Loss of function in SAGA deubiquitinating module caused by Sgf73 H93A mutation: A molecular dynamics study

The Spt-Ada-Gcn5-acetyltransferase (SAGA) deubiquitinating module (DUBm), comprising Ubp8, Sgf11, Sus1, and Sgf73, functions as a deubiquitinase. Data from recent biomolecular experiments have indicated that the H93A mutation in Sgf73 abrogates the enzyme function without interfering with module formation. Interestingly Sgf73 H93 residue is neither involved in the active site nor near the ubiquitin substrate binding site but is capable of influencing the active site through an allosteric mechanism. In this study, molecular dynamics simulations were used to analyze the structural discrepancy between wild-type and H93A mutant of the SAGA DUBm to reveal the interprotein communication pathway linking the mutation site to the catalytic site. We concluded that H93A mutation directly impairs Sgf73's zinc finger motif and further induces a downward movement of Sgf11's N-terminal long α-helix. The structural influence gradually propagates toward Sgf11's C-terminal end and results in the rearrangement of the catalytic triad of Ubp8 protein. The repositioned catalytic Cys-His-Asn triad could no longer execute the deubiquitinating function.