Mutagenesis of human immunodeficiency virus reverse transcriptase p51 subunit defines residues contributing to vinylogous urea inhibition of ribonuclease H activity

J Biol Chem. 2012 Feb 3;287(6):4066-75. doi: 10.1074/jbc.M111.314781. Epub 2011 Nov 21.


The vinylogous urea, NSC727447, was proposed to allosterically inhibit ribonuclease H (RNase H) activity of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) by interacting with the thumb subdomain of its non-catalytic p51 subunit. Proximity of the p51 thumb to the p66 RNase H domain implied that inhibitor binding altered active site geometry, whereas protein footprinting suggested a contribution from α-helix I residues Cys-280 and Lys-281. To more thoroughly characterize the vinylogous urea binding site, horizontal alanine scanning mutagenesis between p51 residues Lys-275 and Thr-286 (comprising α-helix I and portions of the neighboring αH/αI and αI/αJ connecting loops) was combined with a limited vertical scan of Cys-280. A contribution from Cys-280 was strengthened by our observation that all substitutions at this position rendered selectively mutated, reconstituted p66/p51 heterodimers ∼45-fold less sensitive to inhibition. An ∼19-fold reduced IC(50) for p51 mutant T286A coupled with a 2-8-fold increased IC(50) when intervening residues were substituted supports our original proposal of p51 α-helix I as the vinylogous urea binding site. In contrast to these allosteric inhibitors, mutant enzymes retained equivalent sensitivity to the natural product α-hydroxytropolone inhibitor manicol, which x-ray crystallography has demonstrated functions by chelating divalent metal at the p66 RNase H active site. Finally, reduced DNA strand-transfer activity together with increased vinylogous urea sensitivity of p66/p51 heterodimers containing short p51 C-terminal deletions suggests an additional role for the p51 C terminus in nucleic acid binding that is compromised by inhibitor binding.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Amino Acid Substitution
  • Cell Line
  • Crystallography, X-Ray
  • Enzyme Inhibitors / chemistry*
  • HIV-1 / enzymology*
  • HIV-1 / genetics
  • Humans
  • Mutagenesis
  • Mutation, Missense
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Ribonuclease H, Human Immunodeficiency Virus / antagonists & inhibitors*
  • Ribonuclease H, Human Immunodeficiency Virus / chemistry*
  • Ribonuclease H, Human Immunodeficiency Virus / genetics
  • Thiophenes / chemistry*


  • Enzyme Inhibitors
  • NSC 727447
  • Thiophenes
  • Ribonuclease H, Human Immunodeficiency Virus