The “GyrA-box” Is Required for the Ability of DNA Gyrase to Wrap DNA and Catalyze the Supercoiling Reaction

Abstract

DNA gyrase is the only topoisomerase that can introduce negative supercoils into DNA. It is thought that the binding of conventional type II topoisomerases, including topoisomerase IV, to DNA takes place at the catalytic domain across the DNA gate, whereas DNA gyrase binds to DNA not only at the amino-terminal catalytic domain but also at the carboxyl-terminal domain (CTD) of the GyrA subunit. The binding of the GyrA CTD to DNA allows gyrase to wrap DNA around itself and catalyze the supercoiling reaction. Recent structural studies, however, have revealed striking similarities between the GyrA CTD and the ParC CTD, as well as the ability of the ParC CTD to bind and bend DNA. Thus, the molecular basis of gyrase-mediated wrapping of DNA needs to be reexamined. Here, we have conducted a mutational analysis to determine the role of the "GyrA-box," a 7-amino acid-long motif unique to the GyrA CTD, in determining the DNA binding mode of gyrase. Either a deletion of the entire GyrA-box or substitution of the GyrA-box with 7 Ala residues abolishes the ability of gyrase to wrap DNA around itself and catalyze the supercoiling reaction. However, these mutations do not affect the relaxation and decatenation activities of gyrase. Thus, the presence of a GyrA-box allows gyrase to wrap DNA and catalyze the supercoiling reaction. The consequence of the loss of the GyrA-box during evolution of bacterial type II topoisomerases is discussed.DNA topoisomerases are ubiquitous enzymes that alter the linking number of double-stranded DNA. There are two classes of topoisomerases, type I and type II (1, 2). Type I topoisomerases alter the linking number in steps of one by breaking one strand of duplex DNA, passing the other strand through the break, and then resealing the broken strand, whereas type II topoisomerases alter the linking number in steps of two by breaking both strands, passing another segment of the helix through the break, and then resealing the broken strands. The discovery of a novel type II enzyme from Sulfolobus shibatae (3, 4) prompted the division of the type II topoisomerases into the type IIA and type IIB subtypes. All type II topoisomerases, except the S. shibatae topoisomerase VI, belong to type IIA subtype.DNA gyrase (5-7) and topoisomerase (Topo 3 ) IV (8) are type IIA topoisomerases. Gyrase and Topo IV consist of GyrA and GyrB subunits and ParC and ParE subunits, respectively. GyrA and ParC subunits catalyze strand-breakage and reunion reactions, whereas GyrB and ParE subunits hydrolyze ATP. The active forms of gyrase and Topo IV are an ␣ 2 ␤ 2 tetramer, and these topoisomerases bind double-stranded DNA. Topo IV can relax both positive and negative supercoils and catenate and decatenate covalently closed, negatively supercoiled, doublestranded circular (form I) and nicked or gapped, double-stranded circular DNA molecules. Gyrase can supercoil covalently closed, relaxed, double-stranded circular (form IЈ) DNA molecules, catenate and decatenate DNA rings, and, in the absence of ATP, relax negative supercoils (1...

A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs

“…3D). Moreover, the released minicircles showed no sign of supercoiling, a reaction known to be catalyzed by gyrase in this assay (18). The distinguishing ability of gyrase to negatively supercoil DNA relies on the DNA wrapping properties of the GyrA CTD (10).…”

“…1B and Fig. S1), eliminates gyrase's ability to negatively supercoil DNA (10,18,19). The topo IV CTD has been proposed to control enzyme activity not by wrapping DNA around its surface, but by helping to capture a DNA segment in trans for strand passage (14).…”

Mechanisms for Defining Supercoiling Set Point of DNA Gyrase Orthologs

“…The GyrA CTD is thought to constrain a positive supercoil by wrapping a DNA duplex around its surface (9 -12); this wrap is then converted into two negative supercoils upon strand passage (13). A highly conserved amino acid sequence motif, termed the GyrA box (14), maps to the N-terminal region of the CTD in all gyrases and is required for both wrapping and supercoiling functions (15).…”

L’architecture moléculaire complète de l’ADN gyrase révélée par cryo-microscopie électronique

“…La partie centrale comprend trois interfaces protéiques majeures ou « portes », constituées d'un domaine de fixation de l'ATP et d'un domaine de liaison/coupure de l'ADN, à travers lesquelles l'ADN est transporté. Cette interface dimérique est flanquée de deux domaines carboxy-terminaux adoptant un repliement tridimensionnel en forme de disque (b-pinwheel), indispensables à l'introduction de courbures dans l'ADN [4]. L'accumulation des données biochimiques et structurales sur plus de quatre décennies a permis de mettre en évidence l'implication des différents domaines dans le mécanisme de surenroulement de l'ADN.…”