Sandbox Reserved 828: Difference between revisions

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'''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.

Sandbox Reserved 828: Difference between revisions

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+'''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.