Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha

Background: Karyopherin alpha (importin alpha) is an adaptor molecule that recognizes proteins containing nuclear localization signals (NLSs). The pro totypical NLS that is able to bind to karyopherin alpha is that of the SV40 T antigen, and consists of a short positively charged sequence motif. Dist inct classes of NLSs (monopartite and bipartite) have been identified that are only partly conserved with respect to one another but are nevertheless recognized by the same receptor. Results: We report the crystal structures of two peptide complexes of yeast karyopherin alpha (Kap alpha): one with a human c-myc NLS peptide, determi ned at 2.1 Angstrom resolution, and one with a Xenopus nucleoplasmin NLS pe ptide, determined at 2.4 Angstrom resolution. Analysis of these structures reveals the determinants of specificity for the binding of a relatively hyd rophobic monopartite NLS and of a bipartite NLS peptide. The peptides bind Kap alpha in its extended surface groove, which presents a modular array of tandem binding pockets for amino acid residues. Conclusions: Monopaltite and bipartite NLSs bind to a different number of a mino acid binding pockets and make different interactions within them. The relatively hydrophobic monopartite c-myc NLS binds extensively at a few bin ding pockets in a similar manner to that of the SV40 T antigen NLS. In cont rast, the bipartite nucleoplasmin NLS engages the whole array of pockets wi th individually more limited but overall more abundant interactions, which include the NLS two basic clusters and the backbone of its non-conserved li nker region. Versatility in the specific recognition of NLSs relies on the modular.