1KIJ

Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin

Summary for 1KIJ

• Entry DOI: 10.2210/pdb1kij/pdb
• Descriptor: DNA GYRASE SUBUNIT B, NOVOBIOCIN, FORMIC ACID, ... (4 entities in total)
• Functional Keywords: topoisomerase, gyrase b-coumarin complex, isomerase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 2
• Total formula weight: 86760.20

Authors

Lamour, V.,Hoermann, L.,Jeltsch, J.-M.,Oudet, P.,Moras, D. (deposition date: 2001-12-03, release date: 2002-06-03, Last modification date: 2024-02-14)

Primary citation

Lamour, V.,Hoermann, L.,Jeltsch, J.M.,Oudet, P.,Moras, D.
An open conformation of the Thermus thermophilus gyrase B ATP-binding domain.
J.Biol.Chem., 277:18947-18953, 2002

PubMed Abstract: 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-beta,gamma-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.

PubMed: 11850422
DOI: 10.1074/jbc.M111740200

Experimental method

X-RAY DIFFRACTION (2.3 Å)