Structural basis and dynamics of multidrug recognition in a minimal bacterial multidrug resistance system

Significance Multidrug recognition is an important phenomenon that is not well understood. TipA, a bacterial transcriptional regulator, constitutes a minimal multidrug resistance system against numerous thiopeptide antibiotics. We show that motions in the millisecond to microsecond time range form the basis of the TipA multidrug recognition mechanism. This may be common to many multidrug recognition systems. The discovery that the structural antibiotic motifs essential for binding to TipA and to the ribosome are identical makes the multidrug recognition mechanism of TipA a useful model for ribosomal thiopeptide binding and current antibiotic drug development. TipA is a transcriptional regulator found in diverse bacteria. It constitutes a minimal autoregulated multidrug resistance system against numerous thiopeptide antibiotics. Here we report the structures of its drug-binding domain TipAS in complexes with promothiocin A and nosiheptide, and a model of the thiostrepton complex. Drug binding induces a large transition from a partially unfolded to a globin-like structure. The structures rationalize the mechanism of promiscuous, yet specific, drug recognition: ( i ) a four-ring motif present in all known TipA-inducing antibiotics is recognized specifically by conserved TipAS amino acids; and ( ii ) the variable part of the antibiotic is accommodated within a flexible cleft that rigidifies upon drug binding. Remarkably, the identified four-ring motif is also the major interacting part of the antibiotic with the ribosome. Hence the TipA multidrug resistance mechanism is directed against the same chemical motif that inhibits protein synthesis. The observed identity of chemical motifs responsible for antibiotic function and resistance may be a general principle and could help to better define new leads for antibiotics.