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

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Abstract

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 (MtRpsACTD_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 MtRpsACTD_S1(280–368), and analyzed its structural dynamics by NMR spectroscopy. The solution structure of MtRpsACTD_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 MtRpsACTD_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 Rex values exhibit significant chemical or conformational exchange on microsecond to millisecond time scale. Titration of the truncated MtRpsACTD_S1(280–368) with POA shows similar characteristics to titration of MtRpsACTD_S1(280–438) with POA. In addition, diverse length fragments of MtRpsACTD_S1 show various HN resonance signals, and we find that the interaction of MtRpsA(369–481) with MtRpsACTD_S1(280–368) [Kd = (4.25 ± 0.15) mM] is responsible for the structural difference between MtRpsACTD_S1(280–368) and MtRpsACTD_S1. This work may shed light on the underlying molecular mechanism of MtRpsACTD recognizing and binding POA or mRNA, as well as the detailed mechanism of interactions between MtRpsACTD_S1(280–368) and the additional C-terminal MtRpsA(369–481).

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Abbreviations

M. tb :

Mycobacterium tuberculosis

RpsA:

Ribosomal protein S1

MtRpsA:

Ribosomal protein S1 of M. tb

MtRpsACTD_S1:

The C-terminal S1 domain of MtRpsA

MtRpsACTD_S1(280–368):

The region Q280–D368 of MtRpsACTD_S1

MtRpsACTD_S1(280–433):

The residues 280–433 of MtRpsA

MtRpsACTD_S1(280–438):

The residues 280–438 of MtRpsA

MtRpsACTD_S1(280–467):

The residues 280–467 of MtRpsA

MtRpsA(369–481):

The residues 369–481 of MtRpsA

MtRpsA(401–439):

The residues 401–439 of MtRpsA

MtRpsACTD ΔA438 :

An alanine deletion of MtRpsACTD_S1

tmRNA:

Transfer-messenger RNA

PZA:

Pyrazinamide

POA:

Pyrazinoic acid

R 1 :

Longitudinal relaxation rate

R 2 :

Transverse relaxation rate

NOE:

Nuclear Overhauser effect

HSQC:

Heteronuclear singular quantum correlation

RMSD:

Root-mean-square deviation

S 2 :

The square of generalized order parameters

R ex :

Conformational exchange rate

τ m :

The overall rotation correlation time

τ e :

Effective internal correlation time

Kd:

Dissociation constant

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Acknowledgements

This work was supported by Grants from the National Key Research and Development Program of China (2016YFA0500600) and the National Natural Science Foundation of China (31270777, 21778042, 41876072, 91856126). I would like to thank Mr. Xingxing for taking me around the world by bike every day, and BEST WISHES FOR YOU.

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Authors and Affiliations

  1. Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, No. 422, Siming South Road, Xiamen, 361005, Fujian, People’s Republic of China

    Biling Huang, Shihui Fan, Yan Liu, Yufen Zhao, Donghai Lin & Xinli Liao

  2. Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, People’s Republic of China

    Yufen Zhao

  3. Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, People’s Republic of China

    Yufen Zhao

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  1. Biling Huang
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  2. Shihui Fan
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  3. Yan Liu
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Correspondence to Yufen Zhao, Donghai Lin or Xinli Liao.

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Huang, B., Fan, S., Liu, Y. et al. Solution structure and backbone dynamics for S1 domain of ribosomal protein S1 from Mycobacterium tuberculosis. Eur Biophys J 48, 491–501 (2019). https://doi.org/10.1007/s00249-019-01372-5

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