Rules for Nuclear Localization Sequence Recognition by Karyopherin Beta 2

Cell. 2006 Aug 11;126(3):543-58. doi: 10.1016/j.cell.2006.05.049.

Abstract

Karyopherinbeta (Kapbeta) proteins bind nuclear localization and export signals (NLSs and NESs) to mediate nucleocytoplasmic trafficking, a process regulated by Ran GTPase through its nucleotide cycle. Diversity and complexity of signals recognized by Kap betas have prevented prediction of new Kap beta substrates. The structure of Kap beta 2 (also known as Transportin) bound to one of its substrates, the NLS of hnRNP A1, that we report here explains the mechanism of substrate displacement by Ran GTPase. Further analyses reveal three rules for NLS recognition by Kap beta 2: NLSs are structurally disordered in free substrates, have overall basic character, and possess a central hydrophobic or basic motif followed by a C-terminal R/H/KX(2-5)PY consensus sequence. We demonstrate the predictive nature of these rules by identifying NLSs in seven previously known Kap beta 2 substrates and uncovering 81 new candidate substrates, confirming five experimentally. These studies define and validate a new NLS that could not be predicted by primary sequence analysis alone.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Active Transport, Cell Nucleus / genetics
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Amino Acids / genetics*
  • Animals
  • Binding Sites / physiology
  • Cell Nucleus / genetics
  • Cell Nucleus / metabolism*
  • Crystallography, X-Ray
  • Heterogeneous-Nuclear Ribonucleoproteins / chemistry
  • Heterogeneous-Nuclear Ribonucleoproteins / genetics
  • Heterogeneous-Nuclear Ribonucleoproteins / metabolism
  • Humans
  • Macromolecular Substances / chemistry
  • Macromolecular Substances / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Export Signals / genetics*
  • Protein Binding / physiology
  • Protein Structure, Tertiary / physiology
  • beta Karyopherins / chemistry*
  • beta Karyopherins / genetics
  • beta Karyopherins / metabolism
  • ran GTP-Binding Protein / chemistry
  • ran GTP-Binding Protein / genetics
  • ran GTP-Binding Protein / metabolism

Substances

  • Amino Acids
  • Heterogeneous-Nuclear Ribonucleoproteins
  • Macromolecular Substances
  • Nuclear Export Signals
  • RAN protein, human
  • TNPO1 protein, human
  • beta Karyopherins
  • ran GTP-Binding Protein

Associated data

  • PDB/2H4M