Fig. 2.

Structural comparison of the JD with UCH-L3. (A and B) Secondary structure topologies of the JD (A) and UCH-L3 (B) (Protein Data Bank ID code 1UCH). α-Helices are represented by filled circles, and β-strands are represented by triangles. β-Strand direction out from the paper is indicated by left-oriented triangles, and β-strand direction into the paper is indicated by right-oriented triangles. The left lobe of the JD is conserved in UCH-L3 (colored in blue). The main topological differences are observed in the right lobe. The N-terminal α-helices of the JD are “shuffled” as a big insertion between the β2 and β3 strands in UCH-L3. The “substrate-limiting loop,” which crosses over the catalytic site in UCH-L3 (yellow), is missing in the JD. Green letters indicate the positions of the catalytic residues with single-letter amino acid abbreviations. (C and D) Ribbon diagrams of the catalytic sites of the JDs of ataxin-3 (C) and UCH-L3 (D), with the active site residues shown in ball-and-stick models. The catalytic residues have a similar geometric organization in the two proteins, suggesting a similar mechanism of catalysis.