Study of AAA proteins by X-ray protein crystallography

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My lab was the first to determine the structure of the full-length ClpA, which was also the first structure of AAA+ proteins with two AAA+ modules. We also determined the structures of the N-terminal domain (N-domain) of ClpA and its complex with ClpS, an adaptor protein that plays a role in selecting substrates (N-end rule) for degradation. We analyzed the structure of the N-domain and identified potential sites for its interaction with substrates. Recently, my lab has determined structures for a number of N-D1 fragments of the human AAA+ protein p97 ATPase mutants, which were identified in patients suffering from the IBMPFD and were shown to be deficient in polyubiquitin binding. We found for the first time that the N-terminal domains of mutant proteins take a different conformation when the D1-domains are bound with ATP, in sharp contrast with previously observed conformation when the D1 domains were bound with ADP in the wild type enzyme. Our experiments further suggest that mutant proteins most likely have altered the affinities for various nucleotides that lead to the observed erratic conformational alteration. We believe that the new observed conformation in p97 is critical for understanding its function.