True-atomic-resolution insights into the interactions of antibiotic rifampicin and rifamycin derivatives with orphan CYP143 of M.tuberculosis.

Analysis of drug-resistant strains of M.tuberculosis revealed a mutation in cytochrome P450 CYP143 gene located in the ESX-5 secretion cluster. The function of CYP143 is unknown. Available synteny information is insufficient to straightforwardly infer potential CYP143 substrates, because a full set of effector proteins/substrates exported by the ESX-5 secretion system has not yet been identified. Here we found that CYP143 is highly conserved among mycobacteria. We leverage the possible association of the G334A mutation in CYP143 with the development of resistance to test the frontline antitubercular drug rifampicin using purified proteins. Binding of rifampicin does not induce typical P450 spectral response, while the crystal structure at atomic resolution reveals the binding mode in the active site. The drug binds above the heme and adopts "closed" conformation of the ansa chain running almost parallel to the naphthoquinone core. In this conformation the oxygen atom bridging C12 and C29 of the macrocycle makes a hydrogen bond with a water molecule coordinating heme iron. The same binding mode was observed in crystal structures in complex with rifaximin, rifamycin S and two synthetic derivatives. In the ligand-bound state the protein retains an open conformation even in the presence of the redox partner, as evident from the crystal structure of the ternary complex. Despite binding close to the heme, no conversion was observed showing that either the rifamycins or the reduction system, or both, are insufficient to support a full catalytic cycle. These results pave the way to understand the development of rifampicin resistance/tolerance and the role of orphan CYPome of M.tuberculosis.