Functional Characterization of Structural Genomics Proteins in the Crotonase Superfamily

Members of the Crotonase superfamily, a mechanistically diverse family of proteins that share a conserved quaternary structure, can often catalyze more than one reaction. However, the spectrum of activity for its members has not been well studied. We report on measured crotonase and hydrolase activity for eight structural genomics (SG) proteins from the Crotonase superfamily plus two previously characterized proteins, intended as controls: human enoyl CoA hydratase (ECH) and Anabaena β-diketone hydrolase. Like most of the 15,000+ SG protein structures deposited in the Protein Data Bank (PDB), the eight SG proteins are of unknown or uncertain biochemical function. The functional characterization of the eight SG proteins is guided by the Structurally Aligned Local Sites of Activity (SALSA), a local-structure-based computational approach to functional annotation. For human ECH, the turnover number for hydrolase activity is threefold higher than that for ECH activity, although the catalytic efficiency is 160-fold higher for ECH. Three SG proteins originally annotated as ECHs were predicted by SALSA to be hydrolases and are observed to have higher catalytic efficiencies for hydrolase activity than for ECH activity, on par with the previously characterized hydrolase. Among the five SG proteins predicted by SALSA to be ECHs, all but one also show some hydrolase activity; all five exhibit lower ECH activity than the human ECH with respect to the crotonyl-CoA substrate. Here, we show examples demonstrating that SALSA can correct functional misannotations even within enzyme families that display promiscuous activity.