Solution structure of a yeast ubiquitin-like protein Smt3: the role of structurally less defined sequences in protein-protein recognitions.

Smt3 belongs to a growing family of ubiquitin-related proteins involved in posttranslational protein modification. Independent studies demonstrate an essential function of Smt3 in the regulation of nucleocytoplasmic transport, and suggest a role in cell-cycle regulation. Here we report the high-resolution NMR structure of yeast Smt3 in the complex free form. Our comparison of the Smt3 NMR structure with the Smt3 crystal structure in complex with the C-Terminal Ulp1 protease domain revealed large structural differences in the binding surface, which is also involved in the Smt3-Ubc-9 interaction detected by NMR. The structural differences in the region indicate the important functions of conserved residues in less structurally defined sequences.