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The ATP-dependent chaperone/protease complex, ClpAP or ClpXP, plays an important role in the protein degradation in most bacteria or in mitochondria and chloroplast of eukaryotes. ClpP is a proteolytic component that has 14 identical subunits organized in two stacked heptameric rings whereas ClpA and ClpX is a hexameric AAA+ ATPase that binds, denatures, and trasnlocates protein substrates. We have solved the crystal structure of ClpP from Bacillus subtilis (BsClpP) at 2.4 Å resolution and tested proteolytic activity against peptide and protein substrates. The structure of BsClpP was determined by molecular replacement method using that of E. coli ClpP (EcClpP), which is highly characterized ClpP and has 68% homology to BsClpP. The model of BsClpP has been refined to crystallographic R and R-free factors of 24.4 and 28.8 % and shows very similar overall structure with EcClpP. Although the structural and sequential resemblance between E. coli and B. subtilis species is significantly high, ClpX from E. coli is not able to stimulate the proteolytic activity of BsClpP and ClpX from B. subtilis also is not able to stimulate that of EcClpP. It is in stark different to a similar bacterial ATP-dependent protease, HslVU which shows mutual activation through swapped combination.

Structural and biochemical characterization of ClpP fromBacillus subtilis