High-resolution structure of the catalytic domain of avian sarcoma virus integrase

J Mol Biol. 1995 Oct 20;253(2):333-46. doi: 10.1006/jmbi.1995.0556.


Retroviral integrase (IN) functions to insert retroviral DNA into the host cell chromosome in a highly coordinated manner. IN catalyzes two biochemically separable reactions: processing of the viral DNA ends and joining of these ends to the host DNA. Previous studies suggested that these two reactions are chemically similar and are carried out by a single active site that is characterized by a highly conserved constellation of carboxylate residues, the D,D(35)E motif. We report here the crystal structure of the isolated catalytic domain of avian sarcoma virus (ASV) IN, solved using multiwavelength anomalous diffraction data for a selenomethionine derivative and refined at 1.7 A resolution. The protein is a crystallographic dimer with each monomer featuring a five-stranded mixed beta-sheet region surrounded by five alpha-helices. Based on the general fold and the arrangement of catalytic carboxylate residues, it is apparent that ASV IN is a member of a superfamily of proteins that also includes two types of nucleases, RuvC and RNase H. The general fold and the dimer interface are similar to those of the analogous domain of HIV-1 IN, whose crystal structure has been determined at 2.5 A resolution. However, the ASV IN structure is more complete in that all three critical carboxylic acids, Asp64, Asp121 and Glu157, are ordered. The ordered active site and the considerably higher resolution of the present structure are all important to an understanding of the mechanism of retroviral DNA integration, as well as for designing antiviral agents that may be effective against HIV.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Aspartic Acid
  • Avian Sarcoma Viruses / enzymology*
  • Bacterial Proteins / chemistry
  • Binding Sites
  • Crystallization
  • Crystallography, X-Ray
  • DNA Nucleotidyltransferases / chemistry*
  • DNA Nucleotidyltransferases / isolation & purification
  • DNA Nucleotidyltransferases / metabolism
  • Endodeoxyribonucleases / chemistry
  • Escherichia coli Proteins*
  • Glutamic Acid
  • HIV / enzymology
  • Integrases
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Folding*
  • Protein Structure, Secondary*
  • Ribonuclease H / chemistry
  • Sequence Homology, Amino Acid
  • Virus Integration


  • Bacterial Proteins
  • Escherichia coli Proteins
  • Macromolecular Substances
  • ruvC protein, E coli
  • Aspartic Acid
  • Glutamic Acid
  • DNA Nucleotidyltransferases
  • Integrases
  • Endodeoxyribonucleases
  • Ribonuclease H