Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) contains four structural motifs (A, B, C, and D) that are conserved in polymerases from diverse organisms. Motif B interacts with the incoming nucleotide, the template strand, and key active-site residues from other motifs, suggesting that motif B is an important determinant of substrate specificity. To examine the functional role of this region, we performed "random scanning mutagenesis" of 11 motif B residues and screened replication-competent mutants for altered substrate analog sensitivity in culture. Single amino acid replacements throughout the targeted region conferred resistance to lamivudine and/or hypersusceptibility to zidovudine (AZT). Substitutions at residue Q151 increased the sensitivity of HIV-1 to multiple nucleoside analogs, and a subset of these Q151 variants was also hypersusceptible to the pyrophosphate analog phosphonoformic acid (PFA). Other AZT-hypersusceptible mutants were resistant to PFA and are therefore phenotypically similar to PFA-resistant variants selected in vitro and in infected patients. Collectively, these data show that specific amino acid replacements in motif B confer broad-spectrum hypersusceptibility to substrate analog inhibitors. Our results suggest that motif B influences RT-deoxynucleoside triphosphate interactions at multiple steps in the catalytic cycle of polymerization.Conversion of viral RNA to double-stranded DNA by reverse transcriptase (RT) is a defining step in the retroviral life cycle (8) and a key target of therapy for human immunodeficiency virus type 1 (HIV-1) infection (17). The 66-kilodalton subunit of HIV-1 RT contains four motifs (A, B, C, and D) that are similarly arranged in all known structures of replicative DNA and RNA polymerases (21). Three additional structural elements, motifs E and F and premotif A, are also conserved among RTs and viral RNA-dependent RNA polymerases (4,21,45,76). Together, motifs A, B, C, and F and premotif A form a closely packed protein framework that positions the templating nucleotide, the primer terminus, and incoming deoxynucleoside triphosphate (dNTP) at the RT active site (Fig. 1A). Amino acid substitutions within this conserved core can affect dNTP insertion fidelity, susceptibility to nucleoside analogs, and/or discrimination against ribonucleoside triphosphates (rNTPs) during DNA synthesis (40,49,64,72). Thus, these motifs influence the stringency and specificity of substrate incorporation by RT.Motif B is of particular interest because of its central position in the RT core structure (Fig. 1) (12, 24). Motif B contacts the template strand, the incoming dNTP, and each of the other motifs in the core structure (premotif A and motifs A, C, and F) (Fig. 1A), including residues within these other motifs that are known to affect dNTP substrate recognition (Fig. 1B) (12, 24). The importance of motif B in substrate selection is evident from studies of HIV-1 mutants resistant to nucleoside analogs (49, 72). Two amino acid substitutions in motif B a...