Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2

J Mol Biol. 2004 Nov 19;344(2):303-10. doi: 10.1016/j.jmb.2004.09.043.


Nuclear transport carriers interact with proteins of the nuclear pore complex (NPC) to transport their cargo across the nuclear envelope. One such carrier is nuclear transport factor 2 (NTF2), whose import cargo is the small GTPase Ran. A domain highly homologous to the small NTF2 protein (14kDa) is also found in a number of additional proteins, which together make up the NTF2 domain containing superfamily of proteins. Using structural, computational and biochemical analysis we have identified a functional site that is present throughout this superfamily, and our results indicate that this site functions as an NPC binding site in NTF2. Previously we showed that a D23A mutant of NTF2 exhibits increased affinity for the NPC. The mechanism of this mutation, however, was unknown as this region of NTF2 had not been implicated in binding to NPC proteins. Here we show that the D23A mutation in NTF2 does not result in gross structural changes affecting other known NPC binding sites. Instead, the D23 residue is located in an evolutionarily important region in the NTF2 domain containing superfamily, that in NTF2, is involved in binding to the NPC.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Active Transport, Cell Nucleus
  • Alanine / metabolism
  • Amino Acid Substitution
  • Binding Sites
  • Cell Nucleus / metabolism*
  • Computational Biology*
  • Crystallography, X-Ray
  • Dimerization
  • Escherichia coli / genetics
  • Evolution, Molecular
  • HeLa Cells
  • Humans
  • Hydrogen Bonding
  • Models, Molecular
  • Nuclear Pore / metabolism*
  • Nucleocytoplasmic Transport Proteins / chemistry*
  • Nucleocytoplasmic Transport Proteins / genetics
  • Nucleocytoplasmic Transport Proteins / metabolism*
  • Point Mutation
  • Protein Binding
  • Protein Structure, Tertiary
  • Structure-Activity Relationship
  • ran GTP-Binding Protein / metabolism


  • Nucleocytoplasmic Transport Proteins
  • ran GTP-Binding Protein
  • Alanine