title: Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase.
abstract: Topoisomerase IV and DNA gyrase are related bacterial type II topoisomerases that utilize the free energy from ATP hydrolysis to catalyze topological changes in the bacterial genome. The essential function of DNA gyrase is the introduction of negative DNA supercoils into the genome, whereas the essential function of topoisomerase IV is to decatenate daughter chromosomes following replication. Here, we report the crystal structures of a 43-kDa N-terminal fragment of Escherichia coli topoisomerase IV ParE subunit complexed with adenylyl-imidodiphosphate at 2.0-A resolution and a 24-kDa N-terminal fragment of the ParE subunit complexed with novobiocin at 2.1-A resolution. The solved ParE structures are strikingly similar to the known gyrase B (GyrB) subunit structures. We also identified single-position equivalent amino acid residues in ParE (M74) and in GyrB (I78) that, when exchanged, increased the potency of novobiocin against topoisomerase IV by nearly 20-fold (to 12 nM). The corresponding exchange in gyrase (I78 M) yielded a 20-fold decrease in the potency of novobiocin (to 1.0 micro M). These data offer an explanation for the observation that novobiocin is significantly less potent against topoisomerase IV than against DNA gyrase. Additionally, the enzyme kinetic parameters were affected. In gyrase, the ATP K(m) increased approximately 5-fold and the V(max) decreased approximately 30%. In contrast, the topoisomerase IV ATP K(m) decreased by a factor of 6, and the V(max) increased approximately 2-fold from the wild-type values. These data demonstrate that the ParE M74 and GyrB I78 side chains impart opposite effects on the enzyme's substrate affinity and catalytic efficiency.
authors.affiliation: Vertex Pharmaceuticals Incorporated, Cambridge, Massachusetts 02139, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Bellon
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Parsons
authors.forename: Yunyi
authors.initials: Y
authors.lastname: Wei
authors.forename: Koto
authors.initials: K
authors.lastname: Hayakawa
authors.forename: Lora L
authors.initials: LL
authors.lastname: Swenson
authors.forename: Paul S
authors.initials: PS
authors.lastname: Charifson
authors.forename: Judith A
authors.initials: JA
authors.lastname: Lippke
authors.forename: Robert
authors.initials: R
authors.lastname: Aldape
authors.forename: Christian H
authors.initials: CH
authors.lastname: Gross
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D027101:DNA Topoisomerase IV / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000235:genetics; D024881:Drug Resistance, Bacterial; D004926:Escherichia coli / Q000201:enzymology*; D007700:Kinetics; D008958:Models, Molecular; D009675:Novobiocin / Q000494:pharmacology*; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000378:metabolism; D013329:Structure-Activity Relationship; D059005:Topoisomerase II Inhibitors
chemical_list: D000900:Anti-Bacterial Agents; D011994:Recombinant Proteins; D059005:Topoisomerase II Inhibitors; D009675:Novobiocin; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases; D027101:DNA Topoisomerase IV