The antibiotic cyclomarin blocks arginine-phosphate-induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis

J Biol Chem. 2018 Jun 1;293(22):8379-8393. doi: 10.1074/jbc.RA118.002251. Epub 2018 Apr 9.


Mycobacterium tuberculosis can remain dormant in the host, an ability that explains the failure of many current tuberculosis treatments. Recently, the natural products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein substrates, such as proteins containing phosphorylated arginine residues, to the ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these dynamics are caused by conformational changes and do not result from unfolding or oligomerization of this domain. Cyclomarin binding to this domain specifically blocked these N-terminal dynamics. On the basis of these results, we propose a mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics, which modulates the chaperone enzymatic activity leading eventually to cell death.

Keywords: Mycobacterium tuberculosis; antibiotic action; antibiotic resistance; chaperone; natural product; nuclear magnetic resonance (NMR); protease; small-angle X-ray scattering (SAXS).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Arginine / analogs & derivatives*
  • Arginine / pharmacology
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Cell Death
  • Crystallography, X-Ray
  • Gene Expression Regulation, Bacterial / drug effects
  • Heat-Shock Proteins / chemistry*
  • Heat-Shock Proteins / metabolism*
  • Ion Transport
  • Mycobacterium tuberculosis / drug effects*
  • Oligopeptides / pharmacology*
  • Organophosphorus Compounds / pharmacology
  • Phosphorylation
  • Protein Conformation
  • Protein Domains
  • Tuberculosis / drug therapy*
  • Tuberculosis / metabolism
  • Tuberculosis / microbiology


  • Anti-Bacterial Agents
  • Bacterial Proteins
  • ClpC1 protein, Mycobacterium tuberculosis
  • Heat-Shock Proteins
  • Oligopeptides
  • Organophosphorus Compounds
  • cyclomarin A
  • phospho-L-arginine
  • Arginine

Associated data

  • PDB/3j3s
  • PDB/3wdb
  • PDB/3wdc
  • PDB/5hbn
  • PDB/6em9