Solution structure of the DNA binding domain of HIV-1 integrase

Biochemistry. 1995 Aug 8;34(31):9826-33. doi: 10.1021/bi00031a002.


The solution structure of the DNA binding domain of HIV-1 integrase (residues 220-270) has been determined by multidimensional NMR spectroscopy. The protein is a dimer in solution, and each subunit is composed of a five-stranded beta-barrel with a topology very similar to that of the SH3 domain. The dimer is formed by a stacked beta-interface comprising strands 2, 3, and 4, with the two triple-stranded antiparallel beta-sheets, one from each subunit, oriented antiparallel to each other. One surface of the dimer, bounded by the loop between strands beta 1 and beta 2, forms a saddle-shaped groove with dimensions of approximately 24 x 23 x 12 A in cross section. Lys264, which has been shown from mutational data to be involved in DNA binding, protrudes from this surface, implicating the saddle-shaped groove as the potential DNA binding site.

Publication types

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

MeSH terms

  • Adaptor Proteins, Signal Transducing*
  • Amino Acid Sequence
  • Binding Sites
  • DNA Nucleotidyltransferases / chemistry*
  • DNA Nucleotidyltransferases / genetics
  • DNA Nucleotidyltransferases / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • Escherichia coli / genetics
  • GRB2 Adaptor Protein
  • HIV-1 / enzymology*
  • Integrases
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Peptide Fragments / chemistry*
  • Peptide Fragments / genetics
  • Protein Conformation
  • Proteins / chemistry
  • Recombinant Proteins / chemistry
  • Sequence Homology
  • Solutions
  • Spectrin / chemistry


  • Adaptor Proteins, Signal Transducing
  • DNA-Binding Proteins
  • GRB2 Adaptor Protein
  • Peptide Fragments
  • Proteins
  • Recombinant Proteins
  • Solutions
  • Spectrin
  • DNA Nucleotidyltransferases
  • Integrases