Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-α

Nuclear localization signals (NLSs) contain one or two clusters of basic residues and are recognized by the import receptor importin-. There are two NLS-binding sites (major and minor) on importin- and the major NLS-binding site is considered to be the primary binding site. Here, we used crystallographic and biochemical methods to investigate the binding between importin- and predicted minor site-specific' NLSs: four peptide library-derived peptides, and the NLS from mouse RNA helicase II/Gu. The crystal structures reveal that these atypical NLSs indeed preferentially bind to the minor NLS-binding site. Unlike previously characterized NLSs, the C-terminal residues of these NLSs form an -helical turn, stabilized by internal H-bond and cation- interactions between the aromatic residues from the NLSs and the positively charged residues from importin-. This helical turn sterically hinders binding at the major NLS-binding site, explaining the minor-site preference. Our data suggest the sequence RXXKR[K/X][F/Y/W]XXAF as the optimal minor NLS-binding site-specific motif, which may help identify novel proteins with atypical NLSs.