Figure 8. Proposed debranching model.

(A) Surface depiction of UCH37 showing the canonical S1 (cS1) ubiquitin (Ub)-binding site and the new K48-specific binding sites identified in this study. (B) Proposed mechanism for chain debranching using the K48-specific binding sites. The K48-linked portion of a branched chain engages the K48-specific Ub-binding sites in two different orientations: one with the proximal Ub (Ub^prox) docked at the α5–6 motif and the other with the distal Ub (Ub^dist) bound to that site. As the docking models show (Figure 4H), the K48 isopeptide bond is less obstructed and closer to the catalytic C88 residue when the K48 Ub^dist moiety is bound to α5–6 and Ub^prox is bound near the L181 region. In this orientation, the other Ub^dist at the branchpoint is positioned near the frontside of the enzyme. With K48 isopeptide bond cleavage occurring on the backside, the α5–6 motif would serve as the noncanonical S1 (ncS1) site and the L181 region would be the ncS1´ site.