Crystal structure of the breakage–reunion domain of DNA gyrase

Morais-Cabral, J.H.; Jackson, Andrew P.; Smith, Clare V.; Shikotra, Nita; Maxwell, Anthony; Liddington, Robert

doi:10.1038/42294

Cited by 426 publications

(199 citation statements)

References 3 publications

Supporting

Mentioning

194

Contrasting

Unclassified

Order By: Relevance

“…Our present observations as well as our previous study of BaP DE-2 dG adducts (15) underline recent progress in the understanding of the molecular contacts between topoisomerases and their DNA substrates (7,8,15,(48)(49)(50), and the potential of such structures to elucidate the molecular interactions of various ligands, including carcinogenic adducts as well as antibacterial and anticancer drugs.…”

Section: Discussionsupporting

confidence: 78%

Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[ a ]- pyrene diol epoxide adducts at the 6-amino group of adenine

Pommier

Laco

Kohlhagen

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

DNA topoisomerase I (top1) is the target of potent anticancer agents, including camptothecins and DNA intercalators, which reversibly stabilize (trap) top1 catalytic intermediates (cleavage complexes). The aim of the present study was to define the structural relationship between the site(s) of covalently bound intercalating agents, whose solution conformations in DNA are known, and the site(s) of top1 cleavage. Two diastereomeric pairs of oligonucleotide 22-mers, derived from a sequence used to determine the crystal structure of top1-DNA complexes, were synthesized. One pair contained either a trans-opened 10R-or 10S-benzo[a]pyrene 7,8-diol 9,10-epoxide adduct at the N 6 -amino group of a central 2 -deoxyadenosine residue in the scissile strand, and the other pair contained the same two adducts in the nonscissile strand. These adducts were derived from the (؉)-(7R,8S,9S,10R)-and (؊)-(7S,8R,9R,10S)-7,8-diol 9,10-epoxides in which the benzylic 7-hydroxyl group and the epoxide oxygen are trans. On the basis of analogy with known solution conformations of duplex oligonucleotides containing these adducts, we conclude that top1 cleavage complexes are trapped when the hydrocarbon adduct is intercalated between the base pairs flanking a preexisting top1 cleavage site, or between the base pairs immediately downstream (3 relative to the scissile strand) from this site. We propose a model with the ؉1 base rotated out of the duplex, and in which the intercalated adduct prevents religation of the corresponding nucleotide at the 5 end of the cleaved DNA. These results suggest mechanisms whereby intercalating agents interfere with the normal function of human top1. D NA topoisomerase I (top1) is an essential enzyme in higher eukaryotes (1, 2). It can relax DNA supercoiling and relieve torsional strain during DNA processing, including replication, transcription, and repair. It can also perform intermolecular religation leading to DNA recombinations (3, 4). The catalytic intermediate of top1 is a cleavage complex in which a tyrosine (Tyr-723 for human top1) in the enzyme attacks a DNA phosphodiester and forms a covalent bond to the phosphorus at the 3Ј side of the cleavage site while a 5Ј-hydroxyl is generated at the other side (1, 2). The reaction occurs with short duplex oligodeoxynucleotides (5, 6), as evidenced by recent crystal structures of top1-DNA complexes (7,8).top1 is the cellular target of several anticancer drugs, including the camptothecins, which have recently been approved by the Food and Drug Administration for the treatment of colon and ovarian carcinomas. The anticancer activity of these drugs results from the trapping of top1 cleavage complexes such that the enzyme is reversibly inactivated as it cleaves DNA (9-11). These agents are often referred to as ''top1 poisons.'' They represent an exemplary case of pharmacological interference whereby the drug stabilizes the interactions of two macromolecules (i.e., top1 and DNA) by formation of a ternary complex. Because of the clinical efficacy of camptothecins, no...

show abstract

Section: Discussionsupporting

confidence: 78%

Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[ a ]- pyrene diol epoxide adducts at the 6-amino group of adenine

Pommier

Laco

Kohlhagen

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Ser 83 of gyrA is the amino acid most frequently changed in strains with high levels of quinolone resistance, although other mutations in either gyrA or gyrB can lead to quinolone resistance (15) 953 and hypersensitivity to etoposide (19). To investigate the basis for the differential responses of the top2 S740W , we analyzed the base sequence preference (20 -23) and stability of the top2 cleavage complexes in the absence and presence of top2-targeting drugs.…”

Section: A Sermentioning

confidence: 99%

Mutation of a Conserved Serine Residue in a Quinolone-resistant Type II Topoisomerase Alters the Enzyme-DNA and Drug Interactions

Strumberg

Nitiss²,

Rose³

et al. 1999

Journal of Biological Chemistry

View full text Add to dashboard Cite

A Ser740 3 Trp mutation in yeast topoisomerase II (top2) and of the equivalent Ser 83 in gyrase results in resistance to quinolones and confers hypersensitivity to etoposide (VP-16). We characterized the cleavage complexes induced by the top2 S740W in the human c-myc gene. In addition to resistance to the fluoroquinolone CP-115,953, top2 S740W induced novel DNA cleavage sites in the presence of VP-16, azatoxin, amsacrine, and mitoxantrone. Analysis of the VP-16 sites indicated that the changes in the cleavage pattern were reflected by alterations in base preference. C at position ؊2 and G at position ؉6 were observed for the top2 S740W in addition to the previously reported C؊1 and G؉5 for the wildtype top2. The VP-16-induced top2 S740W cleavage complexes were also more stable. The most stable sites had strong preference for C؊1, whereas the most reversible sites showed no base preference at positions ؊1 or ؊2. Different patterns of DNA cleavage were also observed in the absence of drug and in the presence of calcium. These results indicate that the Ser 740 3 Trp mutation alters the DNA recognition of top2, enhances its DNA binding, and markedly affects its interactions with inhibitors. Thus, residue 740 of top2 appears critical for both DNA and drug interactions.DNA topoisomerases are enzymes that catalyze changes in the topology of DNA via a mechanism involving the transient breakage and rejoining of phosphodiester bonds in the DNA backbone (1). Studies in both prokaryotic and eukaryotic cells have demonstrated the importance of topoisomerases in transcription, DNA replication, and chromosome segregation. The type II topoisomerases, which make transient double-strand breaks and change the linking number of DNA in steps of two, play key roles in chromosome structure. In eukaryotic cells, these enzymes are essential for chromosome condensation/decondensation and decatenation of chromosome loops during mitosis (2, 3).Topoisomerase II (top2) 1 has also been identified as a major target of chemotherapeutic agents that are specifically active against prokaryotic (4) or cancer cells (5-8). Fluoroquinolones are antibacterial agents that target DNA gyrase (the prokaryotic type II topoisomerase) (9), whereas a variety of DNAintercalating agents such as anthracyclines, amsacrine, and mitoxantrone and nonintercalating agents such as the epipodophyllotoxin etoposide (VP-16) are active against eukaryotic top2 and are clinically important anti-cancer agents (5-8).Azatoxin is also a nonintercalative top2 poison (10).Recently, it has been shown that 6,8-difluoro-7-(4Ј-hydroxyphenyl)-1-cyclopropyl-4-quinolone-3-carboxylic acid (CP-115, 953), a fluoroquinolone closely related to ciprofloxacin, is highly toxic to mammalian cells in culture (11,12). Studies in yeast demonstrated that top2 is the primary physiological target for this quinolone (13). Unlike etoposide, which stabilizes top2-mediated DNA cleavage primarily by inhibiting the religation reaction of top2, CP-115,953 stabilizes DNA cleavage by enhancing the forward rate o...

show abstract

“…1). Structures of fragments of Escherichia coli GyrB (4) and GyrA (5,6), and of a fusion of parts of GyrB and GyrA (7) have been determined, but the overall architecture of gyrase remains unknown. DNA supercoiling by gyrase occurs via a strandpassage mechanism (8)(9)(10)(11).…”

mentioning

confidence: 99%

“…DNA supercoiling by gyrase occurs via a strandpassage mechanism (8)(9)(10)(11). A double-stranded DNA segment binds to the DNA-gate (5,12), close to the catalytic tyrosines that perform the cleavage reaction. Cleavage of this gate DNA (G-segment) generates a gap through which a second DNA segment (T-segment) is transported.…”

mentioning

confidence: 99%

DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage

Gubaev

Klostermeier

2011

Proc. Natl. Acad. Sci. U.S.A.

147

View full text Add to dashboard Cite

DNA gyrase introduces negative supercoils into DNA in an ATPdependent reaction. DNA supercoiling is catalyzed by a strandpassage mechanism, in which a T-segment of DNA is passed through the gap in a transiently cleaved G-segment. Strand passage requires the coordinated closing and opening of three protein interfaces in gyrase, the N-gate, DNA-gate, and C-gate. We show here that DNA binding to the DNA-gate of gyrase and wrapping of DNA around the C-terminal domains of GyrA induces a narrowing of the N-gate. This half-closed state prepares capture of a T-segment in the upper cavity of gyrase. Subsequent N-gate closure upon binding of ATP then poises the reaction toward strand passage. The N-gate reopens after ATP hydrolysis, allowing for further catalytic cycles. DNA binding, cleavage, and wrapping and N-gate narrowing are intimately linked events that coordinate conformational changes at the DNA and the N-gate.gyrase dynamics | nucleotide-induced conformational changes | topoisomerase mechanism | DNA wrapping | negative supercoiling

show abstract

Crystal structure of the breakage–reunion domain of DNA gyrase

Cited by 426 publications

References 3 publications

Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[ a ]- pyrene diol epoxide adducts at the 6-amino group of adenine

Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[ a ]- pyrene diol epoxide adducts at the 6-amino group of adenine

Mutation of a Conserved Serine Residue in a Quinolone-resistant Type II Topoisomerase Alters the Enzyme-DNA and Drug Interactions

DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage

Contact Info

Product

Resources

About