DNA gyrase forms an A 2 B 2 tetramer involved in DNA replication, repair, recombination, and transcription in which the B subunit catalyzes ATP hydrolysis. The Thermus thermophilus and Escherichia coli gyrases are homologues and present the same catalytic activity. When compared with that of the E. coli 43K-5-adenylyl-,␥-imidodiphosphate complex, the crystal structure of Gyrase B 43K ATPase domain in complex with novobiocin, one of the most potent inhibitors of gyrase shows large conformational changes of the subdomains within the dimer. The stabilization of loop 98 -118 closing the active site through dimeric contacts and interaction with domain 2 allows to observe novobiocin-protein interactions that could not be seen in the 24K-inhibitor complexes. Furthermore, this loop adopts a position which defines an "open" conformation of the active site in absence of ATP, in contrast with the "closed" conformation adopted upon ATP binding. All together, these results indicate how the subdomains may propagate conformational changes from the active site and provide crucial information for the design of more specific inhibitors.Type II topoisomerases are enzymes essential for chromosome segregation and cell division due to their ability to modify the topological forms of procaryotic and eukaryotic DNA (1). The topoisomerases II share sequence, functional, and structural similarities and this knowledge comes mostly from complementary comparative studies done on the procaryotic and eukaryotic enzymes (2-5). At difference with the eukaryotic enzyme, the bacterial enzyme named gyrase, catalyzes the negative supercoiling of DNA and consists of two proteins, namely GyrB and GyrA associated into a A 2 B 2 oligomer. ATP binding and hydrolysis in the N-terminal part of the B subunit appears to be required for protein-protein interactions and recycling of the enzyme (6). This part of the protein also contains the entry site for the DNA T-segment (7-9) and studies have shown that this domain behaves as an ATP-operated clamp which binds DNA during the supercoiling cycle (10).Recent structural studies on yeast topoisomerase II have shown that the domains of this modular enzyme are capable of wide conformational changes which could be correlated with the topoisomerization mechanism (4). Nevertheless, the structure of the whole enzyme is not known. Up to now, the only structural information from the ATP-binding site comes from the Escherichia coli 43K complex with ADPPNP (6, 11). Most of the residues which bind the ATP molecule lie in the 24-kDa N-terminal region between residues 1 and 220 (domain 1), but there are two residues (Gln 335 and Lys 337 ) in domain 2 (residues 220 -392) which also contact the ATP molecule. Although the role of these highly conserved residues remains unclear, mutational studies have pointed out their role in the hydrolysis of ATP and they are thought to be implicated in the transmission of conformational changes upon ATP hydrolysis (12, 13). The loop closing the active site and comprising residues 98 to 118 ...
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