNA crossings is significant, especially in low salt media containing Mg(II), and that this mode of binding strongly affects DNA knotting, it appears that stabilization of DNA crossovers by the eukaryotic type II enzyme is not directly related to its DNA transport activity.
Energy coupling in DNA gyrase and the mechanism of action of novobiocin.
TLDR
It is postulate that ATP and App[NH]p are allosteric effectors of a conformational change of gyrase that leads to one round of supercoiling and that cyclic conformational changes accompanying alteration in nucleotide affinity also seem to be a common feature of energy transduction in other diverse processes including muscle contraction, protein synthesis, and oxidative phosphorylation.
Identification of the breakage-reunion subunit of T4 DNA topoisomerase.
DNA gyrase action involves the introduction of transient double-strand breaks into DNA.
TLDR
Evidence that transient double-strand breaks are also involved in the supercoiling and relaxing activities of DNA gyrase is derived from experiments showing that the linking number of circular DNA is changed in steps of two.
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