3WDE: Mutant N-terminal Domain of Mycobacterium Tuberculosis Clpc1, F80y, Bound to Cyclomarin a

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.
PDB ID: 3WDEDownload
MMDB ID: 113481
PDB Deposition Date: 2013/6/14
Updated in MMDB: 2013/12
Experimental Method:
x-ray diffraction
Resolution: 1.44  Å
Source Organism:
Similar Structures:
Biological Unit for 3WDE: dimeric; determined by author and by software (PISA)
Molecular Components in 3WDE
Label Count Molecule
Protein (1 molecule)
Probable Atp-dependent CLP Protease Atp-binding Subunit
Molecule annotation
Nucleotide(1 molecule)
Cyclomarin a
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

Citing MMDB