Crystal Structure of a pol α Family Replication DNA Polymerase from Bacteriophage RB69

amino acid sequence of the bacteriophage RB69 DNA and T. A. Steitz* † ‡ polymerase (gp43), whose structure is reported here, is * Department of Molecular Biophysics and 63% identical to that of its homolog from T4 phage and Biochemistry is similar to the primary structures of several pol ␣ family † Department of Chemistry DNA polymerases (Wang et al., 1995). U-shaped polymerase domain geometry that has been likened to the shape of a hand with " thumb, " " palm, " and " fingers " subdomains (Ollis et al., 1985; Kohlstaedt Summary et al., 1992). The thumb interacts across the minor groove of product duplex DNA, while the palm contains The 2.8 A ˚ resolution crystal structure of the bacterio-the polymerase catalytic site; the fingers interact with phage RB69 gp43, a member of the eukaryotic pol ␣ the template strand and perhaps with the deoxynucleo-family of replicative DNA polymerases, shares some side triphosphate. While the structure of mammalian similarities with other polymerases but shows many DNA polymerase ␤ (pol ␤) exhibits an analogous hand-differences. Although its palm domain has the same topology as other polymerases, except rat DNA poly-Sawaya et al., 1994), it is not structurally homologous merase ␤, one of the three carboxylates required for to pol I, RT, or T7 RNA polymerase (T7 RNAP) (Steitz et nucleotidyl transfer is located on a different ␤ strand. al., 1994) but rather belongs to another family of nucleoti-The structures of the fingers and thumb domains are dyl transferases (Holm and Sander, 1995; Yue et al., unrelated to all other known polymerase structures. 1996). The editing 3؅–5؅ exonuclease domain of gp43 is ho-The structures of the polymerase domains of pol I, mologous to that of E. coli DNA polymerase I but lies RT, and T7 RNAP (Ollis et al., 1985; Kohlstaedt et al., on the opposite side of the polymerase active site. An extended structure-based alignment of eukaryotic show a surprising amount of diversity, although the cata-DNA polymerase sequences provides structural in-lytic palm domains of all three are sufficiently similar to sights that should be applicable to most eukaryotic imply homology. In contrast, their thumb-domain struc-DNA polymerases. tures are not alike, and the structures of only the pol I and RNA pol fingers domains are similar. Amino acid Introduction sequence comparisons hint at additional structural variations between these polymerases and the pol ␣ family, The structures of four polynucleotide polymerases have …