Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a Parkinson disease-associated, putative cysteine protease found abundantly and selectively expressed in neurons. The crystal structure of apo UCHL1 showed that the active-site residues are not aligned in a canonical form, with the nucleophilic cysteine being 7.7 Ă
from the general base histidine, an arrangement consistent with an inactive form of the enzyme. Here we report the crystal structures of the wild type and two Parkinson disease-associated variants of the enzyme, S18Y and I93M, bound to a ubiquitin-based suicide substrate, ubiquitin vinyl methyl ester. These structures reveal that ubiquitin vinyl methyl ester binds primarily at two sites on the enzyme, with its carboxy terminus at the active site and with its amino-terminal ÎČ-hairpin at the distal site-a surface-exposed hydrophobic crevice 17 Ă
away from the active site. Binding at the distal site initiates a cascade of side-chain movements in the enzyme that starts at a highly conserved, surface-exposed phenylalanine and is relayed to the active site resulting in the reorientation and proximal placement of the general base within 4 Ă
of the catalytic cysteine, an arrangement found in productive cysteine proteases. Mutation of the distal-site, surface-exposed phenylalanine to alanine reduces ubiquitin binding and severely impairs the catalytic activity of the enzyme. These results suggest that the activity of UCHL1 may be regulated by its own substrate.deubiquitinating enzyme | enzyme suicide substrate complex | neurodegeneration | ubiquitination U CHL1, a member of the UCH (ubiquitin C-terminal hydrolase) family of deubiquitinating enzymes (DUBs), is a 223-amino acid protein found abundantly and selectively expressed in brain, constituting up to 1-2% of total brain protein (1, 2). In vivo studies suggest that UCHL1 is involved in regulation of ubiquitin pool, apoptosis, and learning and memory, and its absence in mice because of spontaneous intragenic deletions yields phenotypes with neurological defects (3). Mutations in UCHL1 have been implicated in Parkinson disease (PD). A point mutation near the active site that changes Ile93 to Met (I93M) has been linked to an increased risk of developing an autosomaldominant form of PD (4). Conversely, a common S18Y polymorphism reduces susceptibility to PD (5, 6) and Alzheimer's disease (7). In addition to its association with neurodegenerative diseases, abnormal expression of UCHL1 is found in many forms of cancer, including lung, colorectal, and pancreatic cancers, and may be related to tumor progression (8, 9). The normal function of UCHL1, however, is not known. Also unknown are how the activity of this abundant neuronal enzyme is regulated and what its true physiological substrates are, although biochemical studies have indicated that UCHL1 can accept short-peptide (α or ϔ-amino-linked) or small-molecule C-terminal conjugates of ubiquitin as substrates, cleaving, as its name suggests, the amide bond following immediately after the C-terminal glycine (Gly7...