Fig. 3: Structure and specificity of Otu2 binding to eS7-monoubiquitinated 40S.
From: Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2
a molecular model of the Otu2 N-terminal hairpin (α1- α2) bound in a pocket formed by h44 (ES12), the loop between h7 and h8, h9 (ES3a) and eS8 as well as of Otu2 α3 bound to eS8. A thumbnail in the top left corner indicates the location of zoomed regions within the Otu2-40S complex. rf right foot, lf left foot. b view as in a, showing density for the Otu2 α1- α2 hairpin (transparent orange with fitted model) in its binding pocket (solid map). Interacting residues are labeled. c side view focusing on the Otu2 α3-eS8 interaction site. d molecular model of the extended Otu2 OTU domain and α4 bound to Lys83-monoubiquitinated eS7 and ES6e. e zoom view focusing on the model for the active site of OTU domain targeting the ubiquitinated-eS7-Lys83 residue. The dotted circle shows the protease site with the catalytic triad (Cys178, His300 and Asn302) of Otu2 and its substrate, ubiquitinated eS7-Lys83. The minor ubiquitination site eS7-Lys84 is also shown. Ub ubiquitin. f zoom on the eS7-Lys83 ubiquitination site (eS7 and the C-terminus of monoubiquitin shown as electron potential map) contacted by Pro174 (in loop β1-α6), Trp248 (loop α8-α9) and Tyr295 (loop β4-β5) of the OTU domain (shown as model). g “Open book” view displaying the hydrophobic contact interface between the Otu2 OTU-S1 site and ubiquitin. Hydrophobic regions are shown in yellow, hydrophilic in cyan. h SDS gel of an in vitro deubiquitination assay using purified Otu2 and di-ubiquitin with indicated linkage types. We obtained essentially the same results in at least three independent experiments. The original gel image for (h) is provided in the Source Data file. Ub ubiquitin.
