Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases

2005 ◽  
Vol 33 (6) ◽  
pp. 1460 ◽  
Author(s):  
L. Costenaro ◽  
A. Maxwell ◽  
S. Mitelheiser ◽  
A.D. Bates
Keyword(s):  
Atp Hydrolysis ◽  
Dna Topoisomerases ◽  
Dna Strand ◽  
Strand Passage

Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases

2005 ◽  
Vol 33 (6) ◽  
pp. 1460-1464 ◽  
Author(s):  
A. Maxwell ◽  
L. Costenaro ◽  
S. Mitelheiser ◽  
A.D. Bates
Keyword(s):  
Atp Hydrolysis ◽  
Dna Gyrase ◽  
Energy Coupling ◽  
Dna Topoisomerases ◽  
Structural Work ◽  
Structural Details ◽  
Negative Supercoiling ◽  
Topo Ii ◽  
Dna Strand ◽  
Strand Passage

Type IIA topos (topoisomerases) catalyse topological conversions of DNA through the passage of one double strand through a transient break in another. In the case of the archetypal enzyme, DNA gyrase, it has always been apparent that the enzyme couples the free energy of ATP hydrolysis to the introduction of negative supercoiling, and the structural details of this process are now becoming clearer. The homologous type IIA enzymes such as topo IV and eukaryotic topo II also require ATP and it has more recently been shown that the energy of hydrolysis is coupled to a reduction of supercoiling or catenation (linking) beyond equilibrium. The mechanism behind this effect is less clear. We review the energy coupling process in both classes of enzyme and describe recent mechanistic and structural work on gyrase that addresses the mechanism of energy coupling.

scholarly journals CryoEM structures of open dimers of Gyrase A in complex with DNA illuminate mechanism of strand passage

2018 ◽  
Author(s):  
Katarzyna M. Soczek ◽  
Tim Grant ◽  
Peter B. Rosenthal ◽  
Alfonso Mondragon
Keyword(s):  
Conformational Changes ◽  
Dna Cleavage ◽  
Atp Hydrolysis ◽  
Unique Type ◽  
Dna Molecule ◽  
Gyrase A ◽  
A Subunit ◽  
Important Intermediate ◽  
Dna Strand ◽  
Strand Passage

AbstractGyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.16 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.

scholarly journals CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Katarzyna M Soczek ◽  
Tim Grant ◽  
Peter B Rosenthal ◽  
Alfonso Mondragón
Keyword(s):  
Conformational Changes ◽  
Dna Cleavage ◽  
Atp Hydrolysis ◽  
Unique Type ◽  
Dna Molecule ◽  
Gyrase A ◽  
A Subunit ◽  
Important Intermediate ◽  
Dna Strand ◽  
Strand Passage

Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.2 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.

scholarly journals Characterization of an ATP-dependent DNA strand transferase from human cells.

1987 ◽  
Vol 7 (9) ◽  
pp. 3124-3130 ◽  
Author(s):  
D Ganea ◽  
P Moore ◽  
L Chekuri ◽  
R Kucherlapati
Keyword(s):  
Dna Sequences ◽  
Atp Hydrolysis ◽  
Reca Protein ◽  
Strand Exchange ◽  
Cell Nuclei ◽  
In Vitro Recombination ◽  
Dna Strand ◽  
Exchange Activity

We have characterized an enzymatic activity from human cell nuclei which is capable of catalyzing strand exchange between homologous DNA sequences. The strand exchange activity was Mg2+ dependent and required ATP hydrolysis. In addition, it was capable of promoting reannealing of homologous DNA sequences and could form nucleoprotein networks in a fashion reminiscent of purified bacterial RecA protein. Using an in vitro recombination assay, we also showed that the strand exchange activity was biologically important. The factor(s) responsible for the activity has been partially purified.

scholarly journals Hindering the Strand Passage Reaction of Human Topoisomerase IIα without Disturbing DNA Cleavage, ATP Hydrolysis, or the Operation of the N-terminal Clamp

2004 ◽  
Vol 279 (27) ◽  
pp. 28093-28099 ◽  
Author(s):  
Vibe H. Oestergaard ◽  
Laura Giangiacomo ◽  
Lotte Bjergbaek ◽  
Birgitta R. Knudsen ◽  
Anni H. Andersen
Keyword(s):  
Dna Cleavage ◽  
Atp Hydrolysis ◽  
Topoisomerase Iiα ◽  
Strand Passage

Effects of the DNA intercalators 4'-(9-acridinylamino)methanesulfon-m-anisidide and 2-methyl-9-hydroxyellipticinium on topoisomerase II mediated DNA strand cleavage and strand passage

Biochemistry ◽  
1985 ◽  
Vol 24 (23) ◽  
pp. 6410-6416 ◽  
Author(s):  
Yves Pommier ◽  
Jon K. Minford ◽  
Ronald E. Schwartz ◽  
Leonard A. Zwelling ◽  
Kurt W. Kohn
Keyword(s):  
Topoisomerase Ii ◽  
Dna Intercalators ◽  
Dna Strand ◽  
Strand Passage

The role of ATP in the reactions of type II DNA topoisomerases

2010 ◽  
Vol 38 (2) ◽  
pp. 438-442 ◽  
Author(s):  
Andrew D. Bates ◽  
Anthony Maxwell
Keyword(s):  
Atp Hydrolysis ◽  
Dna Gyrase ◽  
Dna Topology ◽  
Type Ii ◽  
Free Energies ◽  
Dna Topoisomerases ◽  
Type Ii Dna Topoisomerases ◽  
Topology Simplification ◽  
Hydrolysis Of

Type II DNA topoisomerases catalyse changes in DNA topology in reactions coupled to the hydrolysis of ATP. In the case of DNA gyrase, which can introduce supercoils into DNA, the requirement for free energy is clear. However, the non-supercoiling type II enzymes carry out reactions that are apparently energetically favourable, so their requirement for ATP hydrolysis is not so obvious. It has been shown that many of these enzymes (the type IIA family) can simplify the topology of their DNA substrates to a level beyond that expected at equilibrium. Although this seems to explain their usage of ATP, we show that the free energies involved in topology simplification are very small (<0.2% of that available from ATP) and we argue that topology simplification may simply be an evolutionary relic.

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