DNA topoisomerase IIA dimer, Human
|PDB structures||RCSB PDB PDBe PDBsum|
DNA gyrase, also known as topoisomerase II or simply as gyrase, is an enzyme that relieves strain while double-stranded DNA is being unwound by helicase. This causes negative supercoiling of the DNA. The gyrase supercoils (or relaxes positive supercoils) into DNA by looping the template so as to form a crossing, then cutting one of the double helices and passing the other through it before releasing the break, changing the linking number by two in each enzymatic step. This process occurs in prokaryotes (in particular, in bacteria), whose single circular DNA is cut by DNA gyrase and the two ends are then twisted around each other to form supercoils. Gyrase has been found in the apicoplast of the malarial parasite Plasmodium falciparum, a unicellular eukaryote. Bacterial DNA gyrase is the target of many antibiotics, including nalidixic acid, novobiocin, and ciprofloxacin.
The unique ability of gyrase to introduce negative supercoils into DNA is what allows bacterial DNA to have free negative supercoils. The ability of gyrase to relax positive supercoils comes into play during DNA replication and prokaryotic transcription. The right-handed nature of the DNA double helix causes positive supercoils to accumulate ahead of a translocating enzyme, in the case of DNA replication, a DNA polymerase. The ability of gyrase (and topoisomerase IV) to relax positive supercoils allows superhelical tension ahead of the polymerase to be released so that replication can continue.
Mechanochemical model of gyrase activity
A single molecule study has characterized gyrase activity as a function of DNA tension (applied force) and ATP, and proposed a mechanochemical model. Upon binding to DNA (the "Gyrase-DNA" state), there is a competition between DNA wrapping and dissociation, where increasing DNA tension increases the probability of dissociation. Upon wrapping and ATP hydrolysis, two negative supercoils are introduced into the template, providing opportunities for subsequent wrapping and supercoiling events. The number of superhelical turns introduced into an initially relaxed circular DNA has been calculated to be approximately equal to the number of ATP molecules hydrolyzed by gyrase. Therefore, it can be suggested that two ATP molecules are hydrolyzed per cycle of reaction by gyrase, leading to the introduction of a linking difference of -2.
Inhibition by antibiotics
Gyrase is present in prokaryotes and some eukaryotes, but the enzymes are not entirely similar in structure or sequence, and have different affinities for different molecules. This makes gyrase a good target for antibiotics. Two classes of antibiotics that inhibit gyrase are:
- The aminocoumarins (including novobiocin). Aminocoumarins work by competitive inhibition of energy transduction of DNA gyrase by binding to the ATPase active site located on the GyrB subunit.
- The quinolones (including nalidixic acid and ciprofloxacin). Quinolones bind to these enzymes and prevent them from decatenation replicating DNA. Quinolone-resistant bacteria frequently harbor mutated topoisomerases that resist quinolone binding.
DNA gyrase has two subunits, which in turn have two subunits each, i.e. 2A and 2B subunits. The A and B subunits together bind to DNA, hydrolyze ATP, and introduce negative supertwists. The A subunit carries out nicking of DNA, B subunit introduces negative supercoils, and then A subunit reseals the strands. Fluoroquinolones bind to the A subunit and interfere with its strand cutting and resealing function.
The subunit A is selectively inactivated by antibiotics such as oxolinic and nalidixic acids. The subunit B is selectively inactivated by antibiotics such as coumermycin A1 and novobiocin. Inhibition of either subunit blocks supertwisting activity.
- Wigley, D.B.; Davies, G.J.; Dodson, E.J.; Maxwell, A; Dodson, G (1991). "Crystal structure of an N-terminal fragment of the DNA gyrase B protein". Nature. 351 (6328): 624–629. Bibcode:1991Natur.351..624W. doi:10.1038/351624a0. PMID 1646964.
- Morais Cabral, J. H.; Jackson, A. P.; Smith, C. V.; Shikotra, N; Maxwell, A; Liddington, R. C. (1997). "Crystal structure of the breakage-reunion domain of DNA gyrase". Nature. 388 (6645): 903–6. Bibcode:1997Natur.388..903M. doi:10.1038/42294. PMID 9278055.
- "Molecular Cloning of Apicoplast-Targeted Plasmodium falciparum DNA Gyrase Genes: Unique Intrinsic ATPase Activity and ATP-Independent Dimerization of PfGyrB Subunit". Eukaryotic Cell: 398–412. 2007.
- Dar, A.; Prusty, D.; Mondal, N.; Dhar, S. K. (2009). "A unique 45 amino acid region in the Toprim domain of Plasmodium falciparum GyraseB is essential for its activity. (2009)". Eukaryotic Cell. 11 (8): 1759–69. doi:10.1128/ec.00149-09.
- Gore J, Bryant Z, Stone MD, Nollmann M, Cozzarelli NR, Bustamante C, "Mechanochemical Analysis of DNA Gyrase Using Rotor Bead Tracking", Nature 2006 Jan 5 (Vol. 439): 100-104.
- Sugino, Akio (1980-10-07). "The Intrinsic ATPase of DNA Gyrase". Journal of Biological Chemistry. 255 (13).
- Reece, Richard (1991). "DNA Gyrase: Structure and Function". Critical Reviews in Biochemistry and Molecular Biology. 26 (3/4): 335–375. doi:10.3109/10409239109114072. PMID 1657531.
- Engle, E C; Manes, S H; Drlica, K. "Differential effects of antibiotics inhibiting gyrase". Journal of Bacteriology.