Robert Huber
Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany

Abstract:

Within cells or subcellular compartments misfolded and/or short-lived regulatory proteins are degraded by protease machines, cage-forming multi-subunit assemblages. Their proteolytic active sites are sequestered within the particles and located on the inner walls. Access of protein substrates is regulated by protein subcomplexes or protein domains which may assist in substrate unfolding dependent of ATP. Five protease machines will be described displaying different subunit structures, oligomeric states, enzymatic mechanisms, and regulatory properties.

Proteasome

Groll, M., Ditzel, L., Löwe, J., Stock, D., Bochtler, M., Bartunik, H. D. and Huber, R. (1997) Structure of 20S proteasome from yeast at 2.4 Å resolution. Nature 386, 463-471.
Groll, M., Heinemeyer, W., Jäger, S., Ullrich, T., Bochtler, M., Wolf, D. H. and Huber, R. (1999) The catalytic sites of 20S proteasomes and their role in subunit maturation: A mutational and crystallographic study. Proc. Natl. Acad. Sci. USA 96, 10976-10983.
Groll, M., Bajorek, M., Köhler, A., Moroder, L., Rubin, D. M., Huber, R., Glickman, M. H. and Finley, D. (2000) A gated channel into the proteasome core particle. Nature Struct. Biol. 7, 1062-1067.
Groll, M., Schellenberg, B., Bachmann, A. S., Archer, C. R., Huber, R., Powell, T. K., Lindow, S., Kaiser, M. and  Dudler, R. (2008) A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism. Nature 452, 755-758.
Groll, M., Huber, R. and Moroder, L. (2009). The persisting challenge of selective and specific proteasome inhibition. Journal of Peptide Science 15, 58-66.
Clerc, J., Groll, M., Illich, D. J., Bachmann, A. S., Huber, R., Schellenberg, B., Dudler, R. and Kaiser, M. (2009). Synthetic and structural studies on syringolin A and B reveal critical determinants of selectivity and potency of proteasome inhibition. Proc. Natl. Acad. Sci. USA 106, 6507-6512.
Clerc, J., Florea, B. I., Kraus, M., Groll, M., Huber, R., Bachmann, A. S., Dudler, R., Driessen, C., Overkleeft, H. S. and Kaiser, M. (2009). Syringolin A selectively labels the 20 S proteasome in murine EL4 and wild-type and bortezomib-adapted leukaemic cell lines. CHEMBIOCHEM 10, 2638-2643.
Groll, M., Gallastegui, N., Maréchal, X., Le Ravalec, V., Basse, N., Richy, N., Genin, E., Huber, R., Moroder, L., Vidal, J. and Reboud-Ravaux, M. (2010). 20S Proteasome Inhibition: Designing noncovalent linear peptide mimics of the natural product TMC-95A. ChemMedChem 5, 1701-1705.
Gräwert MA, Gallastegui N, Stein M, Schmidt B, Kloetzel PM, Huber R, and Groll M. (2010). Elucidation of the α-Keto-Aldehyde Binding Mechanism: A Lead Structure Motif for Proteasome Inhibition. Angew Chem Int Ed Engl. 2010 Dec 9Epub.

HslV/HslU

Bochtler, M., Hartmann, C., Song, H. K., Bourenkov, G., Bartunik, H. and Huber, R. (2000) The structure of HslU and the ATP-dependent protease HslU-HslV.
Nature 403, 800-805.
Song, H. K., Hartmann, C., Ramachandran, R., Bochtler, M., Behrendt, R., Moroder, L. and Huber, R. (2000) Mutational studies on HslU and its docking mode with HslV. Proc. Natl. Acad. Sci. USA 97, 14103-14108.
Ramachandran, R., Hartmann, C., Song, H. J., Huber, R. and Bochtler, M.(2002) Functional interactions of HslV(ClpQ) with the ATPase HslU(ClpY). Proc. Natl. Acad. Sci. USA 99, 7396-7401.

Tricorn

Brandstetter, H., Kim, J. S., Groll, M. and Huber, R. (2001) Crystal structure of the tricorn protease reveals a protein disassembly line. Nature 414, 466-470.
Kim, J. S., Groll, M., Musiol, H. J., Behrendt, R., Kaiser, M., Moroder, L., Huber, R. and Brandstetter H. (2002) Navigation inside a protease: substrate selection and product exit in the tricorn protease from Thermoplasma acidophilum. J. Mol. Biol. 324, 1041-1050.
Goettig, P., Groll, M., Kim, J. S., Huber, R. and Brandstetter, H. (2002) Structures of the tricorn interacting aminopeptidase F1 with different ligands explain its catalytic mechanism. EMBO J. 21, 5343-5352.

Dipeptidyl peptidase IV
Engel, M., Hoffmann, T., Wagner, L., Wermann, M., Heiser, U., Kiefersauer, R., Huber, R., Bode, W., Demuth, H. U. and Brandstetter, H. (2003) The crystal structure of dipeptidyl peptidase IV (CD26) reveals its functional regulation and enzymatic mechanism.Proc. Natl. Acad. Sci. USA 100, 5063-5068.

DegP(HtrA)
Krojer, T., Garrido-Franco, M., Huber, R., Ehrmann, M., and Clausen, T. (2002) Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine. Nature 416, 455-459.
Krojer, T., Pangerl, K., Kurt, J., Sawa, J., Stingl, C., Mechtler, K., Huber, R., Ehrmann, M. and Clausen, T. (2008) Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins. Proc. Natl. Acad. Sci. USA 105, 7702-7707.
Krojer, T., Sawa, J., Schäfer, E., Saibil, H. R, Ehrmann, M, and Clausen, T. (2008) Structural basis for the regulated protease and chaperone function of DegP. Nature 453, 885-890.
Krojer, T., Sawa, J., Huber, R. and Clausen, T. (2010) HtrA proteases have a conserved activation mechanism that can be triggered by distinct molecular cues. Nat. Struct. Mol. Biol. 17, 844-852.

.