title: Binding of two DNA molecules by type II topoisomerases for decatenation.
abstract: Topoisomerases (topos) maintain DNA topology and influence DNA transaction processes by catalysing relaxation, supercoiling and decatenation reactions. In the cellular milieu, division of labour between different topos ensures topological homeostasis and control of central processes. In Escherichia coli, DNA gyrase is the principal enzyme that carries out negative supercoiling, while topo IV catalyses decatenation, relaxation and unknotting. DNA gyrase apparently has the daunting task of undertaking both the enzyme functions in mycobacteria, where topo IV is absent. We have shown previously that mycobacterial DNA gyrase is an efficient decatenase. Here, we demonstrate that the strong decatenation property of the enzyme is due to its ability to capture two DNA segments in trans. Topo IV, a strong dedicated decatenase of E. coli, also captures two distinct DNA molecules in a similar manner. In contrast, E. coli DNA gyrase, which is a poor decatenase, does not appear to be able to hold two different DNA molecules in a stable complex. The binding of a second DNA molecule to GyrB/ParE is inhibited by ATP and the non-hydrolysable analogue, AMPPNP, and by the substitution of a prominent positively charged residue in the GyrB N-terminal cavity, suggesting that this binding represents a potential T-segment positioned in the cavity. Thus, after the GyrA/ParC mediated initial DNA capture, GyrB/ParE would bind efficiently to a second DNA in trans to form a T-segment prior to nucleotide binding and closure of the gate during decatenation.
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Rupesh
authors.initials: R
authors.lastname: Kumar
authors.forename: Jane E
authors.initials: JE
authors.lastname: Riley
authors.forename: Damian
authors.initials: D
authors.lastname: Parry
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Bates
authors.forename: Valakunja
authors.initials: V
authors.lastname: Nagaraja
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000378:metabolism; D001120:Arginine / Q000737:chemistry; D004247:DNA / Q000378:metabolism*; D027081:DNA Gyrase / Q000378:metabolism*; D027101:DNA Topoisomerase IV / Q000737:chemistry / Q000378:metabolism*; D043864:DNA, Catenated / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D020102:Mycobacterium smegmatis / Q000201:enzymology; D011485:Protein Binding
chemical_list: D043864:DNA, Catenated; D004247:DNA; D001120:Arginine; D000251:Adenosine Triphosphatases; D027101:DNA Topoisomerase IV; D027081:DNA Gyrase