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Structural basis for the regulated protease and chaperone function of DegP

Abstract

All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases.

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Figure 1: The DegP 24 particle.
Figure 2: Regulation of protease activity by oligomer reassembly.
Figure 3: Function of DegP in OMP biogenesis.
Figure 4: Membrane attachment of DegP24.
Figure 5: Cryo-electron microscopy structure of the DegP 12 –OMP complex.

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Primary accessions

Protein Data Bank

Data deposits

The DegP24 structure is deposited in the Protein Data Bank under accession number 3cs0. The fitted model of the electron microscopic three-dimensional map of DegP12–OMP is deposited in the Protein Data Bank under accession number 2zle. The electron-microscopic three-dimensional maps are deposited at the Electron Microscopy Data Bank (http://www.ebi.ac.uk/msd-srv/emsearch/index.html) under accession codes EMD-1504 and EMD-1505 for DegP24–OMP and DegP12–OMP, respectively.

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Acknowledgements

We thank K. Mechtler and I. Steinmacher for assistance with mass spectrometry; the staff at the European Synchrotron Radiation Facility and the Swiss Light Source for assistance with collecting synchrotron data; N. Boisset and R. Trujillo for providing image-processing scripts; L. Wang for support with electron microscopy; D. Houldershaw for computer support; and E. Orlova for discussion. The Research Institute of Molecular Pathology (IMP) is funded by Boehringer Ingelheim. E.S. and H.R.S. were supported by the UK Biotechnology and Biological Sciences Research Council, M.E. by the Deutsche Forschungsgemeinschaft and the Fonds der Chemischen Industrie, T.C. by the EMBO Young Investigator Program, and T.K. and J.S. by the Austrian Science Fund.

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Correspondence to Tim Clausen.

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Supplementary Information

The file contains Supplementary Table 1 and Supplementary Figures S1-S6 with Legends. The Table comprises a summary of X-ray data collection, phasing and refinement statistics. The Figures illustrate the identification and isolation of the DegP/OMP complex (S1), EM images of DegP12/OMP and DegP24/OMP complexes (S2), a structural comparison of the overall dimensions of DegP6 and DegP24 (S3), the intersubunit contacts of different DegP oligomers (S4), the biochemical analysis of oligomer formation and protease activity (S5) and the Fourier shell correlation curves of the EM maps (S6). (PDF 1152 kb)

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Krojer, T., Sawa, J., Schäfer, E. et al. Structural basis for the regulated protease and chaperone function of DegP. Nature 453, 885–890 (2008). https://doi.org/10.1038/nature07004

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