Structural basis for the specificity of ubiquitin C-terminal hydrolases

The release of ubiquitin from attachment to other proteins and adducts is c ritical for ubiquitin biosynthesis, proteasomal degradation and other cellu lar processes, De-ubiquitination is accomplished in part by members of the UCH (ubiquitin C-terminal hydrolase) family of enzymes. We have determined the 2.25 Angstrom resolution crystal structure of the yeast UGH, Yuhl, in a complex with the inhibitor ubiquitin aldehyde (Ubal), The structure mimics the tetrahedral intermediate in the reaction pathway and explains the very high enzyme specificity, Comparison with a related, unliganded UCH structu re indicates that ubiquitin binding is coupled to rearrangements which bloc k the active-site cleft in the absence of authentic substrate. Remarkably, a 21-residue loop that becomes ordered upon binding Ubal lies directly over the active site, Efficiently processed substrates apparently pass through this loop, and constraints on the loop conformation probably function to co ntrol UCH specificity.