Crystal structures of the HsIVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism

Background: The bacterial heat shock locus HsIU ATPase and HsIV peptidase together form an ATP-dependent HsIVU protease. Bacterial HsIVU is a homolog of the eukaryotic 26S proteasome. Crystallographic studies of HsIVU should provide an understanding of ATP-dependent protein unfolding, translocation, and proteolysis by this and other ATP-dependent proteases. Results: We present a 3.0 Angstrom resolution crystal structure of HsIVU with an HsIU hexamer bound at one end of an HsIV dodecamer. The structure shows that the central pores of the ATPase and peptidase are next to each other and aligned. The central pore of HsIU consists of a GYVG motif, which is conserved among protease-associated ATPases. The binding of one HsIU hexamer to one end of an HsIV dodecamer in the 3.0 Angstrom resolution structure opens both HsIV central pores and induces asymmetric changes in HsIV. Conclusions: Analysis of nucleotide binding induced conformational changes in the current and previous HsIU structures suggests a protein unfolding-coupled translocation mechanism. In this mechanism, unfolded polypeptides are threaded through the aligned pores of the ATPase and peptidase and translocated into the peptidase central chamber.