Structural basis of mycobacterial inhibition by cyclomarin A

J Biol Chem. 2013 Oct 25;288(43):30883-91. doi: 10.1074/jbc.M113.493767. Epub 2013 Sep 10.


Cyclomarin A (CymA) was identified as a mycobactericidal compound targeting ClpC1. However, the target was identified based on pulldown experiments and in vitro binding data, without direct functional evidence in mycobacteria. Here we show that CymA specifically binds to the N-terminal domain of ClpC1. In addition we have determined the co-crystal structure of CymA bound to the N-terminal domain of ClpC1 to high resolution. Based on the structure of the complex several mutations were engineered into ClpC1, which showed reduced CymA binding in vitro. The ClpC1 mutants were overexpressed in mycobacteria and two showed resistance to CymA, providing the first direct evidence that ClpC1 is the target of CymA. Phe(80) is important in vitro and in cells for the ClpC1-CymA interaction and this explains why other bacteria are resistant to CymA. A model for how CymA binding to the N-terminal domain of ClpC1 leads to uncontrolled proteolysis by the associated ClpP protease machinery is discussed.

Keywords: ClpC; Crystal Structure; Cyclomarin; Drug Discovery; Enzyme Inhibitors; Enzymes; Natural Products.

MeSH terms

  • Bacterial Proteins / antagonists & inhibitors
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Crystallography, X-Ray
  • Heat-Shock Proteins / antagonists & inhibitors
  • Heat-Shock Proteins / chemistry*
  • Heat-Shock Proteins / genetics
  • Heat-Shock Proteins / metabolism
  • Models, Molecular*
  • Mutation
  • Mycobacterium tuberculosis / chemistry*
  • Mycobacterium tuberculosis / genetics
  • Mycobacterium tuberculosis / metabolism
  • Oligopeptides / chemistry*
  • Oligopeptides / metabolism
  • Protein Binding
  • Protein Structure, Tertiary


  • Bacterial Proteins
  • ClpC1 protein, Mycobacterium tuberculosis
  • Heat-Shock Proteins
  • Oligopeptides
  • cyclomarin A

Associated data

  • PDB/3WDB
  • PDB/3WDC
  • PDB/3WDD
  • PDB/3WDE