Sandbox Reserved 828

From Proteopedia

Introduction :

Gyrase is the only prokaryote DNA topoisomerase II able to introduce negative supercoils in the DNA in order to remove positive supercoils. It catalyses the hydrolysis of two phosphodiester bonds in a DNA segment (called G segment). Then, thanks to ATP dependant conformation changes it enables the passage of another segment (the T segment) through the break, and then religates the broken segment. Gyrase acts prior to the replication (before the replication fork) or other mecanisms requiring loose DNA. In abscence of ATP, like other topoisomerases II, gyrase only relaxes supercoils.

Gyrase is coded by two differents contiguous genes gyrA and GgyrB as it is a 350 kDa A2B2 heterotetramers of two A proteins and two B proteins. The A protein breaks and religates DNA . The B protein has ATPase activity

Structure

The gyrase structure reveals a dimer contact with a grooved concave surface for binding the G segment and a cluster of conserved charged residues surrounding the active-site tyrosines. The A protein breaks and religates DNA as the DNA cleavage core and the CTD lies on it. GyrA59 is the minimal fragment of the A-subunit which, when complexed with the B-subunit, has DNA-cleavage activity. The carboxy-terminal domain of GyrA is required for the introduction of DNA supercoils. Each GyrA59 monomer is composed of two domains at the head region: one similar to the DNA-binding domain of the catabolite-activator protein (CAP), including the helix–turn–helix (HTH) motif; and a second domain with a/bstructure (the ‘tower’ domain) and a single domain with a helical core at the tail region. Two long helices (a14 anda18) emanate from thiscore and connect, together with the C-terminal helix (a19), the head and tail fragments The three connecting helices (a14,a18 anda19) adopt very different conformations, leading to large quaternary movements involving a single hinge-point within the helices and rigid body movements of the head fragments (Fig. 2d).. The tail is structurally conserved although large surface loops emanatingfrom different points give it a different outward appearance

The B protein has the ATPase domain and the Toprim fold on it. Two ATPase domains dimerize to form a closed conformation. The Toprim fold is a Rossmann fold that contains three invariant acidic residues that coordinate magnesium ions involved in DNA cleavage and DNA religation The central core of the protein contains a Toprim fold and a DNA-binding core that contains a winged helix domain (WHD), often referred to as a CAP domain. The catalytic tyrosine lies on this WHD. The DNA-binding core consists of the WHD, which leads to a tower domain. . A coiled-coil region leads to a C-terminal domain that forms the main dimer interface the Toprim domain is flexible and that this flexibility can allow the Toprim domain to coordinate with the WHD to form a competent cleavage complex DNA was bent by ~150 degrees through an invariant isoleucine (in topoisomerase II it is I833 and in gyrase it is I172) The first structure of a C-terminal domain of gyrase was solved by Corbett et al. (Proceedings of the National Academy of Science, 2004, PDB ID = 1SUU) The structures formed a novel beta barrel, which bends DNA by wrapping the nucleic acid around itself. The bending of DNA by gyrase has been proposed as a key mechanism in the ability of gyrase to introduce negative supercoils into the DNA. This is consistent with footprinting data that shows that gyrase has a 140-base-pair footprint. Both gyrase and topoisomerase IV CTDs bend DNA, but only gyrase introduces negative supercoils.