W0013

Structural Analysis of Substrate binding by the Molecular Chaperone DnaK. Xiaotian Zhu, Xun Zhao and Wayne Hendrickson, Kinetix Pharmaceuticals, Inc., Medford, MA 02155 USA

Heat shock protein 70 (hsp70) promotes protein folding, interaction, and translocation by binding to unfolded polypeptides segments. Hsp70 has two functional units: a substrate-binding domain that binds the polypeptide, and an ATPase domain that facilitates substrate exchange. Our recent crystal structure of the substrate binding domain of DnaK, an E. coli hsp70, provides for the first time the structural basis to understand how hsp70 recognizes its substrates. The structure of the substrate binding domain of DnaK consists of a beta sandwich subdomain followed by an alpha helical subdomain. The substrate peptide is captured in DnaK in a defined channel, formed at the interface of the two subdomains. Comparison of the crystal structures of two different substrate peptides in complex with DnaK indicates how thousands of different unfolded proteins can be recognized by one hsp70 molecule. Furthermore, the structural flexibility of the alpha helical subdomain in two different crystal forms suggests a mechanism of how substrates may bind to and be released by hsp70.