The Structure of ClpP at 2.3 Å Resolution Suggests a Model for ATP-Dependent Proteolysis

Abstract

We have determined the crystal structure of the proteolytic component of the caseinolytic Clp protease (ClpP) from E. coli at 2.3 A resolution using an ab initio phasing procedure that exploits the internal 14-fold symmetry of the oligomer. The structure of a ClpP monomer has a distinct fold that defines a fifth structural family of serine proteases but a conserved catalytic apparatus. The active protease resembles a hollow, solid-walled cylinder composed of two 7-fold symmetric rings stacked back-to-back. Its 14 proteolytic active sites are located within a central, roughly spherical chamber approximately 51 A in diameter. Access to the proteolytic chamber is controlled by two axial pores, each having a minimum diameter of approximately 10 A. From the structural features of ClpP, we suggest a model for its action in degrading proteins.

Structural Insights into the Conformational Diversity of ClpP from Bacillus subtilis

“…The active site was then analyzed since the catalytic triad (Ser97-His122-Asp171) in ClpP is located in the cleft between the head domain and handle region (Wang et al, 1997). Previously, we reported that the catalytic triads in extended and ADEP-bound activated BsClpP showed very similar conformations, ruling out an allosteric activation mechanism (Lee et al, 2010a).…”

“…In addition to the axial pore, we investigated the active site of ClpP. Previously, several ClpP structures representing inhibited or substrate-bound states have been reported (Kim and Kim, 2008;Szyk and Maurizi, 2006;Wang et al, 1997). The overall shape of all of these structures shows an extended conformation as in the case of DFPinhibited BsClpP, although the active sites and N-terminal segments of the apo and inhibited structures vary depending on the bacterial species.…”

“…All of these protease components are self-compartmentalized proteases that possess catalytic residues located deep inside the molecule, and which are shielded from direct access from the outside. It is unknown how the hydrolyzed products generated inside the protease chamber are efficiently released since all atomic resol-ution structures of HslV, ClpP and the 20S proteasome show virtually no product exit site except for the entrance pores (Bochtler et al, 1999;Groll et al, 1997;Lowe et al, 1995;Song et al, 2000;2003;Sousa et al, 2000;Wang et al, 1997;2001;Yu and Houry, 2007).…”

“…Presently, the structures of ClpPs from a variety of species have been reported (El Bakkouri et al, 2010;Kang et al, 2004;Kim and Kim, 2008;Lee et al, 2010a;Wang et al, 1997;Yu and Houry, 2007). In contrast to the similar overall architectural shape, a ClpP structure from Mycobacterium tuberculosis suggests a flexible ring-ring contact (Ingvarsson et al, 2007).…”

Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor‐binding specificities in different bacterial species

“…[2][3][4] ClpP is a multisubunit serine peptidase, in which the proteolytic active sites reside within a barrel-shaped structure. 5 ClpX is a hexameric AAAþ enzyme (ATPases associated with a variety of cellular activities), which recognizes substrates and uses cycles of ATP-powered conformational changes to unfold the native protein and to translocate the denatured polypeptide into the proteolytic chamber of ClpP for degradation. [6][7][8] ClpX typically identifies substrates by binding to degrons located near the protein termini.…”