The iUSP domain of Sad1 aligns well with known USP structures. (A) The finger, palm, and thumb subdomains of Sad1's iUSP domain (slate blue) are circled and the blocking loops indicated. (B) Structural alignment of the Sad1 iUSP domain to the USP domain from H. sapiens USP2 (lime) bound to ubiquitin (PDB ID 2HD5), where ubiquitin was removed afterward for clarity. The structural alignment was produced in Pymol. (C) Transparent surface representation of USP2 bound to ubiquitin (raspberry). The cup-like surface, which binds to the globular fold of ubiquitin, and the catalytic cleft, which binds to the C-terminal tail of ubiquitin, are highlighted. (D) A hypothetical model of the transparent surface representation of Sad1's iUSP domain after a structural alignment of Sad's iUSP domain to USP2 bound to ubiquitin. USP2 was removed to allow modeling of Sad1 iUSP's capacity to accommodate ubiquitin in its partial cup-like surface. (E) A zoomed image of the catalytic cleft from USP2 bound to ubiquitin aligned to Sad1's iUSP domain. The two blocking loops, the QDE loop of USP2 and the homologous PDL loop of Sad1, are labeled to highlight their different conformations. (F) A zoomed image of the catalytic triad from USP2 aligned to the pseudo-catalytic triad of Sad1's iUSP domain shows a high degree of structural similarity.
