SV40 NLS  -  Importin-α

Biological function
Nuclear localization signals (NLSs) facilitate the transport of proteins into the nucleus.

Structural evidence
Monopartite interaction with alternative conformations, which were observed (simultaneously) at specificity-determining subsites of V40 NLS and the N-terminal portion in the minor binding site (staggering one position N-terminally). The structures show the SV40 NLS binds in a very similar manner as mammalian NLS (residues 127-130).

Biochemical evidence
Sequences flanking the basic clusters modulate recognition of the NLS. Proline residues in the flanking regions often appear to have a positive effect on NLS activity, likely by reducing the energetic cost of binding by restraining the NLS sequences in the extended conformation. The more stringent sequence requirements of the basic cluster of the monopartite NLSs are relaxed in the bipartite NLSs, by the second basic cluster compensating for the reduction of favorable contacts in the major site. The autoinhibitory sequence comprising residues 44-54 of importin-α binds to the major NLS binding site, resembling NLS binding. The path of the main chain of residues 47-53 is identical with the path of SV40 and nucleoplasmin NLS residues in the major binding site. Only residues 44-46 bind in a different mode than the analogous nucleoplasmin residues; however, in either case, few favorable interactions are formed in these regions with the protein, and the chains are poorly ordered.

Specificity determining factors: Polar interactions through conserved asparagine sidechains to NLS backbone to determine chain (NLS) direction. Hydrophobic interactions to conserved tryptophanes in shallow grooves. Interactions between basic NLS motifs and the negative charges of importin α.

Mechanism category

Posttranslational modification
Phosphorylation of the T antigen NLS facilitates transport, but does not involve direct interaction with importin-α.

Isoforms, context-dependence
Fuzzy linker modulates specificities of different importin-α isoforms for different cargo proteins.

Alternative binding modes may account for diverse NLS binding by the same receptor and effective competition with mammalian NLSs.