Solution structure and backbone dynamics for S1 domain of ribosomal protein S1 from Mycobacterium tuberculosis

The pro-drug pyrazinamide is hydrolyzed to pyrazinoic acid (POA) in its use for the treatment of tuberculosis. As a molecule with bactericidal activity, POA binds to the C-terminal S1 domain of ribosomal protein S1 from Mycobacterium tuberculosis (MtRpsA^CTD_S1) to inhibit trans-translation. Trans-translation is a critical component of protein synthesis quality control, and is mediated by transfer-messenger RNA. Here, we have determined the solution structure of MtRpsA^CTD_S1(280-368), and analyzed its structural dynamics by NMR spectroscopy. The solution structure of MtRpsA^CTD_S1(280-368) mainly consists of five anti-parallel β strands, two α helices, and two 3₁₀ helices. Backbone dynamics reveals that the overall structure of MtRpsA^CTD_S1(280-368) is rigid, but segment L326-V333 undergoes large amplitude fluctuations on picosecond to nanosecond time scales. In addition, residues V321, H322, V331 and D335 with large R_ex values exhibit significant chemical or conformational exchange on microsecond to millisecond time scale. Titration of the truncated MtRpsA^CTD_S1(280-368) with POA shows similar characteristics to titration of MtRpsA^CTD_S1(280-438) with POA. In addition, diverse length fragments of MtRpsA^CTD_S1 show various HN resonance signals, and we find that the interaction of MtRpsA(369-481) with MtRpsA^CTD_S1(280-368) [Kd = (4.25 ± 0.15) mM] is responsible for the structural difference between MtRpsA^CTD_S1(280-368) and MtRpsA^CTD_S1. This work may shed light on the underlying molecular mechanism of MtRpsA^CTD recognizing and binding POA or mRNA, as well as the detailed mechanism of interactions between MtRpsA^CTD_S1(280-368) and the additional C-terminal MtRpsA(369-481).