Alignment of the conserved sequence motif A (26) of nucleic acid polymerases. The consensus motifs for each polymerase family are based on published compilations for the pol I (26, 28), and pol α (26, 29) families, for the single subunit DNA-dependent RNA polymerases (30), and for RNA-dependent polymerases (27). The motif is aligned on the invariant aspartate residue (white outlined letters, connected by a black vertical bar). The positions that align with Phe-155 of MoMLV reverse transcriptase are connected by a shaded vertical bar. Positions that are almost invariably occupied by a hydrophobic amino acid are designated “h;” hyphens indicate nonconserved positions.

The backbone crystal structures of the polymerase domains of Klenow fragment, HIV-1 reverse transcriptase (RT), and T7 RNA polymerase. In each case the palm subdomain is colored purple, the thumb green, and the fingers blue. The three structures are positioned such that the active site regions of the palm subdomains (with yellow spheres showing the α-carbon positions of the active-site carboxylates) have similar orientations. The locations of residues that influence recognition of the sugar portion of the incoming nucleotide are indicated. Phe-762 of Klenow fragment and Tyr-115 of HIV-1 reverse transcriptase [the homolog of Phe-155 in Moloney murine leukemia virus (MoMLV) reverse transcriptase] are shown in ball-and-stick representation; in T7 RNA polymerase the α-carbon of Tyr-639 is marked by a red sphere. This figure was created by Jimin Wang (Yale University) using raster3d (20, 21).