Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands

@article{Fass1999QuaternaryCI,
  title={Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands},
  author={Deborah Fass and Cynthia E. Bogden and James M. Berger},
  journal={Nature Structural Biology},
  year={1999},
  volume={6},
  pages={322-326}
}
Type II DNA topoisomerases mediate the passage of one DNA duplex through a transient break in another, an event essential for chromosome segregation and cell viability. The active sites of the type II topoisomerase dimer associate covalently with the DNA break-points and must separate by at least the width of the second DNA duplex to accommodate transport. A new structure of the Saccharomyces cerevisiae topoisomerase II DNA-binding and cleavage core suggests that in addition to conformational… 
Structural basis for gate-DNA recognition and bending by type IIA topoisomerases
TLDR
The structure of a complex between the DNA-binding and cleavage core of Saccharomyces cerevisiae Topo II and a gate-DNA segment is presented, revealing that the enzyme enforces a 150° DNA bend through a mechanism similar to that of remodelling proteins such as integration host factor.
New insights into DNA-binding by type IIA topoisomerases.
Control of Strand Scission by Type IIA Topoisomerases
TLDR
This dissertation helps to explain years of biochemical studies, unifies many elements of topo II mechanism and its control by allostery, and has implications for both understanding large ATP-dependent DNA-remodeling molecular machines as a whole, as well as understanding the means by which small molecules target these enzymes for clinical benefit.
Analysis of the eukaryotic topoisomerase II DNA gate: a single-molecule FRET and structural perspective
TLDR
Recent single-molecule fluorescence resonance energy transfer and crystallographic studies that have provided new insight into the dynamics and structure of the topo II DNA gate are highlighted.
Nucleotide-dependent Domain Movement in the ATPase Domain of a Human Type IIA DNA Topoisomerase*
TLDR
Two crystal structures of the ATPase domain of human DNA topoisomerase IIα in different nucleotide-bound states are presented, revealing rigid-body movement of the structural modules within the ATP enzyme domain, suggestive of the motions of a molecular gate.
DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
TLDR
The ability to modulate the extent of DNA cleavage by varying the DNA sequence may be valuable for future structural and mechanistic studies that aim to determine topoisomerase structures with DNA bound in pre- and post-cleavage states and to understand the conformational changes associated with DNA binding and cleavage.
New mechanistic and functional insights into DNA topoisomerases.
TLDR
Recent advances in mechanistic insights into topoisomerases are covered, including a DNA helicase capable of modulating the directionality of strand passage, enabling important functions like reannealing denatured DNA and resolving recombination intermediates.
DNA topoisomerase II and its growing repertoire of biological functions
TLDR
Extensive biochemical and structural studies have provided detailed models of how TOP2 alters DNA structure, and recent molecular studies have greatly expanded knowledge of the biological contexts in which TOP2 functions, such as DNA replication, transcription and chromosome segregation.
A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases
TLDR
The structure of the DNA-binding and cleavage core of Saccharomyces cerevisiae topoisomerase II covalently linked to DNA through its active-site tyrosine at 2.5 Å resolution is presented, revealing for the first time the organization of a cleavage-competent type II topoisomersase configuration.
Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate
TLDR
The authors combine X-ray crystallography and MD simulations and present the structure of the human Top2 DNA-gate in an open conformation, which reveals structural characteristics of its DNA-conducting path and uncovers unexpected yet functionally significant conformational changes associated with gate-opening.
...
...

References

SHOWING 1-10 OF 54 REFERENCES
Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I
TLDR
The three-dimensional structure of the 67K amino-terminal fragment of E. coli DNA topoisomerase I suggests a plausible mechanism by which the organism could catalyse the passage of one DNA strand through a transient break in another strand.
Structural similarities between topoisomerases that cleave one or both DNA strands.
TLDR
Although the type IA and type II topoisomerase structures appear overall quite different from one another, unexpected similarities between several structural elements suggest that members of the two subfamilies may use comparable mechanisms to bind and cleave DNA.
Crystal structure of the breakage–reunion domain of DNA gyrase
DNA gyrase is a type II DNA topoisomerase from bacteria that introduces supercoils into DNA,. It catalyses the breakage of a DNA duplex (the G segment), the passage of another segment (the T segment)
Structure and mechanism of DNA topoisomerase II
The crystal structure of a large fragment of yeast type II DNA topoisomerase reveals a heart-shaped dimeric protein with a large central hole. It provides a molecular model of the enzyme as an
Footprinting of Yeast DNA Topoisomerase II Lysyl Side Chains Involved in Substrate Binding and Interdomainal Interactions*
Footprinting of yeast DNA topoisomerase II and its NH2- and COOH-terminal truncation derivatives was carried out to map the locations of lysyl side chains that are involved in enzyme-DNA interaction,
Tandem regions of yeast DNA topoisomerase II share homology with different subunits of bacterial gyrase.
TLDR
The nucleotide sequence for the Saccharomyces cerevisiae gene TOP2, which encodes DNA topoisomerase II, was compared with the sequence for bacterial DNA gyrase and the homology between the two proteins indicates mechanistic as well as structural similarities, and a probable evolutionary relationship.
Mapping the active site tyrosine of Escherichia coli DNA gyrase.
Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees
The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 90 degrees. This
...
...