At sixes and sevens: Characterization of the symmetry mismatch of the ClpAP chaperone-assisted protease

ClpAP, a typical energy-dependent protease, consists of a proteolytic compo nent (ClpP) and a chaperone-like ATPase (ClpA). ClpP is composed of two app osed heptameric rings, whereas in the presence of ATP or ATP gamma S, ClpA is a single hexameric ring. Formation of ClpAP complexes involves a symmetr y mismatch as sixfold ClpA stacks axially on one or both faces of sevenfold ClpP. We have analyzed these structures by cryo-electron microscopy. Our t hree-dimensional reconstruction of CIpA at 29-Angstrom resolution shows the monomer to be composed of two domains of similar size that, in the hexamer , form two tiers enclosing a large cavity. Cylindrical reconstruction of Cl pAP reveals three compartments: the digestion chamber inside ClpP; a compar tment between ClpP and ClpA; and the cavity inside ClpA. They are connected axially via narrow apertures, implying that substrate proteins should be u nfolded to allow translocation into the digestion chamber. The cavity insid e ClpA is structurally comparable to the "Anfinsen cage" of other chaperone s and may play a role in the unfolding of substrates, A geometrical descrip tion of the symmetry mismatch was obtained by using our model of ClpA and t he crystal structure of ClpP (Wang et al., 1997, Cell 91, 447-456) to ident ify the particular side views presented by both molecules in individual com plexes. The interaction is characterized by a key pair of subunits, one of each protein. A small turn (8.6 degrees = 2 pi/42; equivalent to a 4-Angstr om shift) would transfer the key interaction to another pair of subunits. W e propose that nucleotide hydrolysis results in rotation, facilitating the processive digestion of substrate proteins.