Previously, we reported the three-dimensional molecular interactions of nervonic acid (NA) with mammalian DNA polymerase β (pol β) [Mizushina et al. (1998) J. Biol. Chem. 274, 25599-25607]. By three-dimensional structural model analysis and comparison with the spatial positioning of specific amino acids binding to NA on pol β (Leu11, Lys35, His51, and Thr79), we obtained supplementary information that allowed us to build a structural model of human immunodeficiency virus type-1 reverse transcriptase (HIV-1 RT). In HIV-1 RT, Leu100, Lys65, His235, and Thr386 corresponded to these four amino acid residues. These results suggested that the NA binding domains of pol β and HIV-1 RT are three-dimensionally very similar. The effects of NA on HIV-1 RT are thought to be same as those on pol β in binding to the rhombus of the four amino acid residues. NA dose-dependently inhibited the HIV-1 RT activity. For binding to pol β, the kinetics were competitive when the rhombus was present on the DNA binding site. However, as the rhombus in HIV-1 RT was not present in the DNA binding site, the three-dimensional structure of the DNA binding site must be distorted, and subsequently the enzyme is inhibited non-competitively.